diff --git a/reports/anvil-edge/README.md b/reports/anvil-edge/README.md index c44f5abe0..a86cf983c 100644 --- a/reports/anvil-edge/README.md +++ b/reports/anvil-edge/README.md @@ -13,4 +13,4 @@ After each successful deployment, automated tool tests are also run against the Latest tool tests for each chunk: -
Chunk IDTool ListLatest reportPrevious report
0ToolsetMon Nov 04 06:27:38 2024Mon Oct 28 06:28:11 2024
1ToolsetMon Nov 04 18:33:04 2024Mon Oct 28 18:33:45 2024
2ToolsetTue Nov 05 06:28:13 2024Tue Oct 29 06:27:53 2024
3ToolsetTue Nov 05 18:32:47 2024Tue Oct 29 18:34:14 2024
4ToolsetWed Nov 06 06:27:59 2024Wed Oct 23 06:27:36 2024
5ToolsetWed Nov 06 18:32:51 2024Wed Oct 30 18:34:11 2024
6ToolsetThu Nov 07 06:26:50 2024Thu Oct 31 06:26:39 2024
7ToolsetThu Nov 07 18:38:42 2024Thu Oct 31 18:32:34 2024
8ToolsetFri Nov 08 06:28:01 2024Fri Nov 01 06:27:34 2024
9ToolsetFri Nov 01 18:32:35 2024Fri Oct 25 18:34:46 2024
10ToolsetSat Nov 02 06:24:54 2024Sat Oct 26 06:26:40 2024
11ToolsetSat Nov 02 18:31:34 2024Sat Oct 26 18:32:18 2024
12ToolsetSun Nov 03 06:27:59 2024Sun Oct 27 06:25:17 2024
13ToolsetSun Nov 03 18:32:07 2024Sun Oct 27 18:31:25 2024
+
Chunk IDTool ListLatest reportPrevious report
0ToolsetMon Nov 04 06:27:38 2024Mon Oct 28 06:28:11 2024
1ToolsetMon Nov 04 18:33:04 2024Mon Oct 28 18:33:45 2024
2ToolsetTue Nov 05 06:28:13 2024Tue Oct 29 06:27:53 2024
3ToolsetTue Nov 05 18:32:47 2024Tue Oct 29 18:34:14 2024
4ToolsetWed Nov 06 06:27:59 2024Wed Oct 23 06:27:36 2024
5ToolsetWed Nov 06 18:32:51 2024Wed Oct 30 18:34:11 2024
6ToolsetThu Nov 07 06:26:50 2024Thu Oct 31 06:26:39 2024
7ToolsetThu Nov 07 18:38:42 2024Thu Oct 31 18:32:34 2024
8ToolsetFri Nov 08 06:28:01 2024Fri Nov 01 06:27:34 2024
9ToolsetFri Nov 08 18:33:31 2024Fri Nov 01 18:32:35 2024
10ToolsetSat Nov 02 06:24:54 2024Sat Oct 26 06:26:40 2024
11ToolsetSat Nov 02 18:31:34 2024Sat Oct 26 18:32:18 2024
12ToolsetSun Nov 03 06:27:59 2024Sun Oct 27 06:25:17 2024
13ToolsetSun Nov 03 18:32:07 2024Sun Oct 27 18:31:25 2024
diff --git a/reports/anvil-edge/tool-tests/chunks.json b/reports/anvil-edge/tool-tests/chunks.json index c300ea49f..1b4d27a83 100644 --- a/reports/anvil-edge/tool-tests/chunks.json +++ b/reports/anvil-edge/tool-tests/chunks.json @@ -56,11 +56,11 @@ "date2": "Fri Nov 01 06:27:34 2024" }, "9": { - "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-11-01-18-17-1/results.html", - "date1": "Fri Nov 01 18:32:35 2024", - "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-11-01-18-17-1/tools.yml", - "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-10-25-18-17-1/results.html", - "date2": "Fri Oct 25 18:34:46 2024" + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/results.html", + "date1": "Fri Nov 08 18:33:31 2024", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/tools.yml", + "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-11-01-18-17-1/results.html", + "date2": "Fri Nov 01 18:32:35 2024" }, "10": { "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-11-02-06-10-1/results.html", diff --git a/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/chunk.json b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/chunk.json new file mode 100644 index 000000000..606a04d5f --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/chunk.json @@ -0,0 +1,7 @@ +{ + "9": { + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/results.html", + "date1": "Fri Nov 08 18:33:31 2024", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/tools.yml" + } +} \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/chunk.txt b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/chunk.txt new file mode 100644 index 000000000..ad3379b4a --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/chunk.txt @@ -0,0 +1,26 @@ +-t datamash_reverse --tool-version f198773344e4 +-t deeptools_plot_enrichment --tool-version e65d16fb2724 +-t umi_tools_count --tool-version 8250ea3a1501 +-t umi_tools_count --tool-version b557acca0b56 +-t umi_tools_count --tool-version a535cf1e5da4 +-t bowtie2 --tool-version 09b2cdb7ace5 +-t medaka_consensus_pipeline --tool-version a7228a7ea146 +-t poretools_stats --tool-version 4b17acf9b6ab +-t stringtie --tool-version 1ebd14235b92 +-t samtools_markdup --tool-version 83b8e36e9cbe +-t samtools_markdup --tool-version b5527cc104ab +-t bamtools_filter --tool-version cb20f99fd45b +-t bamtools_filter --tool-version bd735cae4ce6 +-t anndata_manipulate --tool-version 9bd945a03d7b +-t anndata_manipulate --tool-version 3d748954434b +-t salmonquantmerge --tool-version 88c07fc4024c +-t scanpy_remove_confounders --tool-version bf2017df9837 +-t scanpy_compute_graph --tool-version 2401808e20e8 +-t scanpy_compute_graph --tool-version a58d4166805b +-t split_file_on_column --tool-version 37a53100b67e +-t lofreq_indelqual --tool-version 426d707dfc47 +-t bcftools_norm --tool-version c077f71d351f +-t bcftools_plugin_fill_tags --tool-version bf7d6acd9884 +-t vcfallelicprimitives --tool-version 57a16b310fe8 +-t vcfprimers --tool-version 17096387c0e6 +-t ivar_filtervariants --tool-version 7fe36019c073 diff --git a/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/28ca52757f505a15.json b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/28ca52757f505a15.json new file mode 100644 index 000000000..c5732052a --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/28ca52757f505a15.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "28ca52757f505a15", + "history_id": "da7414b0e37eac28", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-11-08T19:08:26.807587", + "update_time": "2024-11-08T19:08:39.496430", + "galaxy_version": "24.1", + "external_id": "gxy-jr97t", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/122/registry.xml' '/galaxy/server/database/jobs_directory/000/122/upload_params.json' '141:/galaxy/server/database/objects/e/7/b/dataset_e7b7875c-20ad-4b39-a910-cf352f7cdc0e_files:/galaxy/server/database/objects/e/7/b/dataset_e7b7875c-20ad-4b39-a910-cf352f7cdc0e.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_irhxrn7r\"", + "files_metadata": "{\"__current_case__\": 36, \"file_type\": \"bam\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"long_reads.bam\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_sp4_tis8\", \"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": "e9cb4075989abeb8", + "src": "hda", + "uuid": "e7b7875c-20ad-4b39-a910-cf352f7cdc0e" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/2cd95566f4d04a2a.json b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/2cd95566f4d04a2a.json new file mode 100644 index 000000000..a46e9b17f --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/2cd95566f4d04a2a.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "2cd95566f4d04a2a", + "history_id": "da7414b0e37eac28", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-11-08T19:02:05.761737", + "update_time": "2024-11-08T19:02:18.074024", + "galaxy_version": "24.1", + "external_id": "gxy-4wscw", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/96/registry.xml' '/galaxy/server/database/jobs_directory/000/96/upload_params.json' '104:/galaxy/server/database/objects/3/1/c/dataset_31cba7c9-425a-4ca4-a36a-e1b95f8ae94d_files:/galaxy/server/database/objects/3/1/c/dataset_31cba7c9-425a-4ca4-a36a-e1b95f8ae94d.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_b37384th\"", + "files_metadata": "{\"__current_case__\": 248, \"file_type\": \"fast5.tar\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"poretools-in1.tar.bz2\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_ao_cevnx\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"fast5.tar\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "1ca8330398e88230", + "src": "hda", + "uuid": "31cba7c9-425a-4ca4-a36a-e1b95f8ae94d" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/38e2156fd7401822.json b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/38e2156fd7401822.json new file mode 100644 index 000000000..1125b31c2 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/38e2156fd7401822.json @@ -0,0 +1,62 @@ +{ + "model_class": "Job", + "id": "38e2156fd7401822", + "history_id": "da7414b0e37eac28", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy4", + "state": "error", + "exit_code": null, + "create_time": "2024-11-08T19:37:00.489978", + "update_time": "2024-11-08T19:37:06.053487", + "galaxy_version": "24.1", + "external_id": "gxy-xfpsb", + "handler": null, + "job_runner_name": null, + "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/7/a/a/dataset_7aaae6d9-5b8e-4c4a-ac0b-c92aad2008a6.dat' > input.vcf.gz && bcftools index input.vcf.gz && ln -s '/galaxy/server/database/objects/5/7/3/dataset_573fcc22-f2c2-4d81-be0d-19d8e9001df9.dat' ref.fa && samtools faidx ref.fa && awk '{ if ($0 !~ />/) {print toupper($0)} else {print $0} }' 'ref.fa' > ref_upper.fa && bcftools norm --fasta-ref ref_upper.fa --check-ref w --do-not-normalize --multiallelics '+both' --strict-filter --site-win 1000 --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/2/c/8/dataset_2c83b419-25a1-4495-a502-bcb398c76eba.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "output_type": "\"v\"", + "sec_default": "{\"site_win\": \"1000\"}", + "sec_restrict": "{\"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}", + "multiallelics": "{\"__current_case__\": 2, \"mode\": \"+\", \"multiallelic_types\": \"both\", \"strict_filter\": true}", + "rm_dup": "\"\"", + "old_rec_tag": "\"\"", + "normalize_indels": "false", + "atomize": "false", + "check_ref": "\"w\"", + "reference_source": "{\"__current_case__\": 1, \"fasta_ref\": {\"values\": [{\"id\": 240, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}" + }, + "inputs": { + "input_file": { + "id": "dc82172fda263ec8", + "src": "hda", + "uuid": "7aaae6d9-5b8e-4c4a-ac0b-c92aad2008a6" + }, + "reference_source|fasta_ref": { + "id": "82ce24234cd1d762", + "src": "hda", + "uuid": "573fcc22-f2c2-4d81-be0d-19d8e9001df9" + } + }, + "outputs": { + "output_file": { + "id": "8edb363bd0a3069a", + "src": "hda", + "uuid": "2c83b419-25a1-4495-a502-bcb398c76eba" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "Lines total/split/realigned/skipped:\t26/0/0/0\n", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "Lines total/split/realigned/skipped:\t26/0/0/0\n", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/45abc3d0f8b42070.json b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/45abc3d0f8b42070.json new file mode 100644 index 000000000..6c3ac6d4a --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/45abc3d0f8b42070.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "45abc3d0f8b42070", + "history_id": "da7414b0e37eac28", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-11-08T18:55:57.249760", + "update_time": "2024-11-08T18:56:09.556380", + "galaxy_version": "24.1", + "external_id": "gxy-j8jd7", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/82/registry.xml' '/galaxy/server/database/jobs_directory/000/82/upload_params.json' '84:/galaxy/server/database/objects/8/8/b/dataset_88b2d692-3432-4763-8775-7d213402ad14_files:/galaxy/server/database/objects/8/8/b/dataset_88b2d692-3432-4763-8775-7d213402ad14.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_3znrpibx\"", + "files_metadata": "{\"__current_case__\": 75, \"file_type\": \"fasta\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"bowtie2-fq2.fa\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_fwtxel0e\", \"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": "30453ec4f199ee7d", + "src": "hda", + "uuid": "88b2d692-3432-4763-8775-7d213402ad14" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/75b0d11877e26dbe.json b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/75b0d11877e26dbe.json new file mode 100644 index 000000000..36b64c0ee --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/75b0d11877e26dbe.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "75b0d11877e26dbe", + "history_id": "da7414b0e37eac28", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-11-08T18:50:33.496526", + "update_time": "2024-11-08T18:50:45.672994", + "galaxy_version": "24.1", + "external_id": "gxy-kxcrf", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/52/registry.xml' '/galaxy/server/database/jobs_directory/000/52/upload_params.json' '53:/galaxy/server/database/objects/e/9/6/dataset_e9694852-f518-41a0-98f9-d50d8a670a57_files:/galaxy/server/database/objects/e/9/6/dataset_e9694852-f518-41a0-98f9-d50d8a670a57.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_678yu6q2\"", + "files_metadata": "{\"__current_case__\": 81, \"file_type\": \"fastqsanger\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"bowtie2-fq2.fq\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_nlo5cv8v\", \"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": "e5b1b68f6c1b4f43", + "src": "hda", + "uuid": "e9694852-f518-41a0-98f9-d50d8a670a57" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/87afed66c00a7675.json b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/87afed66c00a7675.json new file mode 100644 index 000000000..9bffca84a --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/87afed66c00a7675.json @@ -0,0 +1,61 @@ +{ + "model_class": "Job", + "id": "87afed66c00a7675", + "history_id": "da7414b0e37eac28", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0", + "state": "error", + "exit_code": null, + "create_time": "2024-11-08T19:07:23.730144", + "update_time": "2024-11-08T19:07:29.338183", + "galaxy_version": "24.1", + "external_id": "gxy-jvrng", + "handler": null, + "job_runner_name": null, + "command_line": "mkdir -p ./special_de_output/sample1/ && ln -s '/galaxy/server/database/objects/b/5/9/dataset_b5948e20-50b6-4e9f-bf48-07845a8d3710.dat' guide.gff && stringtie '/galaxy/server/database/objects/e/f/1/dataset_ef1e9415-0b70-45ee-844d-a778ac4ee621.dat' -o '/galaxy/server/database/objects/d/d/9/dataset_dd909ae8-ad9e-450d-89e3-30605e6a5aff.dat' -p \"${GALAXY_SLOTS:-1}\" -G guide.gff -b ./special_de_output/sample1/ -f '0.17' -m '200' -a '10' -j '1' -c '1' -g '50' -M '1.0' -A '/galaxy/server/database/objects/b/4/6/dataset_b46627df-7520-449d-85d7-60f9a4e3540c.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "adv": "{\"abundance_estimation\": true, \"bdist\": \"50\", \"bundle_fraction\": \"1.0\", \"disable_trimming\": false, \"fraction\": \"0.17\", \"min_anchor_cov\": \"1\", \"min_anchor_len\": \"10\", \"min_bundle_cov\": \"1\", \"min_tlen\": \"200\", \"multi_mapping\": false, \"name_prefix\": null, \"omit_sequences\": \"\", \"point_features\": null}", + "guide": "{\"__current_case__\": 1, \"coverage_file\": false, \"guide_source\": {\"__current_case__\": 1, \"guide_gff_select\": \"history\", \"ref_hist\": {\"values\": [{\"id\": 134, \"src\": \"hda\"}]}}, \"input_estimation\": false, \"special_outputs\": {\"__current_case__\": 2, \"special_outputs_select\": \"no\"}, \"use_guide\": \"yes\"}", + "rna_strandness": "\"\"", + "input_options": "{\"__current_case__\": 0, \"input_bam\": {\"values\": [{\"id\": 133, \"src\": \"hda\"}]}, \"input_mode\": \"short_reads\"}" + }, + "inputs": { + "input_options|input_bam": { + "id": "0875c422d93fe122", + "src": "hda", + "uuid": "ef1e9415-0b70-45ee-844d-a778ac4ee621" + }, + "guide|guide_source|ref_hist": { + "id": "d4aba126f7fdc3f6", + "src": "hda", + "uuid": "b5948e20-50b6-4e9f-bf48-07845a8d3710" + } + }, + "outputs": { + "output_gtf": { + "id": "7807a571f0107626", + "src": "hda", + "uuid": "dd909ae8-ad9e-450d-89e3-30605e6a5aff" + }, + "gene_abundance_estimation": { + "id": "d29a7e08587fb6be", + "src": "hda", + "uuid": "b46627df-7520-449d-85d7-60f9a4e3540c" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/8f3478df74d5586e.json b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/8f3478df74d5586e.json new file mode 100644 index 000000000..e98eddfd5 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/8f3478df74d5586e.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "8f3478df74d5586e", + "history_id": "da7414b0e37eac28", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-11-08T19:24:08.412179", + "update_time": "2024-11-08T19:24:20.559749", + "galaxy_version": "24.1", + "external_id": "gxy-srvnp", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/174/registry.xml' '/galaxy/server/database/jobs_directory/000/174/upload_params.json' '195:/galaxy/server/database/objects/4/7/5/dataset_475ee587-90fd-438b-8ac2-1ecfed15826f_files:/galaxy/server/database/objects/4/7/5/dataset_475ee587-90fd-438b-8ac2-1ecfed15826f.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_qd8qv5or\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"krumsiek11.h5ad\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_oygtuihh\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"auto\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "66940b1e901b3834", + "src": "hda", + "uuid": "475ee587-90fd-438b-8ac2-1ecfed15826f" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/9ec278895232d16d.json b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/9ec278895232d16d.json new file mode 100644 index 000000000..7edee2e79 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/9ec278895232d16d.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "9ec278895232d16d", + "history_id": "da7414b0e37eac28", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-11-08T18:41:11.290673", + "update_time": "2024-11-08T18:41:24.465312", + "galaxy_version": "24.1", + "external_id": "gxy-khhq5", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/20/registry.xml' '/galaxy/server/database/jobs_directory/000/20/upload_params.json' '21:/galaxy/server/database/objects/d/6/9/dataset_d69ee026-ce09-45b5-9fa7-81be30a8fdf3_files:/galaxy/server/database/objects/d/6/9/dataset_d69ee026-ce09-45b5-9fa7-81be30a8fdf3.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_ddb7_43k\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"chr19_gene_tags.bam\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_iowq184k\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"auto\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "95326e6fc2368886", + "src": "hda", + "uuid": "d69ee026-ce09-45b5-9fa7-81be30a8fdf3" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/a0d50995af565d4e.json b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/a0d50995af565d4e.json new file mode 100644 index 000000000..077b5529f --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/a0d50995af565d4e.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "a0d50995af565d4e", + "history_id": "da7414b0e37eac28", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-11-08T19:33:52.975357", + "update_time": "2024-11-08T19:34:05.529904", + "galaxy_version": "24.1", + "external_id": "gxy-7s7vh", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/205/registry.xml' '/galaxy/server/database/jobs_directory/000/205/upload_params.json' '228:/galaxy/server/database/objects/2/5/3/dataset_2539568e-5c61-418f-8cad-22e1872faffb_files:/galaxy/server/database/objects/2/5/3/dataset_2539568e-5c61-418f-8cad-22e1872faffb.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_p6dv0294\"", + "files_metadata": "{\"__current_case__\": 342, \"file_type\": \"vcf\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"norm.vcf\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_xvm6dt3z\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"vcf\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "deb10cdd302a14ef", + "src": "hda", + "uuid": "2539568e-5c61-418f-8cad-22e1872faffb" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/b5c05e39cecb3340.json b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/b5c05e39cecb3340.json new file mode 100644 index 000000000..62ae14a63 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/b5c05e39cecb3340.json @@ -0,0 +1,48 @@ +{ + "model_class": "Job", + "id": "b5c05e39cecb3340", + "history_id": "da7414b0e37eac28", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1", + "state": "error", + "exit_code": null, + "create_time": "2024-11-08T19:27:17.475407", + "update_time": "2024-11-08T19:27:23.111106", + "galaxy_version": "24.1", + "external_id": "gxy-cmqk4", + "handler": null, + "job_runner_name": null, + "command_line": "cat '/galaxy/server/database/jobs_directory/000/186/configs/tmpli09xp_d' && python '/galaxy/server/database/jobs_directory/000/186/configs/tmpli09xp_d'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"h5ad\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "manipulate": "{\"__current_case__\": 7, \"filter\": {\"__current_case__\": 1, \"filter\": \"index\", \"index\": {\"__current_case__\": 0, \"format\": \"text\", \"text\": \"Gata2,EKLF\"}}, \"function\": \"filter\", \"var_obs\": \"var\"}" + }, + "inputs": { + "input": { + "id": "7de9afc393b6bf31", + "src": "hda", + "uuid": "9f368a2f-ba05-4bf2-9f98-21b0d3ccec51" + } + }, + "outputs": { + "anndata": { + "id": "ac4960e8ecd0cb2e", + "src": "hda", + "uuid": "4fd46551-f64e-4179-8c8b-e3b189a89a6d" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/9/f/3/dataset_9f368a2f-ba05-4bf2-9f98-21b0d3ccec51.dat')\n\nfiltered = ['Gata2', 'EKLF']\nprint(filtered)\n\nadata = adata[:,filtered]\n\n\nadata.write('anndata.h5ad')\n['Gata2', 'EKLF']\n", + "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", + "job_stdout": null, + "job_stderr": null, + "stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/9/f/3/dataset_9f368a2f-ba05-4bf2-9f98-21b0d3ccec51.dat')\n\nfiltered = ['Gata2', 'EKLF']\nprint(filtered)\n\nadata = adata[:,filtered]\n\n\nadata.write('anndata.h5ad')\n['Gata2', 'EKLF']\n", + "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/b760d2295e3f99a5.json b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/b760d2295e3f99a5.json new file mode 100644 index 000000000..4a711b9d7 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/b760d2295e3f99a5.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "b760d2295e3f99a5", + "history_id": "da7414b0e37eac28", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-11-08T19:07:30.140568", + "update_time": "2024-11-08T19:07:42.393667", + "galaxy_version": "24.1", + "external_id": "gxy-l6sfp", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/118/registry.xml' '/galaxy/server/database/jobs_directory/000/118/upload_params.json' '137:/galaxy/server/database/objects/5/0/a/dataset_50adf3a1-2df0-4879-97fb-70bb0b629afc_files:/galaxy/server/database/objects/5/0/a/dataset_50adf3a1-2df0-4879-97fb-70bb0b629afc.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_jjiq365t\"", + "files_metadata": "{\"__current_case__\": 36, \"file_type\": \"bam\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"stringtie_in1.bam\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_rwzpk3is\", \"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": "5a20d38e9bb241c0", + "src": "hda", + "uuid": "50adf3a1-2df0-4879-97fb-70bb0b629afc" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/eae541d28ead1c6d.json b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/eae541d28ead1c6d.json new file mode 100644 index 000000000..d8ff28e81 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/eae541d28ead1c6d.json @@ -0,0 +1,55 @@ +{ + "model_class": "Job", + "id": "eae541d28ead1c6d", + "history_id": "da7414b0e37eac28", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2", + "state": "error", + "exit_code": null, + "create_time": "2024-11-08T18:45:35.436093", + "update_time": "2024-11-08T18:45:41.468705", + "galaxy_version": "24.1", + "external_id": "gxy-w4vxt", + "handler": null, + "job_runner_name": null, + "command_line": "ln -sf '/galaxy/server/database/objects/6/e/b/dataset_6ebb3cef-bbeb-44d0-a087-5ac77cea1248.dat' 'input.bam' && ln -sf '/galaxy/server/database/objects/_metadata_files/c/e/7/metadata_ce79e776-9d0c-4db3-9bf5-f9f02e668faf.dat' 'input.bam.bai' && umi_tools count '' --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag 'XF' --skip-tags-regex '^[__Unassigned]' --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed='123456789' -I 'input.bam' -S '/galaxy/server/database/objects/6/0/7/dataset_607b7381-aea4-427b-9e0d-2b6e9c81e40e.dat' --log2stderr", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "log": "false", + "cond_extra": "{\"__current_case__\": 0, \"prepender\": \"none\"}", + "advanced": "{\"random_seed\": \"123456789\"}", + "sc": "{\"assigned_status_tag\": null, \"gene_tag\": \"XF\", \"gene_transcript_map\": null, \"per_cell\": false, \"per_contig\": false, \"skip_tags_regex\": \"^[__|Unassigned]\"}", + "sambam": "{\"chimeric_pairs\": null, \"chrom\": \"\", \"ignore_tlen\": false, \"ignore_umi\": false, \"mapping_quality\": \"0\", \"paired\": false, \"subset\": \"1.0\", \"unmapped_reads\": \"discard\", \"unpaired_reads\": null}", + "umi": "{\"edit_distance_threshold\": \"1\", \"method\": \"directional\", \"read_length\": false, \"soft_clip_threshold\": \"4\", \"spliced_is_unique\": false}", + "bc": "{\"__current_case__\": 2, \"extract_umi_method\": \"umis\"}", + "wide_format_cell_counts": "false" + }, + "inputs": { + "input": { + "id": "eae541d28ead1c6d", + "src": "hda", + "uuid": "6ebb3cef-bbeb-44d0-a087-5ac77cea1248" + } + }, + "outputs": { + "out_counts": { + "id": "5868d5d35892214c", + "src": "hda", + "uuid": "607b7381-aea4-427b-9e0d-2b6e9c81e40e" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "# UMI-tools version: 1.1.2\n# output generated by count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/6/0/7/dataset_607b7381-aea4-427b-9e0d-2b6e9c81e40e.dat --log2stderr\n# job started at Fri Nov 8 18:45:38 2024 on gxy-w4vxt-f9qnc -- 2cd3b257-c856-43a8-9c4a-9f009e9641ab\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XF\n# gene_transcript_map : None\n# get_umi_method : umis\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : directional\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : False\n# per_contig : False\n# per_gene : False\n# random_seed : 123456789\n# read_length : False\n# short_help : None\n# skip_regex : ^[__Unassigned]\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/6/0/7/dataset_607b7381-aea4-427b-9e0d-2b6e9c81e40e.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : False\n2024-11-08 18:45:38,561 INFO command: count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/6/0/7/dataset_607b7381-aea4-427b-9e0d-2b6e9c81e40e.dat --log2stderr\n2024-11-08 18:45:38,589 INFO Input Reads: 1203\n2024-11-08 18:45:38,590 INFO Read skipped - assigned tag matches skip_regex: 120\n2024-11-08 18:45:38,590 INFO Number of (post deduplication) reads counted: 141\n# job finished in 0 seconds at Fri Nov 8 18:45:38 2024 -- 0.90 0.23 0.00 0.00 -- 2cd3b257-c856-43a8-9c4a-9f009e9641ab\n", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "# UMI-tools version: 1.1.2\n# output generated by count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/6/0/7/dataset_607b7381-aea4-427b-9e0d-2b6e9c81e40e.dat --log2stderr\n# job started at Fri Nov 8 18:45:38 2024 on gxy-w4vxt-f9qnc -- 2cd3b257-c856-43a8-9c4a-9f009e9641ab\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XF\n# gene_transcript_map : None\n# get_umi_method : umis\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : directional\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : False\n# per_contig : False\n# per_gene : False\n# random_seed : 123456789\n# read_length : False\n# short_help : None\n# skip_regex : ^[__Unassigned]\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/6/0/7/dataset_607b7381-aea4-427b-9e0d-2b6e9c81e40e.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : False\n2024-11-08 18:45:38,561 INFO command: count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/6/0/7/dataset_607b7381-aea4-427b-9e0d-2b6e9c81e40e.dat --log2stderr\n2024-11-08 18:45:38,589 INFO Input Reads: 1203\n2024-11-08 18:45:38,590 INFO Read skipped - assigned tag matches skip_regex: 120\n2024-11-08 18:45:38,590 INFO Number of (post deduplication) reads counted: 141\n# job finished in 0 seconds at Fri Nov 8 18:45:38 2024 -- 0.90 0.23 0.00 0.00 -- 2cd3b257-c856-43a8-9c4a-9f009e9641ab\n", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/f31638072f02b299.json b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/f31638072f02b299.json new file mode 100644 index 000000000..d1dfab739 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/errors/f31638072f02b299.json @@ -0,0 +1,56 @@ +{ + "model_class": "Job", + "id": "f31638072f02b299", + "history_id": "da7414b0e37eac28", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0", + "state": "error", + "exit_code": null, + "create_time": "2024-11-08T19:09:02.889346", + "update_time": "2024-11-08T19:09:09.634784", + "galaxy_version": "24.1", + "external_id": "gxy-6dvdf", + "handler": null, + "job_runner_name": null, + "command_line": "mkdir -p ./special_de_output/sample1/ && stringtie '/galaxy/server/database/objects/d/8/7/dataset_d8771fc1-c251-4061-8b41-eb887ab6b50d.dat' '/galaxy/server/database/objects/d/5/d/dataset_d5de7dbd-1178-48de-bdfc-f8df69f9c14f.dat' -E 25 -o '/galaxy/server/database/objects/3/7/1/dataset_3718ca85-c02c-4622-9dcb-62b695a35a2c.dat' -p \"${GALAXY_SLOTS:-1}\" -f '0.01' -m '200' -a '10' -j '1' -c '1' -g '50' -M '1.0'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "adv": "{\"abundance_estimation\": false, \"bdist\": \"50\", \"bundle_fraction\": \"1.0\", \"disable_trimming\": false, \"fraction\": \"0.01\", \"min_anchor_cov\": \"1\", \"min_anchor_len\": \"10\", \"min_bundle_cov\": \"1\", \"min_tlen\": \"200\", \"multi_mapping\": false, \"name_prefix\": null, \"omit_sequences\": \"\", \"point_features\": null}", + "guide": "{\"__current_case__\": 0, \"use_guide\": \"no\"}", + "rna_strandness": "\"\"", + "input_options": "{\"__current_case__\": 2, \"error_splice\": \"25\", \"input_bam_long\": {\"values\": [{\"id\": 143, \"src\": \"hda\"}]}, \"input_bam_short\": {\"values\": [{\"id\": 142, \"src\": \"hda\"}]}, \"input_mode\": \"mixed_reads\"}" + }, + "inputs": { + "input_options|input_bam_short": { + "id": "cc9d8bb46765f933", + "src": "hda", + "uuid": "d8771fc1-c251-4061-8b41-eb887ab6b50d" + }, + 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2024-11-08T19:38:05.423826 upload1 +f0d8602f1349bb9a ok 2024-11-08T19:38:05.392991 upload1 +8e42b1fbf985c94c ok 2024-11-08T19:37:43.444939 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy4 +4c694d23b823468b ok 2024-11-08T19:37:28.969248 upload1 +0a6da04fcad59fe6 ok 2024-11-08T19:37:28.229185 upload1 +38e2156fd7401822 error 2024-11-08T19:37:06.053487 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy4 +454e5a69a5cfe987 ok 2024-11-08T19:37:00.133632 upload1 +4516f1481323ade4 ok 2024-11-08T19:37:00.125723 upload1 +7e9b3f6181d9f21f ok 2024-11-08T19:36:36.339275 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy4 +d79761699b67b292 ok 2024-11-08T19:36:21.726162 upload1 +e84d5d005471e063 ok 2024-11-08T19:36:21.636227 upload1 +d2999df588b66189 ok 2024-11-08T19:35:59.795672 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy4 +e6cf843f0a1421be ok 2024-11-08T19:35:12.347129 upload1 +af6164418604b1ed ok 2024-11-08T19:35:12.339159 upload1 +a88d5e16219380b4 ok 2024-11-08T19:34:50.322541 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy4 +8943e16a55fb7a9a ok 2024-11-08T19:34:28.617571 upload1 +ac4960e8ecd0cb2e ok 2024-11-08T19:34:26.588433 upload1 +7de9afc393b6bf31 ok 2024-11-08T19:34:14.528594 upload1 +a0d50995af565d4e error 2024-11-08T19:34:05.529904 upload1 +c88976d64d6b5b93 ok 2024-11-08T19:33:50.943437 toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1 +7faebc7c2663f710 ok 2024-11-08T19:33:35.782581 upload1 +e527b0ee28d9e436 ok 2024-11-08T19:33:13.459817 toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1 +e2bab181a597196a ok 2024-11-08T19:32:59.029507 upload1 +70f2fecc01fed51e ok 2024-11-08T19:32:58.003789 upload1 +07ef8540660ce7c0 ok 2024-11-08T19:32:35.002495 toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1 +34104ebdd97e7c12 ok 2024-11-08T19:32:08.739109 upload1 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2024-11-08T19:27:44.318533 upload1 +b5c05e39cecb3340 error 2024-11-08T19:27:23.111106 toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1 +32c6704a17157385 ok 2024-11-08T19:27:17.063804 upload1 +d0332b419eb36ef4 ok 2024-11-08T19:26:54.920542 toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1 +d2214987cb2d8b80 ok 2024-11-08T19:26:38.256314 upload1 +c366515eb0712963 ok 2024-11-08T19:26:38.131082 upload1 +0072ef120b730b6a ok 2024-11-08T19:26:14.419181 toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1 +b6408abd5e224f8b ok 2024-11-08T19:25:57.895780 upload1 +a05816edfcbf43cd ok 2024-11-08T19:25:57.847777 upload1 +616fd04f6b296dbe ok 2024-11-08T19:25:34.699351 toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1 +a8abc5f9b6912fd7 ok 2024-11-08T19:25:19.374598 upload1 +737b3033e5b6550c ok 2024-11-08T19:24:58.195598 toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1 +4538c8da25243180 ok 2024-11-08T19:24:42.171160 upload1 +8f3478df74d5586e error 2024-11-08T19:24:20.559749 upload1 +e9cea873a02f585b ok 2024-11-08T19:24:07.515594 toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1 +3e4c9827a204efc2 ok 2024-11-08T19:23:51.191747 upload1 +af8afe74309bcaf6 ok 2024-11-08T19:23:29.053724 toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1 +a002b3ceaced54b4 ok 2024-11-08T19:23:12.851092 upload1 +b444036e30a94ba8 ok 2024-11-08T19:22:50.687565 toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1 +94a364b2476b42ce ok 2024-11-08T19:22:35.560994 upload1 +1e79b5996263aba4 ok 2024-11-08T19:22:13.285132 toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1 +4b993ff91e7ec0d0 ok 2024-11-08T19:21:57.108959 upload1 +ffaed0ea0cfde573 ok 2024-11-08T19:21:34.820073 toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1 +6941a67834a7dc0d ok 2024-11-08T19:21:19.620804 upload1 +74798f5cd5fbe7e1 ok 2024-11-08T19:20:58.630259 toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1 +64bb9a27eebe46a5 ok 2024-11-08T19:20:42.632839 upload1 +449cf9cc7d01dc92 ok 2024-11-08T19:20:20.243807 toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1 +63c2ba7411f9dc82 ok 2024-11-08T19:20:03.877088 upload1 +0f8a361424c463d6 ok 2024-11-08T19:20:02.997166 upload1 +3b1d785838fcf855 ok 2024-11-08T19:19:40.426822 toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1 +a26c5048a128464f ok 2024-11-08T19:19:23.409808 upload1 +edcc5d810d7f2cbe ok 2024-11-08T19:19:23.342428 upload1 +7b35e56724bdc701 ok 2024-11-08T19:18:59.684994 toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1 +538f8a97f78e293e ok 2024-11-08T19:18:43.369847 upload1 +237e69e4ea734e4b ok 2024-11-08T19:18:21.123802 toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1 +a2f86245bd71b4cb ok 2024-11-08T19:18:05.053818 upload1 +dba0a91ab7c50a76 ok 2024-11-08T19:17:42.733994 toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1 +fa3b2a0beafdfdbd ok 2024-11-08T19:17:26.710993 upload1 +6da69afd6692ab80 ok 2024-11-08T19:17:04.370097 toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1 +84e25ac3b5653ceb ok 2024-11-08T19:16:49.254810 upload1 +58dccf0d0bd14a40 ok 2024-11-08T19:16:27.888678 toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1 +479f81759fe14964 ok 2024-11-08T19:16:11.713112 upload1 +290b901b9cbb0bd1 ok 2024-11-08T19:15:49.528638 toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1 +7764c94f267f71be ok 2024-11-08T19:15:22.066810 upload1 +93d2fe7f03087140 ok 2024-11-08T19:14:57.757725 toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2 +cc9d8bb46765f933 ok 2024-11-08T19:14:42.765594 upload1 +e9cb4075989abeb8 ok 2024-11-08T19:14:21.410268 toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2 +3ddf019855fbe017 ok 2024-11-08T19:14:06.272637 upload1 +c0004b57c32be191 ok 2024-11-08T19:13:43.836994 toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2 +2371d722a17c0d64 ok 2024-11-08T19:13:29.854906 upload1 +5a20d38e9bb241c0 ok 2024-11-08T19:13:07.795407 toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2 +d29a7e08587fb6be ok 2024-11-08T19:12:52.697812 upload1 +7807a571f0107626 ok 2024-11-08T19:12:29.569329 toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2 +d4aba126f7fdc3f6 ok 2024-11-08T19:12:15.306186 upload1 +0875c422d93fe122 ok 2024-11-08T19:11:54.128286 toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2 +800f121972d7125d ok 2024-11-08T19:11:39.147330 upload1 +87a90ca5ab392bca ok 2024-11-08T19:11:16.765811 toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2 +5507ca7bde5d08ca ok 2024-11-08T19:11:01.649650 upload1 +313122af5a7398a2 ok 2024-11-08T19:10:39.645826 toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2 +467b61757452b047 ok 2024-11-08T19:10:08.238788 upload1 +e9997d48d76616b2 ok 2024-11-08T19:09:45.964194 toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0 +6f41adfb187630ce ok 2024-11-08T19:09:31.795308 upload1 +f31638072f02b299 error 2024-11-08T19:09:09.634784 toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0 +9bb1cfbf7563a675 ok 2024-11-08T19:09:02.636976 upload1 +54b93943e9609524 ok 2024-11-08T19:09:02.490474 upload1 +28ca52757f505a15 error 2024-11-08T19:08:39.496430 upload1 +ce14c2d285f898d3 ok 2024-11-08T19:08:26.250010 upload1 +1c0b833cfd710b29 ok 2024-11-08T19:08:03.446278 upload1 +b48563d4d6a24bed ok 2024-11-08T19:07:51.550974 upload1 +b760d2295e3f99a5 error 2024-11-08T19:07:42.393667 upload1 +87afed66c00a7675 error 2024-11-08T19:07:29.338183 toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0 +60e8d7b20ea99c2a ok 2024-11-08T19:07:23.435697 upload1 +6ec9315ee735f78a ok 2024-11-08T19:07:22.620400 upload1 +b5df49ef3bf6281c ok 2024-11-08T19:06:58.930304 toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0 +d9e73d5a86ad4a25 ok 2024-11-08T19:06:43.728845 upload1 +b19cc830d5a63129 ok 2024-11-08T19:06:42.895257 upload1 +83aa9bcb838125e8 ok 2024-11-08T19:06:18.459266 toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0 +c5b19d90d64a0b32 ok 2024-11-08T19:06:02.523075 upload1 +34911ce9f087078e ok 2024-11-08T19:06:02.513418 upload1 +2c1230cb190434eb ok 2024-11-08T19:05:39.697538 toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0 +5fbfe2bbff639746 ok 2024-11-08T19:05:24.719999 upload1 +2274d9bc56091239 ok 2024-11-08T19:05:24.675723 upload1 +d869f24cd4bd8272 ok 2024-11-08T19:05:01.632608 toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0 +fe99532e009efcc7 ok 2024-11-08T19:04:46.968835 upload1 +1ca8330398e88230 ok 2024-11-08T19:04:45.869664 upload1 +353d17e8e5600932 ok 2024-11-08T19:04:22.626779 toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0 +85364758e151e809 ok 2024-11-08T19:04:08.702971 upload1 +9f31ce1d612eb955 ok 2024-11-08T19:03:46.397979 toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0 +59675abcf37151b8 ok 2024-11-08T19:03:18.028584 upload1 +7963421e6419d1b8 ok 2024-11-08T19:02:54.597265 toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0 +05703a60fce6b467 ok 2024-11-08T19:02:39.672585 upload1 +2cd95566f4d04a2a error 2024-11-08T19:02:18.074024 upload1 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2024-11-08T18:54:14.126879 upload1 +b290ad1616cef64a ok 2024-11-08T18:54:12.860316 upload1 +3efd9b08baf135dc ok 2024-11-08T18:53:45.817293 toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1 +48d443965fb79661 ok 2024-11-08T18:53:30.736982 upload1 +b39762222150b9fa ok 2024-11-08T18:53:30.679221 upload1 +933ce35b72edc64e ok 2024-11-08T18:53:30.668413 upload1 +d7119413a306e9b0 ok 2024-11-08T18:53:02.933226 toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1 +c700bc1b046f6d9a ok 2024-11-08T18:52:47.318235 upload1 +fb05b536cd69771d ok 2024-11-08T18:52:47.309515 upload1 +61add0d864102c44 ok 2024-11-08T18:52:24.501831 toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1 +2dae2f5e3e0f7ea7 ok 2024-11-08T18:52:08.839811 upload1 +7c5036351dc570af ok 2024-11-08T18:52:08.112023 upload1 +12f723b97d4a53c5 ok 2024-11-08T18:52:07.964285 upload1 +e40492d06caf609c ok 2024-11-08T18:51:40.640452 toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1 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toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2 +ed16242a8734824d ok 2024-11-08T18:44:56.749068 upload1 +c38e9d52f41984f4 ok 2024-11-08T18:44:34.406820 toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2 +7d230e8f17fedba0 ok 2024-11-08T18:44:19.433774 upload1 +1ba321c08a66f6e6 ok 2024-11-08T18:43:56.507865 toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2 +9a6057cd21099aeb ok 2024-11-08T18:43:41.586058 upload1 +562134ea0f434c69 ok 2024-11-08T18:43:19.149120 toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2 +69a419b0dfadf9ae ok 2024-11-08T18:43:03.959733 upload1 +5a76110036291e09 ok 2024-11-08T18:42:41.875542 toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2 +f493aa5161845cb8 ok 2024-11-08T18:42:26.888580 upload1 +63e82ac14c91a36d ok 2024-11-08T18:42:05.438328 toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2 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2024-11-08T18:38:23.894768 upload1 +18f545ab1e4ded21 ok 2024-11-08T18:38:01.636413 toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2 +05730410412536ea ok 2024-11-08T18:37:45.642221 upload1 +e9b0e4d46bcc827e ok 2024-11-08T18:37:20.446190 toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2 +3df03115672c8d19 ok 2024-11-08T18:36:49.008692 upload1 +33e5e4773222c037 ok 2024-11-08T18:36:25.819161 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/3.5.4+galaxy0 +a9975e93915e7608 ok 2024-11-08T18:35:49.805292 upload1 +e5042d7292e14fe6 ok 2024-11-08T18:35:49.614231 upload1 +94c8c8b52917d0da ok 2024-11-08T18:35:25.705137 toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.8+galaxy0 +da7414b0e37eac28 ok 2024-11-08T18:34:37.399986 upload1 diff --git a/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/results.html b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/results.html new file mode 100644 index 000000000..a0089023f --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/results.html @@ -0,0 +1,291 @@ + + + + + + + Test Results (powered by Planemo) + + + + + + + + + + +
+
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+ + + + + + + \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/results.json b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/results.json new file mode 100644 index 000000000..ba3aa73c5 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/results.json @@ -0,0 +1 @@ +{"version": "0.1", "suitename": "Galaxy Tool Tests", "results": {"total": 107, "errors": 14, "failures": 13, "skips": 2}, "tests": [{"id": "anndata_manipulate/0.7.5+galaxy1-0", "has_data": true, "data": {"tool_id": "anndata_manipulate", "tool_version": "0.7.5+galaxy1", "test_index": 0, "time_seconds": 49.2726891040802, "inputs": {"input": {"src": "hda", "id": "ffaed0ea0cfde573"}, "manipulate|other_adatas": {"src": "hda", "id": "ffaed0ea0cfde573"}, "manipulate|join": "inner", "manipulate|batch_key": "batch", "manipulate|index_unique": "-", "manipulate|function": "concatenate"}, "job": {"model_class": "Job", "id": "290b901b9cbb0bd1", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:15:22.400791", "update_time": "2024-11-08T19:15:49.528638", "galaxy_version": "24.1", "external_id": "gxy-mbjfm", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/145/configs/tmp7g4oki7k' && python '/galaxy/server/database/jobs_directory/000/145/configs/tmp7g4oki7k'", "user_email": "tests@fake.org", "command_version": "anndata version: 0.7.5\n\nloompy version: 2.0.17", "params": {"__input_ext": "\"h5ad\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "manipulate": "{\"__current_case__\": 0, \"batch_key\": \"batch\", \"function\": \"concatenate\", \"index_unique\": \"-\", \"join\": \"inner\", \"other_adatas\": {\"values\": [{\"id\": 165, \"src\": \"hda\"}]}}"}, "inputs": {"input": {"id": "ffaed0ea0cfde573", "src": "hda", "uuid": "99654ca5-797a-4ecc-8c5d-9998d7235698"}, "manipulate|other_adatas": {"id": "ffaed0ea0cfde573", "src": "hda", "uuid": "99654ca5-797a-4ecc-8c5d-9998d7235698"}, "manipulate|other_adatas1": {"id": "ffaed0ea0cfde573", "src": "hda", "uuid": "99654ca5-797a-4ecc-8c5d-9998d7235698"}}, "outputs": {"anndata": {"id": "4b993ff91e7ec0d0", "src": "hda", "uuid": "f66a9266-b0bb-4bf0-a1ca-6b901c14e9a9"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/9/9/6/dataset_99654ca5-797a-4ecc-8c5d-9998d7235698.dat')\n\nadata_0 = ad.read('/galaxy/server/database/objects/9/9/6/dataset_99654ca5-797a-4ecc-8c5d-9998d7235698.dat')\nadata = adata.concatenate(\n adata_0,\n join='inner',\n index_unique='-',\n batch_key='batch')\n\n\nadata.write('anndata.h5ad')\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/9/9/6/dataset_99654ca5-797a-4ecc-8c5d-9998d7235698.dat')\n\nadata_0 = ad.read('/galaxy/server/database/objects/9/9/6/dataset_99654ca5-797a-4ecc-8c5d-9998d7235698.dat')\nadata = adata.concatenate(\n adata_0,\n join='inner',\n index_unique='-',\n batch_key='batch')\n\n\nadata.write('anndata.h5ad')\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-08 19:15:35", "plugin": "core", "name": "end_epoch", "raw_value": "1731093335.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:15:34", "plugin": "core", "name": "start_epoch", "raw_value": "1731093334.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "anndata_manipulate/0.7.5+galaxy1-0", "has_data": true, "data": {"tool_id": "anndata_manipulate", "tool_version": "0.7.5+galaxy1", "test_index": 0, "time_seconds": 36.521424531936646, "inputs": {"input": {"src": "hda", "id": "458491cc6e2be8a7"}, "manipulate|other_adatas": {"src": "hda", "id": "458491cc6e2be8a7"}, "manipulate|join": "inner", "manipulate|batch_key": "batch", "manipulate|index_unique": "-", "manipulate|function": "concatenate"}, "job": {"model_class": "Job", "id": "b444036e30a94ba8", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:22:35.696176", "update_time": "2024-11-08T19:22:50.687565", "galaxy_version": "24.1", "external_id": "gxy-qqvzs", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/169/configs/tmp7mhnohc3' && python '/galaxy/server/database/jobs_directory/000/169/configs/tmp7mhnohc3'", "user_email": "tests@fake.org", "command_version": "anndata version: 0.7.5\n\nloompy version: 2.0.17", "params": {"__input_ext": "\"h5ad\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "manipulate": "{\"__current_case__\": 0, \"batch_key\": \"batch\", \"function\": \"concatenate\", \"index_unique\": \"-\", \"join\": \"inner\", \"other_adatas\": {\"values\": [{\"id\": 189, \"src\": \"hda\"}]}}"}, "inputs": {"input": {"id": "458491cc6e2be8a7", "src": "hda", "uuid": "15a75010-66c7-4a30-9089-3eb7d5502ae8"}, "manipulate|other_adatas": {"id": "458491cc6e2be8a7", "src": "hda", "uuid": "15a75010-66c7-4a30-9089-3eb7d5502ae8"}, "manipulate|other_adatas1": {"id": "458491cc6e2be8a7", "src": "hda", "uuid": "15a75010-66c7-4a30-9089-3eb7d5502ae8"}}, "outputs": {"anndata": {"id": "6ed0912ec814c7e1", "src": "hda", "uuid": "8f11bac9-911d-44dd-8e64-17eca236cfb0"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/1/5/a/dataset_15a75010-66c7-4a30-9089-3eb7d5502ae8.dat')\n\nadata_0 = ad.read('/galaxy/server/database/objects/1/5/a/dataset_15a75010-66c7-4a30-9089-3eb7d5502ae8.dat')\nadata = adata.concatenate(\n adata_0,\n join='inner',\n index_unique='-',\n batch_key='batch')\n\n\nadata.write('anndata.h5ad')\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/1/5/a/dataset_15a75010-66c7-4a30-9089-3eb7d5502ae8.dat')\n\nadata_0 = ad.read('/galaxy/server/database/objects/1/5/a/dataset_15a75010-66c7-4a30-9089-3eb7d5502ae8.dat')\nadata = adata.concatenate(\n adata_0,\n join='inner',\n index_unique='-',\n batch_key='batch')\n\n\nadata.write('anndata.h5ad')\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-11-08 19:22:38", "plugin": "core", "name": "end_epoch", "raw_value": "1731093758.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:22:36", "plugin": "core", "name": "start_epoch", "raw_value": "1731093756.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "anndata_manipulate/0.7.5+galaxy1-1", "has_data": true, "data": {"tool_id": "anndata_manipulate", "tool_version": "0.7.5+galaxy1", "test_index": 1, "time_seconds": 38.51513361930847, "inputs": {"input": {"src": "hda", "id": "1e79b5996263aba4"}, "manipulate|join": "-", "manipulate|function": "obs_names_make_unique"}, "job": {"model_class": "Job", "id": "58dccf0d0bd14a40", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:16:12.050570", "update_time": "2024-11-08T19:16:27.888678", "galaxy_version": "24.1", "external_id": "gxy-rvnvz", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/147/configs/tmp6u8_av7q' && python '/galaxy/server/database/jobs_directory/000/147/configs/tmp6u8_av7q'", "user_email": "tests@fake.org", "command_version": "anndata version: 0.7.5\n\nloompy version: 2.0.17", "params": {"__input_ext": "\"h5ad\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "manipulate": "{\"__current_case__\": 1, \"function\": \"obs_names_make_unique\", \"join\": \"-\"}"}, "inputs": {"input": {"id": "1e79b5996263aba4", "src": "hda", "uuid": "4e4d375e-4f2b-4333-99d2-3ad19a03f3f0"}}, "outputs": {"anndata": {"id": "94a364b2476b42ce", "src": "hda", "uuid": "c36a1798-6150-406f-885e-afeecc3502a3"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/4/e/4/dataset_4e4d375e-4f2b-4333-99d2-3ad19a03f3f0.dat')\n\nadata.obs_names_make_unique(join='-')\n\n\nadata.write('anndata.h5ad')\n", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_stdout": "", "job_stderr": "", "stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/4/e/4/dataset_4e4d375e-4f2b-4333-99d2-3ad19a03f3f0.dat')\n\nadata.obs_names_make_unique(join='-')\n\n\nadata.write('anndata.h5ad')\n", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-11-08 19:16:15", "plugin": "core", "name": "end_epoch", "raw_value": "1731093375.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:16:13", "plugin": "core", "name": "start_epoch", "raw_value": "1731093373.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "anndata_manipulate/0.7.5+galaxy1-1", "has_data": true, "data": {"tool_id": "anndata_manipulate", "tool_version": "0.7.5+galaxy1", "test_index": 1, "time_seconds": 38.19416689872742, "inputs": {"input": {"src": "hda", "id": "f1d77499850d3aed"}, "manipulate|join": "-", "manipulate|function": "obs_names_make_unique"}, "job": {"model_class": "Job", "id": "af8afe74309bcaf6", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:23:13.266370", "update_time": "2024-11-08T19:23:29.053724", "galaxy_version": "24.1", "external_id": "gxy-x89z2", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/171/configs/tmpi_smly_i' && python '/galaxy/server/database/jobs_directory/000/171/configs/tmpi_smly_i'", "user_email": "tests@fake.org", "command_version": "anndata version: 0.7.5\n\nloompy version: 2.0.17", "params": {"__input_ext": "\"h5ad\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "manipulate": "{\"__current_case__\": 1, \"function\": \"obs_names_make_unique\", \"join\": \"-\"}"}, "inputs": {"input": {"id": "f1d77499850d3aed", "src": "hda", "uuid": "2970a8c2-184a-49c4-b7ea-f59e7a6db904"}}, "outputs": {"anndata": {"id": "fc7fd7c14d95c4c2", "src": "hda", "uuid": "2af792ce-98c0-47d7-ab5b-53dcf2bc687e"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/2/9/7/dataset_2970a8c2-184a-49c4-b7ea-f59e7a6db904.dat')\n\nadata.obs_names_make_unique(join='-')\n\n\nadata.write('anndata.h5ad')\n", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_stdout": "", "job_stderr": "", "stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/2/9/7/dataset_2970a8c2-184a-49c4-b7ea-f59e7a6db904.dat')\n\nadata.obs_names_make_unique(join='-')\n\n\nadata.write('anndata.h5ad')\n", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-08 19:23:16", "plugin": "core", "name": "end_epoch", "raw_value": "1731093796.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:23:15", "plugin": "core", "name": "start_epoch", "raw_value": "1731093795.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "anndata_manipulate/0.7.5+galaxy1-10", "has_data": true, "data": {"tool_id": "anndata_manipulate", "tool_version": "0.7.5+galaxy1", "test_index": 10, "time_seconds": 38.45858979225159, "inputs": {"input": {"src": "hda", "id": "c9d4301d824436b9"}, "manipulate|function": "save_raw"}, "job": {"model_class": "Job", "id": "1e79b5996263aba4", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:21:57.255502", "update_time": "2024-11-08T19:22:13.285132", "galaxy_version": "24.1", "external_id": "gxy-78f8b", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/167/configs/tmpwf6r_zqp' && python '/galaxy/server/database/jobs_directory/000/167/configs/tmpwf6r_zqp'", "user_email": "tests@fake.org", "command_version": "anndata version: 0.7.5\n\nloompy version: 2.0.17", "params": {"__input_ext": "\"h5ad\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "manipulate": "{\"__current_case__\": 8, \"function\": \"save_raw\"}"}, "inputs": {"input": {"id": "c9d4301d824436b9", "src": "hda", "uuid": "30e708fa-2fa8-4bf0-8a1e-0e7caf9de4d4"}}, "outputs": {"anndata": {"id": "030ab49c7f4d195b", "src": "hda", "uuid": "85ff5807-1513-4e9f-9f75-0a1940398166"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/3/0/e/dataset_30e708fa-2fa8-4bf0-8a1e-0e7caf9de4d4.dat')\n\nadata.raw = adata\n\n\nadata.write('anndata.h5ad')\n", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_stdout": "", "job_stderr": "", "stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/3/0/e/dataset_30e708fa-2fa8-4bf0-8a1e-0e7caf9de4d4.dat')\n\nadata.raw = adata\n\n\nadata.write('anndata.h5ad')\n", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-08 19:22:00", "plugin": "core", "name": "end_epoch", "raw_value": "1731093720.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:21:59", "plugin": "core", "name": "start_epoch", "raw_value": "1731093719.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "anndata_manipulate/0.7.5+galaxy1-10", "has_data": true, "data": {"tool_id": "anndata_manipulate", "tool_version": "0.7.5+galaxy1", "test_index": 10, "time_seconds": 38.81725883483887, "inputs": {"input": {"src": "hda", "id": "af6164418604b1ed"}, "manipulate|function": "save_raw"}, "job": {"model_class": "Job", "id": "6ed0912ec814c7e1", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:28:24.212686", "update_time": "2024-11-08T19:28:40.114154", "galaxy_version": "24.1", "external_id": "gxy-2xsvc", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/190/configs/tmptnad17jy' && python '/galaxy/server/database/jobs_directory/000/190/configs/tmptnad17jy'", "user_email": "tests@fake.org", "command_version": "anndata version: 0.7.5\n\nloompy version: 2.0.17", "params": {"__input_ext": "\"h5ad\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "manipulate": "{\"__current_case__\": 8, \"function\": \"save_raw\"}"}, "inputs": {"input": {"id": "af6164418604b1ed", "src": "hda", "uuid": "6d253761-bcc4-40a0-926c-92183797b8fb"}}, "outputs": {"anndata": {"id": "e6cf843f0a1421be", "src": "hda", "uuid": "7635e260-9c13-4127-b755-f88e82202422"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/6/d/2/dataset_6d253761-bcc4-40a0-926c-92183797b8fb.dat')\n\nadata.raw = adata\n\n\nadata.write('anndata.h5ad')\n", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_stdout": "", "job_stderr": "", "stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/6/d/2/dataset_6d253761-bcc4-40a0-926c-92183797b8fb.dat')\n\nadata.raw = adata\n\n\nadata.write('anndata.h5ad')\n", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-08 19:28:27", "plugin": "core", "name": "end_epoch", "raw_value": "1731094107.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:28:26", "plugin": "core", "name": "start_epoch", "raw_value": "1731094106.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "anndata_manipulate/0.7.5+galaxy1-2", "has_data": true, "data": {"tool_id": "anndata_manipulate", "tool_version": "0.7.5+galaxy1", "test_index": 2, "time_seconds": 36.25518250465393, "inputs": {"input": {"src": "hda", "id": "b444036e30a94ba8"}, "manipulate|join": "-", "manipulate|function": "var_names_make_unique"}, "job": {"model_class": "Job", "id": "6da69afd6692ab80", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:16:49.593962", "update_time": "2024-11-08T19:17:04.370097", "galaxy_version": "24.1", "external_id": "gxy-rnttx", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/149/configs/tmp_5_dqlc4' && python '/galaxy/server/database/jobs_directory/000/149/configs/tmp_5_dqlc4'", "user_email": "tests@fake.org", "command_version": "anndata version: 0.7.5\n\nloompy version: 2.0.17", "params": {"__input_ext": "\"h5ad\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "manipulate": "{\"__current_case__\": 2, \"function\": \"var_names_make_unique\", \"join\": \"-\"}"}, "inputs": {"input": {"id": "b444036e30a94ba8", "src": "hda", "uuid": "7e62f86e-4ae3-4a6c-974b-4b638f69d85b"}}, "outputs": {"anndata": {"id": "a002b3ceaced54b4", "src": "hda", "uuid": "1568e4fa-5c9c-47f7-b1ce-6f06c945d6ab"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/7/e/6/dataset_7e62f86e-4ae3-4a6c-974b-4b638f69d85b.dat')\n\nadata.var_names_make_unique(join='-')\n\n\nadata.write('anndata.h5ad')\n", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_stdout": "", "job_stderr": "", "stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/7/e/6/dataset_7e62f86e-4ae3-4a6c-974b-4b638f69d85b.dat')\n\nadata.var_names_make_unique(join='-')\n\n\nadata.write('anndata.h5ad')\n", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-11-08 19:16:52", "plugin": "core", "name": "end_epoch", "raw_value": "1731093412.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:16:50", "plugin": "core", "name": "start_epoch", "raw_value": "1731093410.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "anndata_manipulate/0.7.5+galaxy1-2", "has_data": true, "data": {"tool_id": "anndata_manipulate", "tool_version": "0.7.5+galaxy1", "test_index": 2, "time_seconds": 38.46866416931152, "inputs": {"input": {"src": "hda", "id": "0057b99aca4835a0"}, "manipulate|join": "-", "manipulate|function": "var_names_make_unique"}, "job": {"model_class": "Job", "id": "e9cea873a02f585b", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:23:51.475483", "update_time": "2024-11-08T19:24:07.515594", "galaxy_version": "24.1", "external_id": "gxy-sr8wf", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/173/configs/tmpfzits521' && python '/galaxy/server/database/jobs_directory/000/173/configs/tmpfzits521'", "user_email": "tests@fake.org", "command_version": "anndata version: 0.7.5\n\nloompy version: 2.0.17", "params": {"__input_ext": "\"h5ad\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "manipulate": "{\"__current_case__\": 2, \"function\": \"var_names_make_unique\", \"join\": \"-\"}"}, "inputs": {"input": {"id": "0057b99aca4835a0", "src": "hda", "uuid": "c49901d4-5618-4f1e-a2fc-8babdf4ed6cd"}}, "outputs": {"anndata": {"id": "daa992d45bf0a66b", "src": "hda", "uuid": "a9d23087-d388-4c65-a4be-a478abd52328"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/c/4/9/dataset_c49901d4-5618-4f1e-a2fc-8babdf4ed6cd.dat')\n\nadata.var_names_make_unique(join='-')\n\n\nadata.write('anndata.h5ad')\n", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_stdout": "", "job_stderr": "", "stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/c/4/9/dataset_c49901d4-5618-4f1e-a2fc-8babdf4ed6cd.dat')\n\nadata.var_names_make_unique(join='-')\n\n\nadata.write('anndata.h5ad')\n", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-11-08 19:23:54", "plugin": "core", "name": "end_epoch", "raw_value": "1731093834.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:23:52", "plugin": "core", "name": "start_epoch", "raw_value": "1731093832.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "anndata_manipulate/0.7.5+galaxy1-3", "has_data": true, "data": {"tool_id": "anndata_manipulate", "tool_version": "0.7.5+galaxy1", "test_index": 3, "time_seconds": 38.21318578720093, "inputs": {"input": {"src": "hda", "id": "af8afe74309bcaf6"}, "manipulate|key": "cell_type", "manipulate|categories": "Er,Ml,Mt, Ne, pr", "manipulate|function": "rename_categories"}, "job": {"model_class": "Job", "id": "dba0a91ab7c50a76", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:17:26.926411", "update_time": "2024-11-08T19:17:42.733994", "galaxy_version": "24.1", "external_id": "gxy-72fcz", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/151/configs/tmpllkc_u6n' && python '/galaxy/server/database/jobs_directory/000/151/configs/tmpllkc_u6n'", "user_email": "tests@fake.org", "command_version": "anndata version: 0.7.5\n\nloompy version: 2.0.17", "params": {"__input_ext": "\"h5ad\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "manipulate": "{\"__current_case__\": 3, \"categories\": \"Er,Ml,Mt, Ne, pr\", \"function\": \"rename_categories\", \"key\": \"cell_type\"}"}, "inputs": {"input": {"id": "af8afe74309bcaf6", "src": "hda", "uuid": "39a4dda2-9435-4386-a1f2-59a2c36f23ca"}}, "outputs": {"anndata": {"id": "3e4c9827a204efc2", "src": "hda", "uuid": "03b81ba6-ef70-41c9-a2ca-59ed8f268f25"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/3/9/a/dataset_39a4dda2-9435-4386-a1f2-59a2c36f23ca.dat')\n\nadata.rename_categories(\n key='cell_type',\n categories=['Er', 'Ml', 'Mt', 'Ne', 'pr'])\n\n\nadata.write('anndata.h5ad')\n", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_stdout": "", "job_stderr": "", "stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/3/9/a/dataset_39a4dda2-9435-4386-a1f2-59a2c36f23ca.dat')\n\nadata.rename_categories(\n key='cell_type',\n categories=['Er', 'Ml', 'Mt', 'Ne', 'pr'])\n\n\nadata.write('anndata.h5ad')\n", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-11-08 19:17:30", "plugin": "core", "name": "end_epoch", "raw_value": "1731093450.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:17:28", "plugin": "core", "name": "start_epoch", "raw_value": "1731093448.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "anndata_manipulate/0.7.5+galaxy1-3", "has_data": true, "data": {"tool_id": "anndata_manipulate", "tool_version": "0.7.5+galaxy1", "test_index": 3, "time_seconds": 12.723973035812378, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "anndata_manipulate/0.7.5+galaxy1-4", "has_data": true, "data": {"tool_id": "anndata_manipulate", "tool_version": "0.7.5+galaxy1", "test_index": 4, "time_seconds": 38.5667929649353, "inputs": {"input": {"src": "hda", "id": "e9cea873a02f585b"}, "manipulate|function": "strings_to_categoricals"}, "job": {"model_class": "Job", "id": "237e69e4ea734e4b", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:18:05.199436", "update_time": "2024-11-08T19:18:21.123802", "galaxy_version": "24.1", "external_id": "gxy-nlxqn", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/153/configs/tmpapxpw5kl' && python '/galaxy/server/database/jobs_directory/000/153/configs/tmpapxpw5kl'", "user_email": "tests@fake.org", "command_version": "anndata version: 0.7.5\n\nloompy version: 2.0.17", "params": {"__input_ext": "\"h5ad\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "manipulate": "{\"__current_case__\": 4, \"function\": \"strings_to_categoricals\"}"}, "inputs": {"input": {"id": "e9cea873a02f585b", "src": "hda", "uuid": "2e142331-a63c-466b-b43e-8e0f5c8a48b1"}}, "outputs": {"anndata": {"id": "8f3478df74d5586e", "src": "hda", "uuid": "f6f1ec1b-8113-4bf5-b8df-57daae20498c"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/2/e/1/dataset_2e142331-a63c-466b-b43e-8e0f5c8a48b1.dat')\n\nadata.strings_to_categoricals()\n\n\nadata.write('anndata.h5ad')\n", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_stdout": "", "job_stderr": "", "stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/2/e/1/dataset_2e142331-a63c-466b-b43e-8e0f5c8a48b1.dat')\n\nadata.strings_to_categoricals()\n\n\nadata.write('anndata.h5ad')\n", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-08 19:18:08", "plugin": "core", "name": "end_epoch", "raw_value": "1731093488.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:18:07", "plugin": "core", "name": "start_epoch", "raw_value": "1731093487.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "anndata_manipulate/0.7.5+galaxy1-4", "has_data": true, "data": {"tool_id": "anndata_manipulate", "tool_version": "0.7.5+galaxy1", "test_index": 4, "time_seconds": 37.817885875701904, "inputs": {"input": {"src": "hda", "id": "ef1a6b50251d9fae"}, "manipulate|function": "strings_to_categoricals"}, "job": {"model_class": "Job", "id": "737b3033e5b6550c", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:24:42.459620", "update_time": "2024-11-08T19:24:58.195598", "galaxy_version": "24.1", "external_id": "gxy-gjjsz", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/176/configs/tmpsbgfx4jn' && python '/galaxy/server/database/jobs_directory/000/176/configs/tmpsbgfx4jn'", "user_email": "tests@fake.org", "command_version": "anndata version: 0.7.5\n\nloompy version: 2.0.17", "params": {"__input_ext": "\"h5ad\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "manipulate": "{\"__current_case__\": 4, \"function\": \"strings_to_categoricals\"}"}, "inputs": {"input": {"id": "ef1a6b50251d9fae", "src": "hda", "uuid": "29c6f498-3a0d-4a92-b30b-fb70a249b2a0"}}, "outputs": {"anndata": {"id": "a62fb4db4837b8ab", "src": "hda", "uuid": "4b9aecb8-6bba-43cd-8996-eee97466ebbd"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/2/9/c/dataset_29c6f498-3a0d-4a92-b30b-fb70a249b2a0.dat')\n\nadata.strings_to_categoricals()\n\n\nadata.write('anndata.h5ad')\n", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_stdout": "", "job_stderr": "", "stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/2/9/c/dataset_29c6f498-3a0d-4a92-b30b-fb70a249b2a0.dat')\n\nadata.strings_to_categoricals()\n\n\nadata.write('anndata.h5ad')\n", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-08 19:24:45", "plugin": "core", "name": "end_epoch", "raw_value": "1731093885.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:24:44", "plugin": "core", "name": "start_epoch", "raw_value": "1731093884.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "anndata_manipulate/0.7.5+galaxy1-5", "has_data": true, "data": {"tool_id": "anndata_manipulate", "tool_version": "0.7.5+galaxy1", "test_index": 5, "time_seconds": 38.478827476501465, "inputs": {"input": {"src": "hda", "id": "4538c8da25243180"}, "manipulate|function": "transpose"}, "job": {"model_class": "Job", "id": "7b35e56724bdc701", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:18:43.738162", "update_time": "2024-11-08T19:18:59.684994", "galaxy_version": "24.1", "external_id": "gxy-cbg9m", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/155/configs/tmp44_srhkc' && python '/galaxy/server/database/jobs_directory/000/155/configs/tmp44_srhkc'", "user_email": "tests@fake.org", "command_version": "anndata version: 0.7.5\n\nloompy version: 2.0.17", "params": {"__input_ext": "\"h5ad\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "manipulate": "{\"__current_case__\": 5, \"function\": \"transpose\"}"}, "inputs": {"input": {"id": "4538c8da25243180", "src": "hda", "uuid": "3e1e2ca6-bb93-4c87-9cf7-1537da2ee671"}}, "outputs": {"anndata": {"id": "737b3033e5b6550c", "src": "hda", "uuid": "a5287124-6172-41a3-b6d6-8559897ee71d"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/3/e/1/dataset_3e1e2ca6-bb93-4c87-9cf7-1537da2ee671.dat')\n\nadata = adata.transpose()\n\n\nadata.write('anndata.h5ad')\n", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nVariable names are not unique. To make them unique, call `.var_names_make_unique`.\n", "job_stdout": "", "job_stderr": "", "stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/3/e/1/dataset_3e1e2ca6-bb93-4c87-9cf7-1537da2ee671.dat')\n\nadata = adata.transpose()\n\n\nadata.write('anndata.h5ad')\n", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nVariable names are not unique. To make them unique, call `.var_names_make_unique`.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-08 19:18:46", "plugin": "core", "name": "end_epoch", "raw_value": "1731093526.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:18:45", "plugin": "core", "name": "start_epoch", "raw_value": "1731093525.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "anndata_manipulate/0.7.5+galaxy1-5", "has_data": true, "data": {"tool_id": "anndata_manipulate", "tool_version": "0.7.5+galaxy1", "test_index": 5, "time_seconds": 36.592214822769165, "inputs": {"input": {"src": "hda", "id": "34104ebdd97e7c12"}, "manipulate|function": "transpose"}, "job": {"model_class": "Job", "id": "616fd04f6b296dbe", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:25:19.707415", "update_time": "2024-11-08T19:25:34.699351", "galaxy_version": "24.1", "external_id": "gxy-692tr", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/178/configs/tmp6ek_tfwd' && python '/galaxy/server/database/jobs_directory/000/178/configs/tmp6ek_tfwd'", "user_email": "tests@fake.org", "command_version": "anndata version: 0.7.5\n\nloompy version: 2.0.17", "params": {"__input_ext": "\"h5ad\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "manipulate": "{\"__current_case__\": 5, \"function\": \"transpose\"}"}, "inputs": {"input": {"id": "34104ebdd97e7c12", "src": "hda", "uuid": "9531cf8f-b823-4a98-b49f-08ad51145f35"}}, "outputs": {"anndata": {"id": "07ef8540660ce7c0", "src": "hda", "uuid": "35f40497-f7df-47c8-a241-f24b80356ef4"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/9/5/3/dataset_9531cf8f-b823-4a98-b49f-08ad51145f35.dat')\n\nadata = adata.transpose()\n\n\nadata.write('anndata.h5ad')\n", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nVariable names are not unique. To make them unique, call `.var_names_make_unique`.\n", "job_stdout": "", "job_stderr": "", "stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/9/5/3/dataset_9531cf8f-b823-4a98-b49f-08ad51145f35.dat')\n\nadata = adata.transpose()\n\n\nadata.write('anndata.h5ad')\n", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nVariable names are not unique. To make them unique, call `.var_names_make_unique`.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-11-08 19:25:22", "plugin": "core", "name": "end_epoch", "raw_value": "1731093922.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:25:20", "plugin": "core", "name": "start_epoch", "raw_value": "1731093920.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "anndata_manipulate/0.7.5+galaxy1-6", "has_data": true, "data": {"tool_id": "anndata_manipulate", "tool_version": "0.7.5+galaxy1", "test_index": 6, "time_seconds": 40.734774351119995, "inputs": {"input": {"src": "hda", "id": "a8abc5f9b6912fd7"}, "manipulate|var_obs": "var", "manipulate|new_annot": {"src": "hda", "id": "616fd04f6b296dbe"}, "manipulate|function": "add_annotation"}, "job": {"model_class": "Job", "id": "3b1d785838fcf855", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:19:23.828534", "update_time": "2024-11-08T19:19:40.426822", "galaxy_version": "24.1", "external_id": "gxy-mtb4h", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/158/configs/tmpyl4h3p9u' && python '/galaxy/server/database/jobs_directory/000/158/configs/tmpyl4h3p9u'", "user_email": "tests@fake.org", "command_version": "anndata version: 0.7.5\n\nloompy version: 2.0.17", "params": {"__input_ext": "\"h5ad\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "manipulate": "{\"__current_case__\": 6, \"function\": \"add_annotation\", \"new_annot\": {\"values\": [{\"id\": 178, \"src\": \"hda\"}]}, \"var_obs\": \"var\"}"}, "inputs": {"input": {"id": "a8abc5f9b6912fd7", "src": "hda", "uuid": "90f9cbae-d305-4ac2-b37f-7d2954a62610"}, "manipulate|new_annot": {"id": "616fd04f6b296dbe", "src": "hda", "uuid": "c3190aad-5352-4a75-9579-4321e7905a09"}}, "outputs": {"anndata": {"id": "b6408abd5e224f8b", "src": "hda", "uuid": "282f0ac9-fcc2-464f-89b1-da48f07fba9b"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/9/0/f/dataset_90f9cbae-d305-4ac2-b37f-7d2954a62610.dat')\n\nimport pandas as pd\nextra_annot_t = pd.read_csv('/galaxy/server/database/objects/c/3/1/dataset_c3190aad-5352-4a75-9579-4321e7905a09.dat', sep='\\t').reset_index(drop=True)\nvar_index = adata.var_names\nvar = pd.concat([adata.var.reset_index(drop=True), extra_annot_t], axis=1)\nvar.index = var_index\nadata.var = var\n\n\nadata.write('anndata.h5ad')\n", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_stdout": "", "job_stderr": "", "stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/9/0/f/dataset_90f9cbae-d305-4ac2-b37f-7d2954a62610.dat')\n\nimport pandas as pd\nextra_annot_t = pd.read_csv('/galaxy/server/database/objects/c/3/1/dataset_c3190aad-5352-4a75-9579-4321e7905a09.dat', sep='\\t').reset_index(drop=True)\nvar_index = adata.var_names\nvar = pd.concat([adata.var.reset_index(drop=True), extra_annot_t], axis=1)\nvar.index = var_index\nadata.var = var\n\n\nadata.write('anndata.h5ad')\n", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-11-08 19:19:27", "plugin": "core", "name": "end_epoch", "raw_value": "1731093567.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:19:25", "plugin": "core", "name": "start_epoch", "raw_value": "1731093565.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "anndata_manipulate/0.7.5+galaxy1-6", "has_data": true, "data": {"tool_id": "anndata_manipulate", "tool_version": "0.7.5+galaxy1", "test_index": 6, "time_seconds": 39.66567873954773, "inputs": {"input": {"src": "hda", "id": "e2bab181a597196a"}, "manipulate|var_obs": "var", "manipulate|new_annot": {"src": "hda", "id": "70f2fecc01fed51e"}, "manipulate|function": "add_annotation"}, "job": {"model_class": "Job", "id": "0072ef120b730b6a", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:25:58.160590", "update_time": "2024-11-08T19:26:14.419181", "galaxy_version": "24.1", "external_id": "gxy-r8kpt", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/181/configs/tmp80v0zht9' && python '/galaxy/server/database/jobs_directory/000/181/configs/tmp80v0zht9'", "user_email": "tests@fake.org", "command_version": "anndata version: 0.7.5\n\nloompy version: 2.0.17", "params": {"__input_ext": "\"h5ad\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "manipulate": "{\"__current_case__\": 6, \"function\": \"add_annotation\", \"new_annot\": {\"values\": [{\"id\": 201, \"src\": \"hda\"}]}, \"var_obs\": \"var\"}"}, "inputs": {"input": {"id": "e2bab181a597196a", "src": "hda", "uuid": "40272ff1-7295-41de-b0df-7c265558a9c5"}, "manipulate|new_annot": {"id": "70f2fecc01fed51e", "src": "hda", "uuid": "754680dd-72d7-427e-9321-c323876c8d18"}}, "outputs": {"anndata": {"id": "e527b0ee28d9e436", "src": "hda", "uuid": "44a8e574-1e99-4e39-ab19-8310712f22e0"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/4/0/2/dataset_40272ff1-7295-41de-b0df-7c265558a9c5.dat')\n\nimport pandas as pd\nextra_annot_t = pd.read_csv('/galaxy/server/database/objects/7/5/4/dataset_754680dd-72d7-427e-9321-c323876c8d18.dat', sep='\\t').reset_index(drop=True)\nvar_index = adata.var_names\nvar = pd.concat([adata.var.reset_index(drop=True), extra_annot_t], axis=1)\nvar.index = var_index\nadata.var = var\n\n\nadata.write('anndata.h5ad')\n", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_stdout": "", "job_stderr": "", "stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/4/0/2/dataset_40272ff1-7295-41de-b0df-7c265558a9c5.dat')\n\nimport pandas as pd\nextra_annot_t = pd.read_csv('/galaxy/server/database/objects/7/5/4/dataset_754680dd-72d7-427e-9321-c323876c8d18.dat', sep='\\t').reset_index(drop=True)\nvar_index = adata.var_names\nvar = pd.concat([adata.var.reset_index(drop=True), extra_annot_t], axis=1)\nvar.index = var_index\nadata.var = var\n\n\nadata.write('anndata.h5ad')\n", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-08 19:26:01", "plugin": "core", "name": "end_epoch", "raw_value": "1731093961.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:26:00", "plugin": "core", "name": "start_epoch", "raw_value": "1731093960.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "anndata_manipulate/0.7.5+galaxy1-7", "has_data": true, "data": {"tool_id": "anndata_manipulate", "tool_version": "0.7.5+galaxy1", "test_index": 7, "time_seconds": 39.82662343978882, "inputs": {"input": {"src": "hda", "id": "a05816edfcbf43cd"}, "manipulate|var_obs": "obs", "manipulate|new_annot": {"src": "hda", "id": "0072ef120b730b6a"}, "manipulate|function": "add_annotation"}, "job": {"model_class": "Job", "id": "449cf9cc7d01dc92", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:20:04.029010", "update_time": "2024-11-08T19:20:20.243807", "galaxy_version": "24.1", "external_id": "gxy-pvxq2", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/161/configs/tmp7piw2_5x' && python '/galaxy/server/database/jobs_directory/000/161/configs/tmp7piw2_5x'", "user_email": "tests@fake.org", "command_version": "anndata version: 0.7.5\n\nloompy version: 2.0.17", "params": {"__input_ext": "\"h5ad\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "manipulate": "{\"__current_case__\": 6, \"function\": \"add_annotation\", \"new_annot\": {\"values\": [{\"id\": 181, \"src\": \"hda\"}]}, \"var_obs\": \"obs\"}"}, "inputs": {"input": {"id": "a05816edfcbf43cd", "src": "hda", "uuid": "cb27b446-2134-4564-b504-9ba95cf63c6c"}, "manipulate|new_annot": {"id": "0072ef120b730b6a", "src": "hda", "uuid": "3d1f2a66-dcf4-4034-adcf-0005ab134335"}}, "outputs": {"anndata": {"id": "c366515eb0712963", "src": "hda", "uuid": "9f2031ee-0c64-4f55-bd7c-aa45b841d097"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/c/b/2/dataset_cb27b446-2134-4564-b504-9ba95cf63c6c.dat')\n\nimport pandas as pd\nextra_annot_t = pd.read_csv('/galaxy/server/database/objects/3/d/1/dataset_3d1f2a66-dcf4-4034-adcf-0005ab134335.dat', sep='\\t').reset_index(drop=True)\nobs_index = adata.obs.index\nobs = pd.concat([adata.obs.reset_index(drop=True), extra_annot_t], axis=1)\nobs.index = obs_index\nadata.obs = obs\n\n\nadata.write('anndata.h5ad')\n", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n... storing 'annot2' as categorical\n", "job_stdout": "", "job_stderr": "", "stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/c/b/2/dataset_cb27b446-2134-4564-b504-9ba95cf63c6c.dat')\n\nimport pandas as pd\nextra_annot_t = pd.read_csv('/galaxy/server/database/objects/3/d/1/dataset_3d1f2a66-dcf4-4034-adcf-0005ab134335.dat', sep='\\t').reset_index(drop=True)\nobs_index = adata.obs.index\nobs = pd.concat([adata.obs.reset_index(drop=True), extra_annot_t], axis=1)\nobs.index = obs_index\nadata.obs = obs\n\n\nadata.write('anndata.h5ad')\n", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n... storing 'annot2' as categorical\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-08 19:20:06", "plugin": "core", "name": "end_epoch", "raw_value": "1731093606.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:20:05", "plugin": "core", "name": "start_epoch", "raw_value": "1731093605.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "anndata_manipulate/0.7.5+galaxy1-7", "has_data": true, "data": {"tool_id": "anndata_manipulate", "tool_version": "0.7.5+galaxy1", "test_index": 7, "time_seconds": 40.40920972824097, "inputs": {"input": {"src": "hda", "id": "7faebc7c2663f710"}, "manipulate|var_obs": "obs", "manipulate|new_annot": {"src": "hda", "id": "c88976d64d6b5b93"}, "manipulate|function": "add_annotation"}, "job": {"model_class": "Job", "id": "d0332b419eb36ef4", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:26:38.638204", "update_time": "2024-11-08T19:26:54.920542", "galaxy_version": "24.1", "external_id": "gxy-kbm2p", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/184/configs/tmpoyfb1vt1' && python '/galaxy/server/database/jobs_directory/000/184/configs/tmpoyfb1vt1'", "user_email": "tests@fake.org", "command_version": "anndata version: 0.7.5\n\nloompy version: 2.0.17", "params": {"__input_ext": "\"h5ad\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "manipulate": "{\"__current_case__\": 6, \"function\": \"add_annotation\", \"new_annot\": {\"values\": [{\"id\": 204, \"src\": \"hda\"}]}, \"var_obs\": \"obs\"}"}, "inputs": {"input": {"id": "7faebc7c2663f710", "src": "hda", "uuid": "6e8a2c32-8e32-4b9d-8a37-d8f37048dcca"}, "manipulate|new_annot": {"id": "c88976d64d6b5b93", "src": "hda", "uuid": "670af8b8-eb35-46cf-9276-86648620d30f"}}, "outputs": {"anndata": {"id": "a0d50995af565d4e", "src": "hda", "uuid": "3443ec2a-36e8-4931-aee0-d2141ff5dd15"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/6/e/8/dataset_6e8a2c32-8e32-4b9d-8a37-d8f37048dcca.dat')\n\nimport pandas as pd\nextra_annot_t = pd.read_csv('/galaxy/server/database/objects/6/7/0/dataset_670af8b8-eb35-46cf-9276-86648620d30f.dat', sep='\\t').reset_index(drop=True)\nobs_index = adata.obs.index\nobs = pd.concat([adata.obs.reset_index(drop=True), extra_annot_t], axis=1)\nobs.index = obs_index\nadata.obs = obs\n\n\nadata.write('anndata.h5ad')\n", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n... storing 'annot2' as categorical\n", "job_stdout": "", "job_stderr": "", "stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/6/e/8/dataset_6e8a2c32-8e32-4b9d-8a37-d8f37048dcca.dat')\n\nimport pandas as pd\nextra_annot_t = pd.read_csv('/galaxy/server/database/objects/6/7/0/dataset_670af8b8-eb35-46cf-9276-86648620d30f.dat', sep='\\t').reset_index(drop=True)\nobs_index = adata.obs.index\nobs = pd.concat([adata.obs.reset_index(drop=True), extra_annot_t], axis=1)\nobs.index = obs_index\nadata.obs = obs\n\n\nadata.write('anndata.h5ad')\n", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n... storing 'annot2' as categorical\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-11-08 19:26:42", "plugin": "core", "name": "end_epoch", "raw_value": "1731094002.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:26:40", "plugin": "core", "name": "start_epoch", "raw_value": "1731094000.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "anndata_manipulate/0.7.5+galaxy1-8", "has_data": true, "data": {"tool_id": "anndata_manipulate", "tool_version": "0.7.5+galaxy1", "test_index": 8, "time_seconds": 38.18889379501343, "inputs": {"input": {"src": "hda", "id": "d2214987cb2d8b80"}, "manipulate|var_obs": "var", "manipulate|filter|index|text": "Gata2,EKLF", "manipulate|filter|index|format": "text", "manipulate|filter|filter": "index", "manipulate|function": "filter"}, "job": {"model_class": "Job", "id": "74798f5cd5fbe7e1", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:20:43.025058", "update_time": "2024-11-08T19:20:58.630259", "galaxy_version": "24.1", "external_id": "gxy-dhxz5", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/163/configs/tmpumgi1rhi' && python '/galaxy/server/database/jobs_directory/000/163/configs/tmpumgi1rhi'", "user_email": "tests@fake.org", "command_version": "anndata version: 0.7.5\n\nloompy version: 2.0.17", "params": {"__input_ext": "\"h5ad\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "manipulate": "{\"__current_case__\": 7, \"filter\": {\"__current_case__\": 1, \"filter\": \"index\", \"index\": {\"__current_case__\": 0, \"format\": \"text\", \"text\": \"Gata2,EKLF\"}}, \"function\": \"filter\", \"var_obs\": \"var\"}"}, "inputs": {"input": {"id": "d2214987cb2d8b80", "src": "hda", "uuid": "130ef160-7f0d-44c4-9245-49ba2cda1997"}}, "outputs": {"anndata": {"id": "d0332b419eb36ef4", "src": "hda", "uuid": "57dde9dd-c86a-4da7-8070-96c8dff36ee2"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/1/3/0/dataset_130ef160-7f0d-44c4-9245-49ba2cda1997.dat')\n\nfiltered = ['Gata2', 'EKLF']\nprint(filtered)\n\nadata = adata[:,filtered]\n\n\nadata.write('anndata.h5ad')\n['Gata2', 'EKLF']\n", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_stdout": "", "job_stderr": "", "stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/1/3/0/dataset_130ef160-7f0d-44c4-9245-49ba2cda1997.dat')\n\nfiltered = ['Gata2', 'EKLF']\nprint(filtered)\n\nadata = adata[:,filtered]\n\n\nadata.write('anndata.h5ad')\n['Gata2', 'EKLF']\n", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-08 19:20:45", "plugin": "core", "name": "end_epoch", "raw_value": "1731093645.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:20:44", "plugin": "core", "name": "start_epoch", "raw_value": "1731093644.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "anndata_manipulate/0.7.5+galaxy1-8", "has_data": true, "data": {"tool_id": "anndata_manipulate", "tool_version": "0.7.5+galaxy1", "test_index": 8, "time_seconds": 27.84930443763733, "inputs": {"input": {"src": "hda", "id": "7de9afc393b6bf31"}, "manipulate|var_obs": "var", "manipulate|filter|index|text": "Gata2,EKLF", "manipulate|filter|index|format": "text", "manipulate|filter|filter": "index", "manipulate|function": "filter"}, "job": {"model_class": "Job", "id": "b5c05e39cecb3340", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1", "state": "error", "exit_code": null, "create_time": "2024-11-08T19:27:17.475407", "update_time": "2024-11-08T19:27:23.111106", "galaxy_version": "24.1", "external_id": "gxy-cmqk4", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/186/configs/tmpli09xp_d' && python '/galaxy/server/database/jobs_directory/000/186/configs/tmpli09xp_d'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"h5ad\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "manipulate": "{\"__current_case__\": 7, \"filter\": {\"__current_case__\": 1, \"filter\": \"index\", \"index\": {\"__current_case__\": 0, \"format\": \"text\", \"text\": \"Gata2,EKLF\"}}, \"function\": \"filter\", \"var_obs\": \"var\"}"}, "inputs": {"input": {"id": "7de9afc393b6bf31", "src": "hda", "uuid": "9f368a2f-ba05-4bf2-9f98-21b0d3ccec51"}}, "outputs": {"anndata": {"id": "ac4960e8ecd0cb2e", "src": "hda", "uuid": "4fd46551-f64e-4179-8c8b-e3b189a89a6d"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/9/f/3/dataset_9f368a2f-ba05-4bf2-9f98-21b0d3ccec51.dat')\n\nfiltered = ['Gata2', 'EKLF']\nprint(filtered)\n\nadata = adata[:,filtered]\n\n\nadata.write('anndata.h5ad')\n['Gata2', 'EKLF']\n", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_stdout": null, "job_stderr": null, "stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/9/f/3/dataset_9f368a2f-ba05-4bf2-9f98-21b0d3ccec51.dat')\n\nfiltered = ['Gata2', 'EKLF']\nprint(filtered)\n\nadata = adata[:,filtered]\n\n\nadata.write('anndata.h5ad')\n['Gata2', 'EKLF']\n", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1, exit_code: None, stderr: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1, exit_code: None, stderr: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n."], "status": "failure"}}, {"id": "anndata_manipulate/0.7.5+galaxy1-9", "has_data": true, "data": {"tool_id": "anndata_manipulate", "tool_version": "0.7.5+galaxy1", "test_index": 9, "time_seconds": 36.0217444896698, "inputs": {"input": {"src": "hda", "id": "32c6704a17157385"}, "manipulate|var_obs": "obs", "manipulate|filter|key": "cell_type", "manipulate|filter|filter_key|filter": "equal", "manipulate|filter|filter_key|value": "progenitor", "manipulate|filter|filter_key|type": "text", "manipulate|filter|filter": "key", "manipulate|function": "filter"}, "job": {"model_class": "Job", "id": "ffaed0ea0cfde573", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:21:19.976747", "update_time": "2024-11-08T19:21:34.820073", "galaxy_version": "24.1", "external_id": "gxy-ck58l", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/165/configs/tmplobsuzyt' && python '/galaxy/server/database/jobs_directory/000/165/configs/tmplobsuzyt'", "user_email": "tests@fake.org", "command_version": "anndata version: 0.7.5\n\nloompy version: 2.0.17", "params": {"__input_ext": "\"h5ad\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "manipulate": "{\"__current_case__\": 7, \"filter\": {\"__current_case__\": 0, \"filter\": \"key\", \"filter_key\": {\"__current_case__\": 1, \"filter\": \"equal\", \"type\": \"text\", \"value\": \"progenitor\"}, \"key\": \"cell_type\"}, \"function\": \"filter\", \"var_obs\": \"obs\"}"}, "inputs": {"input": {"id": "32c6704a17157385", "src": "hda", "uuid": "533785d3-0d00-4c21-9bbf-8353c8766054"}}, "outputs": {"anndata": {"id": "b5c05e39cecb3340", "src": "hda", "uuid": "214b265d-ecbf-4531-808f-0a505657f178"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/5/3/3/dataset_533785d3-0d00-4c21-9bbf-8353c8766054.dat')\n\nfiltered = adata.obs['cell_type']\n\nfiltered = filtered == 'progenitor'\n\nprint(filtered)\n\nadata = adata[filtered, :]\n\n\nadata.write('anndata.h5ad')\nindex\n0 True\n1 True\n2 True\n3 True\n4 True\n ... \n155 False\n156 False\n157 False\n158 False\n159 False\nName: cell_type, Length: 640, dtype: bool\n", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_stdout": "", "job_stderr": "", "stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/5/3/3/dataset_533785d3-0d00-4c21-9bbf-8353c8766054.dat')\n\nfiltered = adata.obs['cell_type']\n\nfiltered = filtered == 'progenitor'\n\nprint(filtered)\n\nadata = adata[filtered, :]\n\n\nadata.write('anndata.h5ad')\nindex\n0 True\n1 True\n2 True\n3 True\n4 True\n ... \n155 False\n156 False\n157 False\n158 False\n159 False\nName: cell_type, Length: 640, dtype: bool\n", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-08 19:21:22", "plugin": "core", "name": "end_epoch", "raw_value": "1731093682.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:21:21", "plugin": "core", "name": "start_epoch", "raw_value": "1731093681.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "anndata_manipulate/0.7.5+galaxy1-9", "has_data": true, "data": {"tool_id": "anndata_manipulate", "tool_version": "0.7.5+galaxy1", "test_index": 9, "time_seconds": 38.47697949409485, "inputs": {"input": {"src": "hda", "id": "8943e16a55fb7a9a"}, "manipulate|var_obs": "obs", "manipulate|filter|key": "cell_type", "manipulate|filter|filter_key|filter": "equal", "manipulate|filter|filter_key|value": "progenitor", "manipulate|filter|filter_key|type": "text", "manipulate|filter|filter": "key", "manipulate|function": "filter"}, "job": {"model_class": "Job", "id": "030ab49c7f4d195b", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:27:44.466361", "update_time": "2024-11-08T19:28:01.520483", "galaxy_version": "24.1", "external_id": "gxy-jmbxz", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/188/configs/tmpa39urazy' && python '/galaxy/server/database/jobs_directory/000/188/configs/tmpa39urazy'", "user_email": "tests@fake.org", "command_version": "anndata version: 0.7.5\n\nloompy version: 2.0.17", "params": {"__input_ext": "\"h5ad\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "manipulate": "{\"__current_case__\": 7, \"filter\": {\"__current_case__\": 0, \"filter\": \"key\", \"filter_key\": {\"__current_case__\": 1, \"filter\": \"equal\", \"type\": \"text\", \"value\": \"progenitor\"}, \"key\": \"cell_type\"}, \"function\": \"filter\", \"var_obs\": \"obs\"}"}, "inputs": {"input": {"id": "8943e16a55fb7a9a", "src": "hda", "uuid": "709a1388-26df-46cf-8cda-16ad3d8f0b94"}}, "outputs": {"anndata": {"id": "a88d5e16219380b4", "src": "hda", "uuid": "35da5c37-bf17-4b75-a2b7-0fe55d1ef91c"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/7/0/9/dataset_709a1388-26df-46cf-8cda-16ad3d8f0b94.dat')\n\nfiltered = adata.obs['cell_type']\n\nfiltered = filtered == 'progenitor'\n\nprint(filtered)\n\nadata = adata[filtered, :]\n\n\nadata.write('anndata.h5ad')\nindex\n0 True\n1 True\n2 True\n3 True\n4 True\n ... \n155 False\n156 False\n157 False\n158 False\n159 False\nName: cell_type, Length: 640, dtype: bool\n", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_stdout": "", "job_stderr": "", "stdout": "\n\nimport anndata as ad\n \n \n\nadata = ad.read('/galaxy/server/database/objects/7/0/9/dataset_709a1388-26df-46cf-8cda-16ad3d8f0b94.dat')\n\nfiltered = adata.obs['cell_type']\n\nfiltered = filtered == 'progenitor'\n\nprint(filtered)\n\nadata = adata[filtered, :]\n\n\nadata.write('anndata.h5ad')\nindex\n0 True\n1 True\n2 True\n3 True\n4 True\n ... \n155 False\n156 False\n157 False\n158 False\n159 False\nName: cell_type, Length: 640, dtype: bool\n", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-08 19:27:47", "plugin": "core", "name": "end_epoch", "raw_value": "1731094067.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:27:46", "plugin": "core", "name": "start_epoch", "raw_value": "1731094066.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "bcftools_norm/1.15.1+galaxy4-0", "has_data": true, "data": {"tool_id": "bcftools_norm", "tool_version": "1.15.1+galaxy4", "test_index": 0, "time_seconds": 13.111390829086304, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "bcftools_norm/1.15.1+galaxy4-1", "has_data": true, "data": {"tool_id": "bcftools_norm", "tool_version": "1.15.1+galaxy4", "test_index": 1, "status": "skip"}}, {"id": "bcftools_norm/1.15.1+galaxy4-2", "has_data": true, "data": {"tool_id": "bcftools_norm", "tool_version": "1.15.1+galaxy4", "test_index": 2, "time_seconds": 44.71992588043213, "inputs": {"input_file": {"src": "hda", "id": "3c8904a39cba5a6b"}, "reference_source|fasta_ref": {"src": "hda", "id": "5b1d21b5f08a3268"}, "reference_source|reference_source_selector": "history", "multiallelics|mode": "-", "output_type": "v"}, "job": {"model_class": "Job", "id": "a88d5e16219380b4", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:34:28.898821", "update_time": "2024-11-08T19:34:50.322541", "galaxy_version": "24.1", "external_id": "gxy-c74ch", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/2/1/e/dataset_21ee9367-cec2-4136-9ea1-94f821000066.dat' > input.vcf.gz && bcftools index input.vcf.gz && ln -s '/galaxy/server/database/objects/c/4/d/dataset_c4de3c13-69f2-4835-bcc4-234389e75646.dat' ref.fa && samtools faidx ref.fa && awk '{ if ($0 !~ />/) {print toupper($0)} else {print $0} }' 'ref.fa' > ref_upper.fa && bcftools norm --fasta-ref ref_upper.fa --check-ref w --do-not-normalize --multiallelics '-both' --site-win 1000 --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/d/7/1/dataset_d718fcd0-b6ef-4214-be89-9f0fe7337b08.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_default": "{\"site_win\": \"1000\"}", "sec_restrict": "{\"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}", "multiallelics": "{\"__current_case__\": 1, \"mode\": \"-\", \"multiallelic_types\": \"both\"}", "rm_dup": "\"\"", "old_rec_tag": "\"\"", "normalize_indels": "false", "atomize": "false", "check_ref": "\"w\"", "reference_source": "{\"__current_case__\": 1, \"fasta_ref\": {\"values\": [{\"id\": 231, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"input_file": {"id": "3c8904a39cba5a6b", "src": "hda", "uuid": "21ee9367-cec2-4136-9ea1-94f821000066"}, "reference_source|fasta_ref": {"id": "5b1d21b5f08a3268", "src": "hda", "uuid": "c4de3c13-69f2-4835-bcc4-234389e75646"}}, "outputs": {"output_file": {"id": "85e97f742ca04a70", "src": "hda", "uuid": "d718fcd0-b6ef-4214-be89-9f0fe7337b08"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Lines total/split/realigned/skipped:\t19/7/0/0\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Lines total/split/realigned/skipped:\t19/7/0/0\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-08 19:34:37", "plugin": "core", "name": "end_epoch", "raw_value": "1731094477.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:34:36", "plugin": "core", "name": "start_epoch", "raw_value": "1731094476.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "2", "plugin": "core", "name": "galaxy_slots", "raw_value": "2.0000000"}]}, "status": "success"}}, {"id": "bcftools_norm/1.15.1+galaxy4-3", "has_data": true, "data": {"tool_id": "bcftools_norm", "tool_version": "1.15.1+galaxy4", "test_index": 3, "time_seconds": 69.54261922836304, "inputs": {"input_file": {"src": "hda", "id": "e3071098709962db"}, "reference_source|fasta_ref": {"src": "hda", "id": "03cdf6687ced1934"}, "reference_source|reference_source_selector": "history", "normalize_indels": true, "multiallelics|mode": "-", "output_type": "v"}, "job": {"model_class": "Job", "id": "d2999df588b66189", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:35:12.751395", "update_time": "2024-11-08T19:35:59.795672", "galaxy_version": "24.1", "external_id": "gxy-rffgv", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/6/5/d/dataset_65d78585-59b6-4ce2-bc13-909a56bfe7e8.dat' > input.vcf.gz && bcftools index input.vcf.gz && ln -s '/galaxy/server/database/objects/9/6/c/dataset_96cad425-50e6-488c-8ba8-76e91de04f17.dat' ref.fa && samtools faidx ref.fa && awk '{ if ($0 !~ />/) {print toupper($0)} else {print $0} }' 'ref.fa' > ref_upper.fa && bcftools norm --fasta-ref ref_upper.fa --check-ref w --multiallelics '-both' --site-win 1000 --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/9/f/a/dataset_9fa76214-1f3f-437b-93bf-8c204729de78.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_default": "{\"site_win\": \"1000\"}", "sec_restrict": "{\"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}", "multiallelics": "{\"__current_case__\": 1, \"mode\": \"-\", \"multiallelic_types\": \"both\"}", "rm_dup": "\"\"", "old_rec_tag": "\"\"", "normalize_indels": "true", "atomize": "false", "check_ref": "\"w\"", "reference_source": "{\"__current_case__\": 1, \"fasta_ref\": {\"values\": [{\"id\": 234, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"input_file": {"id": "e3071098709962db", "src": "hda", "uuid": "65d78585-59b6-4ce2-bc13-909a56bfe7e8"}, "reference_source|fasta_ref": {"id": "03cdf6687ced1934", "src": "hda", "uuid": "96cad425-50e6-488c-8ba8-76e91de04f17"}}, "outputs": {"output_file": {"id": "43bff08b1ea05cf5", "src": "hda", "uuid": "9fa76214-1f3f-437b-93bf-8c204729de78"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Lines total/split/realigned/skipped:\t19/7/19/0\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Lines total/split/realigned/skipped:\t19/7/19/0\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-08 19:35:47", "plugin": "core", "name": "end_epoch", "raw_value": "1731094547.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:35:46", "plugin": "core", "name": "start_epoch", "raw_value": "1731094546.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "2", "plugin": "core", "name": "galaxy_slots", "raw_value": "2.0000000"}]}, "status": "success"}}, {"id": "bcftools_norm/1.15.1+galaxy4-4", "has_data": true, "data": {"tool_id": "bcftools_norm", "tool_version": "1.15.1+galaxy4", "test_index": 4, "time_seconds": 36.569010972976685, "inputs": {"input_file": {"src": "hda", "id": "13682044cce8454f"}, "reference_source|fasta_ref": {"src": "hda", "id": "3a7169340542f85f"}, "reference_source|reference_source_selector": "history", "multiallelics|mode": "+", "output_type": "v"}, "job": {"model_class": "Job", "id": "7e9b3f6181d9f21f", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:36:22.068067", "update_time": "2024-11-08T19:36:36.339275", "galaxy_version": "24.1", "external_id": "gxy-pmnk6", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/5/4/d/dataset_54d53a05-bd23-4fc7-acb4-44245a80060e.dat' > input.vcf.gz && bcftools index input.vcf.gz && ln -s '/galaxy/server/database/objects/e/2/e/dataset_e2e1c4f3-2969-4cba-9d06-34c42acf7417.dat' ref.fa && samtools faidx ref.fa && awk '{ if ($0 !~ />/) {print toupper($0)} else {print $0} }' 'ref.fa' > ref_upper.fa && bcftools norm --fasta-ref ref_upper.fa --check-ref w --do-not-normalize --multiallelics '+both' --site-win 1000 --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/e/4/a/dataset_e4ad488a-2698-4acb-9e0d-e80cd4ac5b97.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_default": "{\"site_win\": \"1000\"}", "sec_restrict": "{\"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}", "multiallelics": "{\"__current_case__\": 2, \"mode\": \"+\", \"multiallelic_types\": \"both\", \"strict_filter\": false}", "rm_dup": "\"\"", "old_rec_tag": "\"\"", "normalize_indels": "false", "atomize": "false", "check_ref": "\"w\"", "reference_source": "{\"__current_case__\": 1, \"fasta_ref\": {\"values\": [{\"id\": 237, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"input_file": {"id": "13682044cce8454f", "src": "hda", "uuid": "54d53a05-bd23-4fc7-acb4-44245a80060e"}, "reference_source|fasta_ref": {"id": "3a7169340542f85f", "src": "hda", "uuid": "e2e1c4f3-2969-4cba-9d06-34c42acf7417"}}, "outputs": {"output_file": {"id": "7cf426422c2d642f", "src": "hda", "uuid": "e4ad488a-2698-4acb-9e0d-e80cd4ac5b97"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Lines total/split/realigned/skipped:\t26/0/0/0\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Lines total/split/realigned/skipped:\t26/0/0/0\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-11-08 19:36:23", "plugin": "core", "name": "end_epoch", "raw_value": "1731094583.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:36:23", "plugin": "core", "name": "start_epoch", "raw_value": "1731094583.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "2", "plugin": "core", "name": "galaxy_slots", "raw_value": "2.0000000"}]}, "status": "success"}}, {"id": "bcftools_norm/1.15.1+galaxy4-5", "has_data": true, "data": {"tool_id": "bcftools_norm", "tool_version": "1.15.1+galaxy4", "test_index": 5, "time_seconds": 29.53701162338257, "inputs": {"input_file": {"src": "hda", "id": "dc82172fda263ec8"}, "reference_source|fasta_ref": {"src": "hda", "id": "82ce24234cd1d762"}, "reference_source|reference_source_selector": "history", "multiallelics|strict_filter": true, "multiallelics|mode": "+", "output_type": "v"}, "job": {"model_class": "Job", "id": "38e2156fd7401822", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy4", "state": "error", "exit_code": null, "create_time": "2024-11-08T19:37:00.489978", "update_time": "2024-11-08T19:37:06.053487", "galaxy_version": "24.1", "external_id": "gxy-xfpsb", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/7/a/a/dataset_7aaae6d9-5b8e-4c4a-ac0b-c92aad2008a6.dat' > input.vcf.gz && bcftools index input.vcf.gz && ln -s '/galaxy/server/database/objects/5/7/3/dataset_573fcc22-f2c2-4d81-be0d-19d8e9001df9.dat' ref.fa && samtools faidx ref.fa && awk '{ if ($0 !~ />/) {print toupper($0)} else {print $0} }' 'ref.fa' > ref_upper.fa && bcftools norm --fasta-ref ref_upper.fa --check-ref w --do-not-normalize --multiallelics '+both' --strict-filter --site-win 1000 --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/2/c/8/dataset_2c83b419-25a1-4495-a502-bcb398c76eba.dat'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_default": "{\"site_win\": \"1000\"}", "sec_restrict": "{\"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}", "multiallelics": "{\"__current_case__\": 2, \"mode\": \"+\", \"multiallelic_types\": \"both\", \"strict_filter\": true}", "rm_dup": "\"\"", "old_rec_tag": "\"\"", "normalize_indels": "false", "atomize": "false", "check_ref": "\"w\"", "reference_source": "{\"__current_case__\": 1, \"fasta_ref\": {\"values\": [{\"id\": 240, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"input_file": {"id": "dc82172fda263ec8", "src": "hda", "uuid": "7aaae6d9-5b8e-4c4a-ac0b-c92aad2008a6"}, "reference_source|fasta_ref": {"id": "82ce24234cd1d762", "src": "hda", "uuid": "573fcc22-f2c2-4d81-be0d-19d8e9001df9"}}, "outputs": {"output_file": {"id": "8edb363bd0a3069a", "src": "hda", "uuid": "2c83b419-25a1-4495-a502-bcb398c76eba"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Lines total/split/realigned/skipped:\t26/0/0/0\n", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "Lines total/split/realigned/skipped:\t26/0/0/0\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy4, exit_code: None, stderr: Lines total/split/realigned/skipped:\t26/0/0/0\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy4, exit_code: None, stderr: Lines total/split/realigned/skipped:\t26/0/0/0\n."], "status": "failure"}}, {"id": "bcftools_norm/1.15.1+galaxy4-6", "has_data": true, "data": {"tool_id": "bcftools_norm", "tool_version": "1.15.1+galaxy4", "test_index": 6, "time_seconds": 37.477330923080444, "inputs": {"input_file": {"src": "hda", "id": "4bd637d598287b7c"}, "reference_source|fasta_ref": {"src": "hda", "id": "14ef870889eef4fd"}, "reference_source|reference_source_selector": "history", "check_ref": "ws", "output_type": "v"}, "job": {"model_class": "Job", "id": "8e42b1fbf985c94c", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:37:29.160017", "update_time": "2024-11-08T19:37:43.444939", "galaxy_version": "24.1", "external_id": "gxy-5kj7g", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/c/e/5/dataset_ce55bc55-99e3-456e-9647-dfe79fc6b83a.dat' > input.vcf.gz && bcftools index input.vcf.gz && ln -s '/galaxy/server/database/objects/6/2/2/dataset_6222254f-f099-46f1-8171-1aa172272608.dat' ref.fa && samtools faidx ref.fa && awk '{ if ($0 !~ />/) {print toupper($0)} else {print $0} }' 'ref.fa' > ref_upper.fa && bcftools norm --fasta-ref ref_upper.fa --check-ref ws --do-not-normalize --site-win 1000 --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/3/5/1/dataset_351232a1-2f5e-47fe-8715-a44650e6ab71.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_default": "{\"site_win\": \"1000\"}", "sec_restrict": "{\"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}", "multiallelics": "{\"__current_case__\": 0, \"mode\": \"\"}", "rm_dup": "\"\"", "old_rec_tag": "\"\"", "normalize_indels": "false", "atomize": "false", "check_ref": "\"ws\"", "reference_source": "{\"__current_case__\": 1, \"fasta_ref\": {\"values\": [{\"id\": 243, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"input_file": {"id": "4bd637d598287b7c", "src": "hda", "uuid": "ce55bc55-99e3-456e-9647-dfe79fc6b83a"}, "reference_source|fasta_ref": {"id": "14ef870889eef4fd", "src": "hda", "uuid": "6222254f-f099-46f1-8171-1aa172272608"}}, "outputs": {"output_file": {"id": "a2959836dc102bdc", "src": "hda", "uuid": "351232a1-2f5e-47fe-8715-a44650e6ab71"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Lines total/split/realigned/skipped:\t8/0/0/0\nREF/ALT total/modified/added: \t8/5/3\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Lines total/split/realigned/skipped:\t8/0/0/0\nREF/ALT total/modified/added: \t8/5/3\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-08 19:37:31", "plugin": "core", "name": "end_epoch", "raw_value": "1731094651.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:37:30", "plugin": "core", "name": "start_epoch", "raw_value": "1731094650.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "2", "plugin": "core", "name": "galaxy_slots", "raw_value": "2.0000000"}]}, "status": "success"}}, {"id": "bcftools_norm/1.15.1+galaxy4-7", "has_data": true, "data": {"tool_id": "bcftools_norm", "tool_version": "1.15.1+galaxy4", "test_index": 7, "time_seconds": 36.48306441307068, "inputs": {"input_file": {"src": "hda", "id": "7ff33b1e8f43d4da"}, "reference_source|fasta_ref": {"src": "hda", "id": "da87ba1afe484bc7"}, "reference_source|reference_source_selector": "history", "atomize": true, "normalize_indels": true, "multiallelics|mode": "-", "output_type": "v"}, "job": {"model_class": "Job", "id": "778157054be0b652", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:38:05.738060", "update_time": "2024-11-08T19:38:20.146090", "galaxy_version": "24.1", "external_id": "gxy-9srs2", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/9/1/e/dataset_91eadfc7-f0b7-4b0c-93fa-b40753fbb03b.dat' > input.vcf.gz && bcftools index input.vcf.gz && ln -s '/galaxy/server/database/objects/8/4/8/dataset_8489dd4f-ed00-4dec-be17-3fedee501a8e.dat' ref.fa && samtools faidx ref.fa && awk '{ if ($0 !~ />/) {print toupper($0)} else {print $0} }' 'ref.fa' > ref_upper.fa && bcftools norm --fasta-ref ref_upper.fa --check-ref w --atomize --multiallelics '-both' --site-win 1000 --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/3/4/b/dataset_34b8150e-a0c2-4971-9486-85b8a34780cf.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_default": "{\"site_win\": \"1000\"}", "sec_restrict": "{\"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}", "multiallelics": "{\"__current_case__\": 1, \"mode\": \"-\", \"multiallelic_types\": \"both\"}", "rm_dup": "\"\"", "old_rec_tag": "\"\"", "normalize_indels": "true", "atomize": "true", "check_ref": "\"w\"", "reference_source": "{\"__current_case__\": 1, \"fasta_ref\": {\"values\": [{\"id\": 246, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"input_file": {"id": "7ff33b1e8f43d4da", "src": "hda", "uuid": "91eadfc7-f0b7-4b0c-93fa-b40753fbb03b"}, "reference_source|fasta_ref": {"id": "da87ba1afe484bc7", "src": "hda", "uuid": "8489dd4f-ed00-4dec-be17-3fedee501a8e"}}, "outputs": {"output_file": {"id": "31d18e0f29838dd7", "src": "hda", "uuid": "34b8150e-a0c2-4971-9486-85b8a34780cf"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Lines total/split/realigned/skipped:\t39/20/3/0\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Lines total/split/realigned/skipped:\t39/20/3/0\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-11-08 19:38:07", "plugin": "core", "name": "end_epoch", "raw_value": "1731094687.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:38:07", "plugin": "core", "name": "start_epoch", "raw_value": "1731094687.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "2", "plugin": "core", "name": "galaxy_slots", "raw_value": "2.0000000"}]}, "status": "success"}}, {"id": "bcftools_norm/1.15.1+galaxy4-8", "has_data": true, "data": {"tool_id": "bcftools_norm", "tool_version": "1.15.1+galaxy4", "test_index": 8, "status": "skip"}}, {"id": "bcftools_plugin_fill_tags/1.15.1+galaxy4-0", "has_data": true, "data": {"tool_id": "bcftools_plugin_fill_tags", "tool_version": "1.15.1+galaxy4", "test_index": 0, "time_seconds": 41.27412128448486, "inputs": {"input_file": {"src": "hda", "id": "7e54bd2f1a488fcc"}, "output_type": "v"}, "job": {"model_class": "Job", "id": "073f4e1b7f3e599f", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:38:42.631998", "update_time": "2024-11-08T19:39:02.469213", "galaxy_version": "24.1", "external_id": "gxy-ljjw4", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/f/4/9/dataset_f49ba058-0b78-49a3-ad19-d10907c99f20.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools plugin fill-tags --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/4/8/4/dataset_484bfbbf-bc3a-4c50-a4b4-02b88eeca3cc.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_plugin": "{\"invert_samples\": false, \"invert_samples_file\": false, \"samples\": \"\", \"samples_file\": null, \"tags\": null}", "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": "7e54bd2f1a488fcc", "src": "hda", "uuid": "f49ba058-0b78-49a3-ad19-d10907c99f20"}}, "outputs": {"output_file": {"id": "81b00989d16223c8", "src": "hda", "uuid": "484bfbbf-bc3a-4c50-a4b4-02b88eeca3cc"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-11-08 19:38:49", "plugin": "core", "name": "end_epoch", "raw_value": "1731094729.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:38:49", "plugin": "core", "name": "start_epoch", "raw_value": "1731094729.0000000"}, {"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_plugin_fill_tags/1.15.1+galaxy4-1", "has_data": true, "data": {"tool_id": "bcftools_plugin_fill_tags", "tool_version": "1.15.1+galaxy4", "test_index": 1, "time_seconds": 36.611597299575806, "inputs": {"input_file": {"src": "hda", "id": "eda7c6df5600e0a6"}, "sec_plugin|tags": ["AC_Het", "AC_Hom"], "output_type": "v"}, "job": {"model_class": "Job", "id": "deb10cdd302a14ef", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:39:24.001249", "update_time": "2024-11-08T19:39:38.987268", "galaxy_version": "24.1", "external_id": "gxy-v2wm7", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/f/1/4/dataset_f14a647a-9443-4e5c-a664-8fd0ffa75d01.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools plugin fill-tags --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz -- --tags \"AC_Het,AC_Hom\" > '/galaxy/server/database/objects/e/7/5/dataset_e75f3af6-01e4-4ee7-9a54-307c84054584.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_plugin": "{\"invert_samples\": false, \"invert_samples_file\": false, \"samples\": \"\", \"samples_file\": null, \"tags\": [\"AC_Het\", \"AC_Hom\"]}", "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": "eda7c6df5600e0a6", "src": "hda", "uuid": "f14a647a-9443-4e5c-a664-8fd0ffa75d01"}}, "outputs": {"output_file": {"id": "a20b90c3d8444388", "src": "hda", "uuid": "e75f3af6-01e4-4ee7-9a54-307c84054584"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-11-08 19:39:26", "plugin": "core", "name": "end_epoch", "raw_value": "1731094766.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:39:26", "plugin": "core", "name": "start_epoch", "raw_value": "1731094766.0000000"}, {"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": "bowtie2/2.5.3+galaxy1-0", "has_data": true, "data": {"tool_id": "bowtie2", "tool_version": "2.5.3+galaxy1", "test_index": 0, "time_seconds": 57.6619176864624, "inputs": {"library|input_1": {"src": "hda", "id": "b4697e3bbef3f013"}, "library|input_2": {"src": "hda", "id": "47abc766bdc2613c"}, "library|unaligned_file": false, "library|paired_options|paired_options_selector": "no", "library|type": "paired", "reference_genome|own_file": {"src": "hda", "id": "419fc0c8c5cc1385"}, "reference_genome|source": "history", "analysis_type|analysis_type_selector": "simple"}, "job": {"model_class": "Job", "id": "419fc0c8c5cc1385", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T18:50:02.938674", "update_time": "2024-11-08T18:50:32.302809", "galaxy_version": "24.1", "external_id": "gxy-nrc48", "handler": null, "job_runner_name": null, "command_line": "set -o | grep -q pipefail && set -o pipefail; bowtie2-build --threads ${GALAXY_SLOTS:-4} '/galaxy/server/database/objects/d/c/2/dataset_dc2a7de1-c653-4638-b3fd-2c734351a305.dat' genome && ln -s -f '/galaxy/server/database/objects/d/c/2/dataset_dc2a7de1-c653-4638-b3fd-2c734351a305.dat' genome.fa && ln -f -s '/galaxy/server/database/objects/3/3/c/dataset_33cc5c2a-9a97-43a9-bc61-905f7e7ce283.dat' input_f.fastq && ln -f -s '/galaxy/server/database/objects/2/7/a/dataset_27afa158-c737-40c6-9920-99d56e5717bb.dat' input_r.fastq && THREADS=${GALAXY_SLOTS:-4} && if [ \"$THREADS\" -gt 1 ]; then (( THREADS-- )); fi && bowtie2 -p \"$THREADS\" -x 'genome' -1 'input_f.fastq' -2 'input_r.fastq' | samtools sort -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/0/d/8/dataset_0d83e326-d9ed-41ec-8451-9eee7bbbfd5d.dat'", "user_email": "tests@fake.org", "command_version": "/usr/local/bin/bowtie2-align-s version 2.5.3\n64-bit\nBuilt on fv-az365-785\nWed Jan 17 04:43:48 UTC 2024\nCompiler: gcc version 12.3.0 (conda-forge gcc 12.3.0-3) \nOptions: -O3 -msse2 -funroll-loops -g3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /usr/local/include -fdebug-prefix-map=/opt/conda/conda-bld/bowtie2_1705465427853/work=/usr/local/src/conda/bowtie2-2.5.3 -fdebug-prefix-map=/usr/local=/usr/local/src/conda-prefix -std=c++11 -Wall -Wno-unused-but-set-variable -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -DWITH_ZSTD\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "save_mapping_stats": "false", "sam_options": "{\"__current_case__\": 1, \"sam_options_selector\": \"no\"}", "analysis_type": "{\"__current_case__\": 0, \"analysis_type_selector\": \"simple\", \"presets\": \"no_presets\"}", "rg": "{\"__current_case__\": 3, \"rg_selector\": \"do_not_set\"}", "reference_genome": "{\"__current_case__\": 1, \"own_file\": {\"values\": [{\"id\": 50, \"src\": \"hda\"}]}, \"source\": \"history\"}", "library": "{\"__current_case__\": 1, \"aligned_file\": false, \"input_1\": {\"values\": [{\"id\": 48, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 49, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 1, \"paired_options_selector\": \"no\"}, \"type\": \"paired\", \"unaligned_file\": false}"}, "inputs": {"library|input_2": {"id": "47abc766bdc2613c", "src": "hda", "uuid": "27afa158-c737-40c6-9920-99d56e5717bb"}, "library|input_1": {"id": "b4697e3bbef3f013", "src": "hda", "uuid": "33cc5c2a-9a97-43a9-bc61-905f7e7ce283"}, "reference_genome|own_file": {"id": "419fc0c8c5cc1385", "src": "hda", "uuid": "dc2a7de1-c653-4638-b3fd-2c734351a305"}}, "outputs": {"output": {"id": "0be324c4bbcebbef", "src": "hda", "uuid": "0d83e326-d9ed-41ec-8451-9eee7bbbfd5d"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Settings:\n Output files: \"genome.*.bt2\"\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 Max bucket size: default\n Max bucket size, sqrt multiplier: default\n Max bucket size, len divisor: 32\n Difference-cover sample period: 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 /galaxy/server/database/objects/d/c/2/dataset_dc2a7de1-c653-4638-b3fd-2c734351a305.dat\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\nbmax according to bmaxDivN setting: 517\nUsing parameters --bmax 388 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 388 --dcv 1024\nConstructing suffix-array element generator\nBuilding DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 86 sample suffixes\nGenerating random suffixes\nQSorting 86 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 86 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 12, merged 41; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 6; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 284.672 (target: 387)\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering Ebwt loop\nGetting block 1 of 58\n Reserving size (388) for bucket 1\nGetting block 2 of 58\n Calculating Z arrays for bucket 1\nGetting block 3 of 58\n Reserving size (388) for bucket 2\nGetting block 4 of 58\n Entering block accumulator loop for bucket 1:\n Reserving size (388) for bucket 3\nGetting block 5 of 58\n Calculating Z arrays for bucket 2\n Reserving size (388) for bucket 4\nGetting block 6 of 58\nGetting block 7 of 58\n Calculating Z arrays for bucket 3\n Reserving size (388) for bucket 5\n Calculating Z arrays for bucket 4\n Entering block accumulator loop for bucket 2:\n Reserving size (388) for bucket 6\n Reserving size (388) for bucket 7\n Calculating Z arrays for bucket 5\n bucket 1: 10%\n Calculating Z arrays for bucket 6\n Entering block accumulator loop for bucket 3:\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 4:\n Entering block accumulator loop for bucket 5:\n bucket 1: 20%\n bucket 2: 10%\n Entering block accumulator loop for bucket 6:\n Entering block accumulator loop for bucket 7:\n bucket 1: 30%\n bucket 3: 10%\n bucket 2: 20%\n bucket 5: 10%\n bucket 1: 40%\n bucket 4: 10%\n bucket 3: 20%\n bucket 2: 30%\n bucket 5: 20%\n bucket 1: 50%\n bucket 6: 10%\n bucket 7: 10%\n bucket 2: 40%\n bucket 3: 30%\n bucket 1: 60%\n bucket 5: 30%\n bucket 4: 20%\n bucket 2: 50%\n bucket 3: 40%\n bucket 5: 40%\n bucket 7: 20%\n bucket 1: 70%\n bucket 4: 30%\n bucket 2: 60%\n bucket 6: 20%\n bucket 3: 50%\n bucket 5: 50%\n bucket 1: 80%\n bucket 2: 70%\n bucket 7: 30%\n bucket 3: 60%\n bucket 5: 60%\n bucket 1: 90%\n bucket 4: 40%\n bucket 2: 80%\n bucket 6: 30%\n bucket 3: 70%\n bucket 1: 100%\n bucket 5: 70%\n Sorting block of length 355 for bucket 1\n (Using difference cover)\n bucket 2: 90%\n bucket 7: 40%\n bucket 4: 50%\n bucket 3: 80%\n bucket 5: 80%\n bucket 2: 100%\n bucket 6: 40%\n Sorting block of length 165 for bucket 2\n (Using difference cover)\n bucket 3: 90%\n bucket 5: 90%\n bucket 7: 50%\n bucket 4: 60%\n bucket 3: 100%\n bucket 5: 100%\n Sorting block of length 370 for bucket 3\n (Using difference cover)\n bucket 6: 50%\n Sorting block of length 203 for bucket 5\n (Using difference cover)\n bucket 4: 70%\n bucket 7: 60%\n bucket 6: 60%\n bucket 4: 80%\n bucket 7: 70%\n bucket 6: 70%\n bucket 4: 90%\n bucket 7: 80%\n bucket 4: 100%\n bucket 6: 80%\n Sorting block of length 328 for bucket 4\n (Using difference cover)\n bucket 7: 90%\n bucket 6: 90%\n bucket 7: 100%\n bucket 6: 100%\n Sorting block of length 368 for bucket 7\n (Using difference cover)\n Sorting block of length 339 for bucket 6\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 356 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 166 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 371 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 204 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 369 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 329 for bucket 4\nGetting block 8 of 58\n Reserving size (388) for bucket 8\n Calculating Z arrays for bucket 8\nGetting block 9 of 58\n Reserving size (388) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 8:\n Entering block accumulator loop for bucket 9:\nGetting block 10 of 58\n Reserving size (388) for bucket 10\n bucket 8: 10%\n Calculating Z arrays for bucket 10\n bucket 9: 10%\n Entering block accumulator loop for bucket 10:\n bucket 8: 20%\n bucket 9: 20%\n bucket 8: 30%\n bucket 10: 10%\n bucket 9: 30%\n bucket 8: 40%\n bucket 10: 20%\n bucket 9: 40%\n bucket 8: 50%\n bucket 10: 30%\n bucket 9: 50%\n bucket 8: 60%\n bucket 10: 40%\n bucket 9: 60%\n bucket 8: 70%\n bucket 10: 50%\n bucket 9: 70%\n bucket 8: 80%\n bucket 10: 60%\n bucket 9: 80%\n bucket 8: 90%\n bucket 9: 90%\n bucket 10: 70%\n bucket 8: 100%\n bucket 9: 100%\n Sorting block of length 171 for bucket 8\n (Using difference cover)\n bucket 10: 80%\n Sorting block of length 339 for bucket 9\n (Using difference cover)\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 357 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 172 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 358 for bucket 10\nGetting block 11 of 58\n Reserving size (388) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\nGetting block 12 of 58\n bucket 11: 10%\n Reserving size (388) for bucket 12\n Calculating Z arrays for bucket 12\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 12: 70%\n bucket 11: 90%\n bucket 12: 80%\n bucket 11: 100%\n Sorting block of length 305 for bucket 11\n (Using difference cover)\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 185 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 306 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 186 for bucket 12\nGetting block 13 of 58\n Reserving size (388) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 13:\nGetting block 14 of 58\n Reserving size (388) for bucket 14\n Calculating Z arrays for bucket 14\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 14: 70%\n bucket 13: 70%\n bucket 14: 80%\n bucket 13: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 339 for bucket 14\n (Using difference cover)\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 282 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 283 for bucket 13\nGetting block 15 of 58\n Reserving size (388) for bucket 15\nGetting block 16 of 58\n Calculating Z arrays for bucket 15\n Reserving size (388) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 15:\n Entering block accumulator loop for bucket 16:\n bucket 15: 10%\n bucket 16: 10%\n bucket 15: 20%\n bucket 16: 20%\n bucket 15: 30%\n bucket 16: 30%\n bucket 15: 40%\n bucket 16: 40%\n bucket 15: 50%\n bucket 16: 50%\n bucket 16: 60%\n bucket 15: 60%\n bucket 16: 70%\n bucket 15: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 15: 80%\n bucket 16: 100%\n Sorting block of length 379 for bucket 16\n (Using difference cover)\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 241 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 380 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 242 for bucket 15\nGetting block 17 of 58\n Reserving size (388) 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 215 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 216 for bucket 17\nGetting block 18 of 58\n Reserving size (388) for bucket 18\n Calculating Z arrays for bucket 18\nGetting block 19 of 58\n Entering block accumulator loop for bucket 18:\n Reserving size (388) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 18: 10%\n bucket 19: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 19: 20%\n bucket 18: 40%\n bucket 19: 30%\n bucket 18: 50%\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 18: 100%\n Sorting block of length 378 for bucket 18\n (Using difference cover)\n bucket 19: 70%\n bucket 19: 80%\n Sorting block time: 00:00:00\nReturning block of 379 for bucket 18\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 334 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 335 for bucket 19\nGetting block 20 of 58\n Reserving size (388) for bucket 20\nGetting block 21 of 58\n Calculating Z arrays for bucket 20\n Reserving size (388) 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 bucket 21: 100%\n Sorting block of length 313 for bucket 20\n (Using difference cover)\n Sorting block of length 210 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 211 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 314 for bucket 20\nGetting block 22 of 58\n Reserving size (388) 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 386 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 387 for bucket 22\nGetting block 23 of 58\n Reserving size (388) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n bucket 23: 20%\nGetting block 24 of 58\n Reserving size (388) for bucket 24\n Calculating Z arrays for bucket 24\n bucket 23: 30%\n Entering block accumulator loop for bucket 24:\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 24: 40%\n bucket 23: 70%\n bucket 24: 50%\n bucket 23: 80%\n bucket 24: 60%\n bucket 24: 70%\n bucket 23: 90%\n bucket 24: 80%\n bucket 23: 100%\n Sorting block of length 238 for bucket 23\n (Using difference cover)\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 351 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 239 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 352 for bucket 24\nGetting block 25 of 58\n Reserving size (388) for bucket 25\nGetting block 26 of 58\n Calculating Z arrays for bucket 25\n Reserving size (388) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 25:\n Entering block accumulator loop for bucket 26:\n bucket 25: 10%\n bucket 26: 10%\n bucket 25: 20%\n bucket 26: 20%\n bucket 25: 30%\n bucket 25: 40%\n bucket 26: 30%\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 105 for bucket 25\n (Using difference cover)\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 354 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 106 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 355 for bucket 26\nGetting block 27 of 58\n Reserving size (388) for bucket 27\n Calculating Z arrays for bucket 27\nGetting block 28 of 58\n Reserving size (388) for bucket 28\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 28: 50%\n bucket 27: 60%\n bucket 28: 60%\n bucket 27: 70%\n bucket 28: 70%\n bucket 27: 80%\n bucket 28: 80%\n bucket 27: 90%\n bucket 28: 90%\n bucket 27: 100%\n Sorting block of length 334 for bucket 27\n (Using difference cover)\n bucket 28: 100%\n Sorting block of length 253 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 335 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 254 for bucket 28\nGetting block 29 of 58\n Reserving size (388) 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 289 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 290 for bucket 29\nGetting block 30 of 58\n Reserving size (388) for bucket 30\n Calculating Z arrays for bucket 30\nGetting block 31 of 58\n Reserving size (388) 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 30: 10%\n bucket 31: 10%\n bucket 30: 20%\n bucket 30: 30%\n bucket 31: 20%\n bucket 30: 40%\n bucket 30: 50%\n bucket 31: 30%\n bucket 30: 60%\n bucket 31: 40%\n bucket 30: 70%\n bucket 31: 50%\n bucket 30: 80%\n bucket 31: 60%\n bucket 30: 90%\n bucket 31: 70%\n bucket 30: 100%\n Sorting block of length 345 for bucket 30\n (Using difference cover)\n bucket 31: 80%\n bucket 31: 90%\n Sorting block time: 00:00:00\nReturning block of 346 for bucket 30\n bucket 31: 100%\n Sorting block of length 377 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 378 for bucket 31\nGetting block 32 of 58\n Reserving size (388) for bucket 32\nGetting block 33 of 58\n Calculating Z arrays for buc\n..\nucket 24: 40%\n bucket 23: 50%\n bucket 24: 50%\n bucket 23: 60%\n bucket 24: 60%\n bucket 23: 70%\n bucket 24: 70%\n bucket 23: 80%\n bucket 24: 80%\n bucket 23: 90%\n bucket 24: 90%\n bucket 23: 100%\n Sorting block of length 349 for bucket 23\n (Using difference cover)\n bucket 24: 100%\n Sorting block of length 245 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 246 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 350 for bucket 23\nGetting block 25 of 57\n Reserving size (388) 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 286 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 287 for bucket 25\nGetting block 26 of 57\n Reserving size (388) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\nGetting block 27 of 57\n Reserving size (388) for bucket 27\n Calculating Z arrays for bucket 27\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 26: 90%\n bucket 27: 70%\n bucket 26: 100%\n Sorting block of length 384 for bucket 26\n (Using difference cover)\n bucket 27: 80%\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 359 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 385 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 360 for bucket 27\nGetting block 28 of 57\n Reserving size (388) for bucket 28\n Calculating Z arrays for bucket 28\nGetting block 29 of 57\n Entering block accumulator loop for bucket 28:\n Reserving size (388) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 28: 10%\n bucket 28: 20%\n bucket 29: 10%\n bucket 28: 30%\n bucket 29: 20%\n bucket 28: 40%\n bucket 29: 30%\n bucket 28: 50%\n bucket 29: 40%\n bucket 28: 60%\n bucket 29: 50%\n bucket 28: 70%\n bucket 29: 60%\n bucket 28: 80%\n bucket 29: 70%\n bucket 28: 90%\n bucket 29: 80%\n bucket 28: 100%\n Sorting block of length 387 for bucket 28\n (Using difference cover)\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 195 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 29\nGetting block 30 of 57\n Reserving size (388) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 30:\nGetting block 31 of 57\n bucket 30: 10%\n Reserving size (388) for bucket 31\n Calculating Z arrays for bucket 31\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 31: 30%\n bucket 30: 40%\n bucket 31: 40%\n bucket 30: 50%\n bucket 31: 50%\n bucket 31: 60%\n bucket 30: 60%\n bucket 31: 70%\n bucket 30: 70%\n bucket 31: 80%\n bucket 31: 90%\n bucket 30: 80%\n bucket 31: 100%\n Sorting block of length 310 for bucket 31\n (Using difference cover)\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 257 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 311 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 258 for bucket 30\nGetting block 32 of 57\n Reserving size (388) 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 219 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 220 for bucket 32\nGetting block 33 of 57\n Reserving size (388) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 33:\nGetting block 34 of 57\n Reserving size (388) for bucket 34\n Calculating Z arrays for bucket 34\n bucket 33: 10%\n Entering block accumulator loop for bucket 34:\n bucket 33: 20%\n bucket 34: 10%\n bucket 33: 30%\n bucket 34: 20%\n bucket 33: 40%\n bucket 33: 50%\n bucket 34: 30%\n bucket 33: 60%\n bucket 34: 40%\n bucket 33: 70%\n bucket 33: 80%\n bucket 34: 50%\n bucket 33: 90%\n bucket 33: 100%\n bucket 34: 60%\n Sorting block of length 387 for bucket 33\n (Using difference cover)\n bucket 34: 70%\n bucket 34: 80%\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 33\n bucket 34: 90%\n bucket 34: 100%\n Sorting block of length 275 for bucket 34\n (Using difference cover)\n Sorting block time: 00:00:00\nGetting block 35 of 57\nReturning block of 276 for bucket 34\n Reserving size (388) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 35:\nGetting block 36 of 57\n Reserving size (388) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\n bucket 35: 10%\n bucket 36: 10%\n bucket 35: 20%\n bucket 36: 20%\n bucket 35: 30%\n bucket 36: 30%\n bucket 36: 40%\n bucket 35: 40%\n bucket 36: 50%\n bucket 35: 50%\n bucket 36: 60%\n bucket 35: 60%\n bucket 36: 70%\n bucket 35: 70%\n bucket 36: 80%\n bucket 36: 90%\n bucket 35: 80%\n bucket 36: 100%\n Sorting block of length 150 for bucket 36\n (Using difference cover)\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 350 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 151 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 351 for bucket 35\nGetting block 37 of 57\n Reserving size (388) for bucket 37\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 37:\nGetting block 38 of 57\n Reserving size (388) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 38:\n bucket 37: 10%\n bucket 37: 20%\n bucket 38: 10%\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 38: 60%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 267 for bucket 37\n (Using difference cover)\n bucket 38: 70%\n bucket 38: 80%\n Sorting block time: 00:00:00\nReturning block of 268 for bucket 37\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 337 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 338 for bucket 38\nGetting block 39 of 57\n Reserving size (388) for bucket 39\n Calculating Z arrays for bucket 39\n Entering block accumulator loop for bucket 39:\nGetting block 40 of 57\n Reserving size (388) for bucket 40\n Calculating Z arrays for bucket 40\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 40: 50%\n bucket 39: 50%\n bucket 40: 60%\n bucket 39: 60%\n bucket 40: 70%\n bucket 39: 70%\n bucket 40: 80%\n bucket 39: 80%\n bucket 40: 90%\n bucket 39: 90%\n bucket 40: 100%\n Sorting block of length 379 for bucket 40\n (Using difference cover)\n bucket 39: 100%\n Sorting block of length 387 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 39\n Sorting block time: 00:00:00\nReturning block of 380 for bucket 40\nGetting block 41 of 57\n Reserving size (388) 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 330 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 331 for bucket 41\nGetting block 42 of 57\n Reserving size (388) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\nGetting block 43 of 57\n Reserving size (388) for bucket 43\n Calculating Z arrays for bucket 43\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 43: 20%\n bucket 42: 40%\n bucket 43: 30%\n bucket 42: 50%\n bucket 43: 40%\n bucket 42: 60%\n bucket 42: 70%\n bucket 43: 50%\n bucket 42: 80%\n bucket 43: 60%\n bucket 42: 90%\n bucket 42: 100%\n Sorting block of length 188 for bucket 42\n (Using difference cover)\n bucket 43: 70%\n bucket 43: 80%\n Sorting block time: 00:00:00\nReturning block of 189 for bucket 42\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 321 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 322 for bucket 43\nGetting block 44 of 57\n Reserving size (388) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 44:\nGetting block 45 of 57\n bucket 44: 10%\n Reserving size (388) for bucket 45\n Calculating Z arrays for bucket 45\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 45: 20%\n bucket 44: 50%\n bucket 45: 30%\n bucket 44: 60%\n bucket 45: 40%\n bucket 44: 70%\n bucket 45: 50%\n bucket 44: 80%\n bucket 44: 90%\n bucket 45: 60%\n bucket 44: 100%\n Sorting block of length 366 for bucket 44\n (Using difference cover)\n bucket 45: 70%\n bucket 45: 80%\n Sorting block time: 00:00:00\nReturning block of 367 for bucket 44\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 365 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 366 for bucket 45\nGetting block 46 of 57\n Reserving size (388) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 46:\nGetting block 47 of 57\n Reserving size (388) for bucket 47\n Calculating Z arrays for bucket 47\n bucket 46: 10%\n Entering block accumulator loop for bucket 47:\n bucket 46: 20%\n bucket 46: 30%\n bucket 47: 10%\n bucket 46: 40%\n bucket 47: 20%\n bucket 46: 50%\n bucket 46: 60%\n bucket 47: 30%\n bucket 46: 70%\n bucket 47: 40%\n bucket 46: 80%\n bucket 46: 90%\n bucket 47: 50%\n bucket 46: 100%\n Sorting block of length 253 for bucket 46\n (Using difference cover)\n bucket 47: 60%\n bucket 47: 70%\n Sorting block time: 00:00:00\nReturning block of 254 for bucket 46\n bucket 47: 80%\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 217 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 218 for bucket 47\nGetting block 48 of 57\n Reserving size (388) for bucket 48\n Calculating Z arrays for bucket 48\nGetting block 49 of 57\n Reserving size (388) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 48:\n Entering block accumulator loop for bucket 49:\n bucket 48: 10%\n bucket 49: 10%\n bucket 48: 20%\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 49: 50%\n bucket 48: 60%\n bucket 49: 60%\n bucket 48: 70%\n bucket 49: 70%\n bucket 48: 80%\n bucket 49: 80%\n bucket 48: 90%\n bucket 49: 90%\n bucket 48: 100%\n Sorting block of length 384 for bucket 48\n (Using difference cover)\n bucket 49: 100%\n Sorting block of length 112 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 385 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 49\nGetting block 50 of 57\n Reserving size (388) 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 275 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 276 for bucket 50\nGetting block 51 of 57\n Reserving size (388) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 51:\nGetting block 52 of 57\n bucket 51: 10%\n Reserving size (388) for bucket 52\n Calculating Z arrays for bucket 52\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 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 350 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 378 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 351 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 379 for bucket 52\nGetting block 53 of 57\n Reserving size (388) for bucket 53\nGetting block 54 of 57\n Calculating Z arrays for bucket 53\n Reserving size (388) 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 54: 10%\n bucket 53: 10%\n bucket 53: 20%\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 54: 60%\n bucket 53: 50%\n bucket 54: 70%\n bucket 53: 60%\n bucket 54: 80%\n bucket 53: 70%\n bucket 54: 90%\n bucket 53: 80%\n bucket 54: 100%\n Sorting block of length 237 for bucket 54\n (Using difference cover)\n bucket 53: 90%\n bucket 53: 100%\n Sorting block time: 00:00:00\n Sorting block of length 370 for bucket 53\n (Using difference cover)\nReturning block of 238 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 371 for bucket 53\nGetting block 55 of 57\n Reserving size (388) for bucket 55\n Calculating Z arrays for bucket 55\nGetting block 56 of 57\n Reserving size (388) for bucket 56\n Calculating Z arrays for bucket 56\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 56: 20%\n bucket 55: 20%\n bucket 56: 30%\n bucket 56: 40%\n bucket 55: 30%\n bucket 56: 50%\n bucket 55: 40%\n bucket 56: 60%\n bucket 56: 70%\n bucket 55: 50%\n bucket 56: 80%\n bucket 56: 90%\n bucket 55: 60%\n bucket 56: 100%\n Sorting block of length 270 for bucket 56\n (Using difference cover)\n bucket 55: 70%\n bucket 55: 80%\n Sorting block time: 00:00:00\nReturning block of 271 for bucket 56\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 344 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 345 for bucket 55\nGetting block 57 of 57\n Reserving size (388) 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 132 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 133 for bucket 57\nExited Ebwt loop\nfchr[A]: 0\nfchr[C]: 5124\nfchr[G]: 10305\nfchr[T]: 12474\nfchr[$]: 16568\nExiting Ebwt::buildToDisk()\nReturning from initFromVector\nWrote 4200050 bytes to primary EBWT file: genome.rev.1.bt2.tmp\nWrote 4148 bytes to secondary EBWT file: genome.rev.2.bt2.tmp\nRe-opening _in1 and _in2 as input streams\nReturning from Ebwt constructor\nHeaders:\n len: 16568\n bwtLen: 16569\n sz: 4142\n bwtSz: 4143\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 20\n eftabSz: 80\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 1036\n offsSz: 4144\n lineSz: 64\n sideSz: 64\n sideBwtSz: 48\n sideBwtLen: 192\n numSides: 87\n numLines: 87\n ebwtTotLen: 5568\n ebwtTotSz: 5568\n color: 0\n reverse: 1\nTotal time for backward call to driver() for mirror index: 00:00:00\n", "tool_stderr": "Building a SMALL index\nRenaming genome.3.bt2.tmp to genome.3.bt2\nRenaming genome.4.bt2.tmp to genome.4.bt2\nRenaming genome.1.bt2.tmp to genome.1.bt2\nRenaming genome.2.bt2.tmp to genome.2.bt2\nRenaming genome.rev.1.bt2.tmp to genome.rev.1.bt2\nRenaming genome.rev.2.bt2.tmp to genome.rev.2.bt2\n100 reads; of these:\n 100 (100.00%) were paired; of these:\n 97 (97.00%) aligned concordantly 0 times\n 3 (3.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 97 pairs aligned concordantly 0 times; of these:\n 8 (8.25%) aligned discordantly 1 time\n ----\n 89 pairs aligned 0 times concordantly or discordantly; of these:\n 178 mates make up the pairs; of these:\n 153 (85.96%) aligned 0 times\n 25 (14.04%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n23.50% overall alignment rate\n", "job_stdout": "", "job_stderr": "", "stdout": "Settings:\n Output files: \"genome.*.bt2\"\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 Max bucket size: default\n Max bucket size, sqrt multiplier: default\n Max bucket size, len divisor: 32\n Difference-cover sample period: 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 /galaxy/server/database/objects/d/c/2/dataset_dc2a7de1-c653-4638-b3fd-2c734351a305.dat\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\nbmax according to bmaxDivN setting: 517\nUsing parameters --bmax 388 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 388 --dcv 1024\nConstructing suffix-array element generator\nBuilding DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 86 sample suffixes\nGenerating random suffixes\nQSorting 86 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 86 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 12, merged 41; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 6; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 284.672 (target: 387)\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering Ebwt loop\nGetting block 1 of 58\n Reserving size (388) for bucket 1\nGetting block 2 of 58\n Calculating Z arrays for bucket 1\nGetting block 3 of 58\n Reserving size (388) for bucket 2\nGetting block 4 of 58\n Entering block accumulator loop for bucket 1:\n Reserving size (388) for bucket 3\nGetting block 5 of 58\n Calculating Z arrays for bucket 2\n Reserving size (388) for bucket 4\nGetting block 6 of 58\nGetting block 7 of 58\n Calculating Z arrays for bucket 3\n Reserving size (388) for bucket 5\n Calculating Z arrays for bucket 4\n Entering block accumulator loop for bucket 2:\n Reserving size (388) for bucket 6\n Reserving size (388) for bucket 7\n Calculating Z arrays for bucket 5\n bucket 1: 10%\n Calculating Z arrays for bucket 6\n Entering block accumulator loop for bucket 3:\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 4:\n Entering block accumulator loop for bucket 5:\n bucket 1: 20%\n bucket 2: 10%\n Entering block accumulator loop for bucket 6:\n Entering block accumulator loop for bucket 7:\n bucket 1: 30%\n bucket 3: 10%\n bucket 2: 20%\n bucket 5: 10%\n bucket 1: 40%\n bucket 4: 10%\n bucket 3: 20%\n bucket 2: 30%\n bucket 5: 20%\n bucket 1: 50%\n bucket 6: 10%\n bucket 7: 10%\n bucket 2: 40%\n bucket 3: 30%\n bucket 1: 60%\n bucket 5: 30%\n bucket 4: 20%\n bucket 2: 50%\n bucket 3: 40%\n bucket 5: 40%\n bucket 7: 20%\n bucket 1: 70%\n bucket 4: 30%\n bucket 2: 60%\n bucket 6: 20%\n bucket 3: 50%\n bucket 5: 50%\n bucket 1: 80%\n bucket 2: 70%\n bucket 7: 30%\n bucket 3: 60%\n bucket 5: 60%\n bucket 1: 90%\n bucket 4: 40%\n bucket 2: 80%\n bucket 6: 30%\n bucket 3: 70%\n bucket 1: 100%\n bucket 5: 70%\n Sorting block of length 355 for bucket 1\n (Using difference cover)\n bucket 2: 90%\n bucket 7: 40%\n bucket 4: 50%\n bucket 3: 80%\n bucket 5: 80%\n bucket 2: 100%\n bucket 6: 40%\n Sorting block of length 165 for bucket 2\n (Using difference cover)\n bucket 3: 90%\n bucket 5: 90%\n bucket 7: 50%\n bucket 4: 60%\n bucket 3: 100%\n bucket 5: 100%\n Sorting block of length 370 for bucket 3\n (Using difference cover)\n bucket 6: 50%\n Sorting block of length 203 for bucket 5\n (Using difference cover)\n bucket 4: 70%\n bucket 7: 60%\n bucket 6: 60%\n bucket 4: 80%\n bucket 7: 70%\n bucket 6: 70%\n bucket 4: 90%\n bucket 7: 80%\n bucket 4: 100%\n bucket 6: 80%\n Sorting block of length 328 for bucket 4\n (Using difference cover)\n bucket 7: 90%\n bucket 6: 90%\n bucket 7: 100%\n bucket 6: 100%\n Sorting block of length 368 for bucket 7\n (Using difference cover)\n Sorting block of length 339 for bucket 6\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 356 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 166 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 371 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 204 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 369 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 329 for bucket 4\nGetting block 8 of 58\n Reserving size (388) for bucket 8\n Calculating Z arrays for bucket 8\nGetting block 9 of 58\n Reserving size (388) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 8:\n Entering block accumulator loop for bucket 9:\nGetting block 10 of 58\n Reserving size (388) for bucket 10\n bucket 8: 10%\n Calculating Z arrays for bucket 10\n bucket 9: 10%\n Entering block accumulator loop for bucket 10:\n bucket 8: 20%\n bucket 9: 20%\n bucket 8: 30%\n bucket 10: 10%\n bucket 9: 30%\n bucket 8: 40%\n bucket 10: 20%\n bucket 9: 40%\n bucket 8: 50%\n bucket 10: 30%\n bucket 9: 50%\n bucket 8: 60%\n bucket 10: 40%\n bucket 9: 60%\n bucket 8: 70%\n bucket 10: 50%\n bucket 9: 70%\n bucket 8: 80%\n bucket 10: 60%\n bucket 9: 80%\n bucket 8: 90%\n bucket 9: 90%\n bucket 10: 70%\n bucket 8: 100%\n bucket 9: 100%\n Sorting block of length 171 for bucket 8\n (Using difference cover)\n bucket 10: 80%\n Sorting block of length 339 for bucket 9\n (Using difference cover)\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 357 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 172 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 358 for bucket 10\nGetting block 11 of 58\n Reserving size (388) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\nGetting block 12 of 58\n bucket 11: 10%\n Reserving size (388) for bucket 12\n Calculating Z arrays for bucket 12\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 12: 70%\n bucket 11: 90%\n bucket 12: 80%\n bucket 11: 100%\n Sorting block of length 305 for bucket 11\n (Using difference cover)\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 185 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 306 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 186 for bucket 12\nGetting block 13 of 58\n Reserving size (388) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 13:\nGetting block 14 of 58\n Reserving size (388) for bucket 14\n Calculating Z arrays for bucket 14\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 14: 70%\n bucket 13: 70%\n bucket 14: 80%\n bucket 13: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 339 for bucket 14\n (Using difference cover)\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 282 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 283 for bucket 13\nGetting block 15 of 58\n Reserving size (388) for bucket 15\nGetting block 16 of 58\n Calculating Z arrays for bucket 15\n Reserving size (388) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 15:\n Entering block accumulator loop for bucket 16:\n bucket 15: 10%\n bucket 16: 10%\n bucket 15: 20%\n bucket 16: 20%\n bucket 15: 30%\n bucket 16: 30%\n bucket 15: 40%\n bucket 16: 40%\n bucket 15: 50%\n bucket 16: 50%\n bucket 16: 60%\n bucket 15: 60%\n bucket 16: 70%\n bucket 15: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 15: 80%\n bucket 16: 100%\n Sorting block of length 379 for bucket 16\n (Using difference cover)\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 241 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 380 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 242 for bucket 15\nGetting block 17 of 58\n Reserving size (388) 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 215 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 216 for bucket 17\nGetting block 18 of 58\n Reserving size (388) for bucket 18\n Calculating Z arrays for bucket 18\nGetting block 19 of 58\n Entering block accumulator loop for bucket 18:\n Reserving size (388) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 18: 10%\n bucket 19: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 19: 20%\n bucket 18: 40%\n bucket 19: 30%\n bucket 18: 50%\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 18: 100%\n Sorting block of length 378 for bucket 18\n (Using difference cover)\n bucket 19: 70%\n bucket 19: 80%\n Sorting block time: 00:00:00\nReturning block of 379 for bucket 18\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 334 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 335 for bucket 19\nGetting block 20 of 58\n Reserving size (388) for bucket 20\nGetting block 21 of 58\n Calculating Z arrays for bucket 20\n Reserving size (388) 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 bucket 21: 100%\n Sorting block of length 313 for bucket 20\n (Using difference cover)\n Sorting block of length 210 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 211 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 314 for bucket 20\nGetting block 22 of 58\n Reserving size (388) 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 386 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 387 for bucket 22\nGetting block 23 of 58\n Reserving size (388) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n bucket 23: 20%\nGetting block 24 of 58\n Reserving size (388) for bucket 24\n Calculating Z arrays for bucket 24\n bucket 23: 30%\n Entering block accumulator loop for bucket 24:\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 24: 40%\n bucket 23: 70%\n bucket 24: 50%\n bucket 23: 80%\n bucket 24: 60%\n bucket 24: 70%\n bucket 23: 90%\n bucket 24: 80%\n bucket 23: 100%\n Sorting block of length 238 for bucket 23\n (Using difference cover)\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 351 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 239 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 352 for bucket 24\nGetting block 25 of 58\n Reserving size (388) for bucket 25\nGetting block 26 of 58\n Calculating Z arrays for bucket 25\n Reserving size (388) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 25:\n Entering block accumulator loop for bucket 26:\n bucket 25: 10%\n bucket 26: 10%\n bucket 25: 20%\n bucket 26: 20%\n bucket 25: 30%\n bucket 25: 40%\n bucket 26: 30%\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 105 for bucket 25\n (Using difference cover)\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 354 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 106 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 355 for bucket 26\nGetting block 27 of 58\n Reserving size (388) for bucket 27\n Calculating Z arrays for bucket 27\nGetting block 28 of 58\n Reserving size (388) for bucket 28\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 28: 50%\n bucket 27: 60%\n bucket 28: 60%\n bucket 27: 70%\n bucket 28: 70%\n bucket 27: 80%\n bucket 28: 80%\n bucket 27: 90%\n bucket 28: 90%\n bucket 27: 100%\n Sorting block of length 334 for bucket 27\n (Using difference cover)\n bucket 28: 100%\n Sorting block of length 253 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 335 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 254 for bucket 28\nGetting block 29 of 58\n Reserving size (388) 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 289 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 290 for bucket 29\nGetting block 30 of 58\n Reserving size (388) for bucket 30\n Calculating Z arrays for bucket 30\nGetting block 31 of 58\n Reserving size (388) 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 30: 10%\n bucket 31: 10%\n bucket 30: 20%\n bucket 30: 30%\n bucket 31: 20%\n bucket 30: 40%\n bucket 30: 50%\n bucket 31: 30%\n bucket 30: 60%\n bucket 31: 40%\n bucket 30: 70%\n bucket 31: 50%\n bucket 30: 80%\n bucket 31: 60%\n bucket 30: 90%\n bucket 31: 70%\n bucket 30: 100%\n Sorting block of length 345 for bucket 30\n (Using difference cover)\n bucket 31: 80%\n bucket 31: 90%\n Sorting block time: 00:00:00\nReturning block of 346 for bucket 30\n bucket 31: 100%\n Sorting block of length 377 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 378 for bucket 31\nGetting block 32 of 58\n Reserving size (388) for bucket 32\nGetting block 33 of 58\n Calculating Z arrays for buc\n..\nucket 24: 40%\n bucket 23: 50%\n bucket 24: 50%\n bucket 23: 60%\n bucket 24: 60%\n bucket 23: 70%\n bucket 24: 70%\n bucket 23: 80%\n bucket 24: 80%\n bucket 23: 90%\n bucket 24: 90%\n bucket 23: 100%\n Sorting block of length 349 for bucket 23\n (Using difference cover)\n bucket 24: 100%\n Sorting block of length 245 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 246 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 350 for bucket 23\nGetting block 25 of 57\n Reserving size (388) 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 286 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 287 for bucket 25\nGetting block 26 of 57\n Reserving size (388) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\nGetting block 27 of 57\n Reserving size (388) for bucket 27\n Calculating Z arrays for bucket 27\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 26: 90%\n bucket 27: 70%\n bucket 26: 100%\n Sorting block of length 384 for bucket 26\n (Using difference cover)\n bucket 27: 80%\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 359 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 385 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 360 for bucket 27\nGetting block 28 of 57\n Reserving size (388) for bucket 28\n Calculating Z arrays for bucket 28\nGetting block 29 of 57\n Entering block accumulator loop for bucket 28:\n Reserving size (388) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 28: 10%\n bucket 28: 20%\n bucket 29: 10%\n bucket 28: 30%\n bucket 29: 20%\n bucket 28: 40%\n bucket 29: 30%\n bucket 28: 50%\n bucket 29: 40%\n bucket 28: 60%\n bucket 29: 50%\n bucket 28: 70%\n bucket 29: 60%\n bucket 28: 80%\n bucket 29: 70%\n bucket 28: 90%\n bucket 29: 80%\n bucket 28: 100%\n Sorting block of length 387 for bucket 28\n (Using difference cover)\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 195 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 29\nGetting block 30 of 57\n Reserving size (388) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 30:\nGetting block 31 of 57\n bucket 30: 10%\n Reserving size (388) for bucket 31\n Calculating Z arrays for bucket 31\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 31: 30%\n bucket 30: 40%\n bucket 31: 40%\n bucket 30: 50%\n bucket 31: 50%\n bucket 31: 60%\n bucket 30: 60%\n bucket 31: 70%\n bucket 30: 70%\n bucket 31: 80%\n bucket 31: 90%\n bucket 30: 80%\n bucket 31: 100%\n Sorting block of length 310 for bucket 31\n (Using difference cover)\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 257 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 311 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 258 for bucket 30\nGetting block 32 of 57\n Reserving size (388) 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 219 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 220 for bucket 32\nGetting block 33 of 57\n Reserving size (388) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 33:\nGetting block 34 of 57\n Reserving size (388) for bucket 34\n Calculating Z arrays for bucket 34\n bucket 33: 10%\n Entering block accumulator loop for bucket 34:\n bucket 33: 20%\n bucket 34: 10%\n bucket 33: 30%\n bucket 34: 20%\n bucket 33: 40%\n bucket 33: 50%\n bucket 34: 30%\n bucket 33: 60%\n bucket 34: 40%\n bucket 33: 70%\n bucket 33: 80%\n bucket 34: 50%\n bucket 33: 90%\n bucket 33: 100%\n bucket 34: 60%\n Sorting block of length 387 for bucket 33\n (Using difference cover)\n bucket 34: 70%\n bucket 34: 80%\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 33\n bucket 34: 90%\n bucket 34: 100%\n Sorting block of length 275 for bucket 34\n (Using difference cover)\n Sorting block time: 00:00:00\nGetting block 35 of 57\nReturning block of 276 for bucket 34\n Reserving size (388) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 35:\nGetting block 36 of 57\n Reserving size (388) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\n bucket 35: 10%\n bucket 36: 10%\n bucket 35: 20%\n bucket 36: 20%\n bucket 35: 30%\n bucket 36: 30%\n bucket 36: 40%\n bucket 35: 40%\n bucket 36: 50%\n bucket 35: 50%\n bucket 36: 60%\n bucket 35: 60%\n bucket 36: 70%\n bucket 35: 70%\n bucket 36: 80%\n bucket 36: 90%\n bucket 35: 80%\n bucket 36: 100%\n Sorting block of length 150 for bucket 36\n (Using difference cover)\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 350 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 151 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 351 for bucket 35\nGetting block 37 of 57\n Reserving size (388) for bucket 37\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 37:\nGetting block 38 of 57\n Reserving size (388) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 38:\n bucket 37: 10%\n bucket 37: 20%\n bucket 38: 10%\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 38: 60%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 267 for bucket 37\n (Using difference cover)\n bucket 38: 70%\n bucket 38: 80%\n Sorting block time: 00:00:00\nReturning block of 268 for bucket 37\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 337 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 338 for bucket 38\nGetting block 39 of 57\n Reserving size (388) for bucket 39\n Calculating Z arrays for bucket 39\n Entering block accumulator loop for bucket 39:\nGetting block 40 of 57\n Reserving size (388) for bucket 40\n Calculating Z arrays for bucket 40\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 40: 50%\n bucket 39: 50%\n bucket 40: 60%\n bucket 39: 60%\n bucket 40: 70%\n bucket 39: 70%\n bucket 40: 80%\n bucket 39: 80%\n bucket 40: 90%\n bucket 39: 90%\n bucket 40: 100%\n Sorting block of length 379 for bucket 40\n (Using difference cover)\n bucket 39: 100%\n Sorting block of length 387 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 39\n Sorting block time: 00:00:00\nReturning block of 380 for bucket 40\nGetting block 41 of 57\n Reserving size (388) 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 330 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 331 for bucket 41\nGetting block 42 of 57\n Reserving size (388) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\nGetting block 43 of 57\n Reserving size (388) for bucket 43\n Calculating Z arrays for bucket 43\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 43: 20%\n bucket 42: 40%\n bucket 43: 30%\n bucket 42: 50%\n bucket 43: 40%\n bucket 42: 60%\n bucket 42: 70%\n bucket 43: 50%\n bucket 42: 80%\n bucket 43: 60%\n bucket 42: 90%\n bucket 42: 100%\n Sorting block of length 188 for bucket 42\n (Using difference cover)\n bucket 43: 70%\n bucket 43: 80%\n Sorting block time: 00:00:00\nReturning block of 189 for bucket 42\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 321 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 322 for bucket 43\nGetting block 44 of 57\n Reserving size (388) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 44:\nGetting block 45 of 57\n bucket 44: 10%\n Reserving size (388) for bucket 45\n Calculating Z arrays for bucket 45\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 45: 20%\n bucket 44: 50%\n bucket 45: 30%\n bucket 44: 60%\n bucket 45: 40%\n bucket 44: 70%\n bucket 45: 50%\n bucket 44: 80%\n bucket 44: 90%\n bucket 45: 60%\n bucket 44: 100%\n Sorting block of length 366 for bucket 44\n (Using difference cover)\n bucket 45: 70%\n bucket 45: 80%\n Sorting block time: 00:00:00\nReturning block of 367 for bucket 44\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 365 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 366 for bucket 45\nGetting block 46 of 57\n Reserving size (388) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 46:\nGetting block 47 of 57\n Reserving size (388) for bucket 47\n Calculating Z arrays for bucket 47\n bucket 46: 10%\n Entering block accumulator loop for bucket 47:\n bucket 46: 20%\n bucket 46: 30%\n bucket 47: 10%\n bucket 46: 40%\n bucket 47: 20%\n bucket 46: 50%\n bucket 46: 60%\n bucket 47: 30%\n bucket 46: 70%\n bucket 47: 40%\n bucket 46: 80%\n bucket 46: 90%\n bucket 47: 50%\n bucket 46: 100%\n Sorting block of length 253 for bucket 46\n (Using difference cover)\n bucket 47: 60%\n bucket 47: 70%\n Sorting block time: 00:00:00\nReturning block of 254 for bucket 46\n bucket 47: 80%\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 217 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 218 for bucket 47\nGetting block 48 of 57\n Reserving size (388) for bucket 48\n Calculating Z arrays for bucket 48\nGetting block 49 of 57\n Reserving size (388) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 48:\n Entering block accumulator loop for bucket 49:\n bucket 48: 10%\n bucket 49: 10%\n bucket 48: 20%\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 49: 50%\n bucket 48: 60%\n bucket 49: 60%\n bucket 48: 70%\n bucket 49: 70%\n bucket 48: 80%\n bucket 49: 80%\n bucket 48: 90%\n bucket 49: 90%\n bucket 48: 100%\n Sorting block of length 384 for bucket 48\n (Using difference cover)\n bucket 49: 100%\n Sorting block of length 112 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 385 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 49\nGetting block 50 of 57\n Reserving size (388) 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 275 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 276 for bucket 50\nGetting block 51 of 57\n Reserving size (388) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 51:\nGetting block 52 of 57\n bucket 51: 10%\n Reserving size (388) for bucket 52\n Calculating Z arrays for bucket 52\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 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 350 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 378 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 351 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 379 for bucket 52\nGetting block 53 of 57\n Reserving size (388) for bucket 53\nGetting block 54 of 57\n Calculating Z arrays for bucket 53\n Reserving size (388) 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 54: 10%\n bucket 53: 10%\n bucket 53: 20%\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 54: 60%\n bucket 53: 50%\n bucket 54: 70%\n bucket 53: 60%\n bucket 54: 80%\n bucket 53: 70%\n bucket 54: 90%\n bucket 53: 80%\n bucket 54: 100%\n Sorting block of length 237 for bucket 54\n (Using difference cover)\n bucket 53: 90%\n bucket 53: 100%\n Sorting block time: 00:00:00\n Sorting block of length 370 for bucket 53\n (Using difference cover)\nReturning block of 238 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 371 for bucket 53\nGetting block 55 of 57\n Reserving size (388) for bucket 55\n Calculating Z arrays for bucket 55\nGetting block 56 of 57\n Reserving size (388) for bucket 56\n Calculating Z arrays for bucket 56\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 56: 20%\n bucket 55: 20%\n bucket 56: 30%\n bucket 56: 40%\n bucket 55: 30%\n bucket 56: 50%\n bucket 55: 40%\n bucket 56: 60%\n bucket 56: 70%\n bucket 55: 50%\n bucket 56: 80%\n bucket 56: 90%\n bucket 55: 60%\n bucket 56: 100%\n Sorting block of length 270 for bucket 56\n (Using difference cover)\n bucket 55: 70%\n bucket 55: 80%\n Sorting block time: 00:00:00\nReturning block of 271 for bucket 56\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 344 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 345 for bucket 55\nGetting block 57 of 57\n Reserving size (388) 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 132 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 133 for bucket 57\nExited Ebwt loop\nfchr[A]: 0\nfchr[C]: 5124\nfchr[G]: 10305\nfchr[T]: 12474\nfchr[$]: 16568\nExiting Ebwt::buildToDisk()\nReturning from initFromVector\nWrote 4200050 bytes to primary EBWT file: genome.rev.1.bt2.tmp\nWrote 4148 bytes to secondary EBWT file: genome.rev.2.bt2.tmp\nRe-opening _in1 and _in2 as input streams\nReturning from Ebwt constructor\nHeaders:\n len: 16568\n bwtLen: 16569\n sz: 4142\n bwtSz: 4143\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 20\n eftabSz: 80\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 1036\n offsSz: 4144\n lineSz: 64\n sideSz: 64\n sideBwtSz: 48\n sideBwtLen: 192\n numSides: 87\n numLines: 87\n ebwtTotLen: 5568\n ebwtTotSz: 5568\n color: 0\n reverse: 1\nTotal time for backward call to driver() for mirror index: 00:00:00\n", "stderr": "Building a SMALL index\nRenaming genome.3.bt2.tmp to genome.3.bt2\nRenaming genome.4.bt2.tmp to genome.4.bt2\nRenaming genome.1.bt2.tmp to genome.1.bt2\nRenaming genome.2.bt2.tmp to genome.2.bt2\nRenaming genome.rev.1.bt2.tmp to genome.rev.1.bt2\nRenaming genome.rev.2.bt2.tmp to genome.rev.2.bt2\n100 reads; of these:\n 100 (100.00%) were paired; of these:\n 97 (97.00%) aligned concordantly 0 times\n 3 (3.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 97 pairs aligned concordantly 0 times; of these:\n 8 (8.25%) aligned discordantly 1 time\n ----\n 89 pairs aligned 0 times concordantly or discordantly; of these:\n 178 mates make up the pairs; of these:\n 153 (85.96%) aligned 0 times\n 25 (14.04%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n23.50% overall alignment rate\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-08 18:50:17", "plugin": "core", "name": "end_epoch", "raw_value": "1731091817.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 18:50:16", "plugin": "core", "name": "start_epoch", "raw_value": "1731091816.0000000"}, {"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": "bowtie2/2.5.3+galaxy1-1", "has_data": true, "data": {"tool_id": "bowtie2", "tool_version": "2.5.3+galaxy1", "test_index": 1, "time_seconds": 22.464369297027588, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "bowtie2/2.5.3+galaxy1-2", "has_data": true, "data": {"tool_id": "bowtie2", "tool_version": "2.5.3+galaxy1", "test_index": 2, "time_seconds": 45.79890775680542, "inputs": {"library|input_1": {"src": "hda", "id": "4813877bd5190163"}, "library|input_2": {"src": "hda", "id": "dd7732fe27a01988"}, "library|unaligned_file": false, "library|paired_options|paired_options_selector": "no", "library|type": "paired", "reference_genome|own_file": {"src": "hda", "id": "e40492d06caf609c"}, "reference_genome|source": "history", "rg|read_group_id_conditional|ID": "rg1", "rg|PL": "CAPILLARY", "rg|rg_selector": "set", "analysis_type|analysis_type_selector": "simple"}, "job": {"model_class": "Job", "id": "e40492d06caf609c", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T18:51:23.071642", "update_time": "2024-11-08T18:51:40.640452", "galaxy_version": "24.1", "external_id": "gxy-22qpm", "handler": null, "job_runner_name": null, "command_line": "set -o | grep -q pipefail && set -o pipefail; bowtie2-build --threads ${GALAXY_SLOTS:-4} '/galaxy/server/database/objects/2/7/3/dataset_273eac40-e006-4876-bbd7-7aa74081e483.dat' genome && ln -s -f '/galaxy/server/database/objects/2/7/3/dataset_273eac40-e006-4876-bbd7-7aa74081e483.dat' genome.fa && ln -f -s '/galaxy/server/database/objects/d/b/c/dataset_dbcb942a-49df-4364-8ad2-c13c9a237d2f.dat' input_f.fastq && ln -f -s '/galaxy/server/database/objects/3/2/5/dataset_3257dd66-bd8f-42d1-9f0b-c8472d48ef83.dat' input_r.fastq && THREADS=${GALAXY_SLOTS:-4} && if [ \"$THREADS\" -gt 1 ]; then (( THREADS-- )); fi && bowtie2 -p \"$THREADS\" -x 'genome' -1 'input_f.fastq' -2 'input_r.fastq' --rg-id \"rg1\" --rg \"PL:CAPILLARY\" | samtools sort -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/e/4/9/dataset_e490c7c0-3490-46a9-98f5-a8092288d4ef.dat'", "user_email": "tests@fake.org", "command_version": "/usr/local/bin/bowtie2-align-s version 2.5.3\n64-bit\nBuilt on fv-az365-785\nWed Jan 17 04:43:48 UTC 2024\nCompiler: gcc version 12.3.0 (conda-forge gcc 12.3.0-3) \nOptions: -O3 -msse2 -funroll-loops -g3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /usr/local/include -fdebug-prefix-map=/opt/conda/conda-bld/bowtie2_1705465427853/work=/usr/local/src/conda/bowtie2-2.5.3 -fdebug-prefix-map=/usr/local=/usr/local/src/conda-prefix -std=c++11 -Wall -Wno-unused-but-set-variable -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -DWITH_ZSTD\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "save_mapping_stats": "false", "sam_options": "{\"__current_case__\": 1, \"sam_options_selector\": \"no\"}", "analysis_type": "{\"__current_case__\": 0, \"analysis_type_selector\": \"simple\", \"presets\": \"no_presets\"}", "rg": "{\"CN\": null, \"DS\": null, \"DT\": null, \"FO\": null, \"KS\": null, \"PG\": null, \"PI\": \"\", \"PL\": \"CAPILLARY\", \"PU\": null, \"__current_case__\": 1, \"read_group_id_conditional\": {\"ID\": \"rg1\", \"__current_case__\": 1, \"do_auto_name\": false}, \"read_group_lb_conditional\": {\"LB\": null, \"__current_case__\": 1, \"do_auto_name\": false}, \"read_group_sm_conditional\": {\"SM\": \"\", \"__current_case__\": 1, \"do_auto_name\": false}, \"rg_selector\": \"set\"}", "reference_genome": "{\"__current_case__\": 1, \"own_file\": {\"values\": [{\"id\": 57, \"src\": \"hda\"}]}, \"source\": \"history\"}", "library": "{\"__current_case__\": 1, \"aligned_file\": false, \"input_1\": {\"values\": [{\"id\": 55, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 56, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 1, \"paired_options_selector\": \"no\"}, \"type\": \"paired\", \"unaligned_file\": false}"}, "inputs": {"library|input_2": {"id": "dd7732fe27a01988", "src": "hda", "uuid": "3257dd66-bd8f-42d1-9f0b-c8472d48ef83"}, "library|input_1": {"id": "4813877bd5190163", "src": "hda", "uuid": "dbcb942a-49df-4364-8ad2-c13c9a237d2f"}, "reference_genome|own_file": {"id": "e40492d06caf609c", "src": "hda", "uuid": "273eac40-e006-4876-bbd7-7aa74081e483"}}, "outputs": {"output": {"id": "7c5036351dc570af", "src": "hda", "uuid": "e490c7c0-3490-46a9-98f5-a8092288d4ef"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Settings:\n Output files: \"genome.*.bt2\"\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 Max bucket size: default\n Max bucket size, sqrt multiplier: default\n Max bucket size, len divisor: 32\n Difference-cover sample period: 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 /galaxy/server/database/objects/2/7/3/dataset_273eac40-e006-4876-bbd7-7aa74081e483.dat\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\nbmax according to bmaxDivN setting: 517\nUsing parameters --bmax 388 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 388 --dcv 1024\nConstructing suffix-array element generator\nBuilding DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 86 sample suffixes\nGenerating random suffixes\nQSorting 86 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 86 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 12, merged 41; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 6; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 284.672 (target: 387)\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering Ebwt loop\nGetting block 1 of 58\n Reserving size (388) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 2 of 58\nGetting block 3 of 58\n Entering block accumulator loop for bucket 1:\n Reserving size (388) for bucket 2\n Reserving size (388) for bucket 3\nGetting block 4 of 58\nGetting block 5 of 58\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 3\n Reserving size (388) for bucket 4\nGetting block 6 of 58\n Reserving size (388) for bucket 5\nGetting block 7 of 58\n bucket 1: 10%\n Calculating Z arrays for bucket 4\n Reserving size (388) for bucket 6\n Entering block accumulator loop for bucket 3:\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 2:\n Reserving size (388) for bucket 7\n bucket 1: 20%\n Entering block accumulator loop for bucket 4:\n Calculating Z arrays for bucket 6\n Calculating Z arrays for bucket 7\n bucket 1: 30%\n Entering block accumulator loop for bucket 5:\n bucket 3: 10%\n bucket 1: 40%\n Entering block accumulator loop for bucket 6:\n Entering block accumulator loop for bucket 7:\n bucket 5: 10%\n bucket 2: 10%\n bucket 4: 10%\n bucket 1: 50%\n bucket 3: 20%\n bucket 5: 20%\n bucket 1: 60%\n bucket 3: 30%\n bucket 2: 20%\n bucket 6: 10%\n bucket 5: 30%\n bucket 7: 10%\n bucket 4: 20%\n bucket 1: 70%\n bucket 3: 40%\n bucket 5: 40%\n bucket 2: 30%\n bucket 1: 80%\n bucket 6: 20%\n bucket 3: 50%\n bucket 4: 30%\n bucket 2: 40%\n bucket 5: 50%\n bucket 7: 20%\n bucket 1: 90%\n bucket 3: 60%\n bucket 6: 30%\n bucket 5: 60%\n bucket 2: 50%\n bucket 1: 100%\n bucket 4: 40%\n Sorting block of length 355 for bucket 1\n (Using difference cover)\n bucket 3: 70%\n bucket 7: 30%\n bucket 5: 70%\n bucket 2: 60%\n bucket 6: 40%\n bucket 3: 80%\n bucket 4: 50%\n bucket 5: 80%\n bucket 2: 70%\n bucket 7: 40%\n bucket 3: 90%\n bucket 2: 80%\n bucket 5: 90%\n bucket 6: 50%\n bucket 4: 60%\n bucket 3: 100%\n Sorting block of length 370 for bucket 3\n (Using difference cover)\n bucket 2: 90%\n bucket 5: 100%\n bucket 7: 50%\n Sorting block of length 203 for bucket 5\n (Using difference cover)\n bucket 6: 60%\n bucket 4: 70%\n bucket 2: 100%\n Sorting block of length 165 for bucket 2\n (Using difference cover)\n bucket 7: 60%\n bucket 6: 70%\n bucket 4: 80%\n Sorting block time: 00:00:00\nReturning block of 356 for bucket 1\n bucket 7: 70%\n bucket 6: 80%\n bucket 4: 90%\n bucket 7: 80%\n bucket 4: 100%\n bucket 6: 90%\n Sorting block of length 328 for bucket 4\n (Using difference cover)\n bucket 7: 90%\n bucket 6: 100%\n Sorting block of length 339 for bucket 6\n (Using difference cover)\n bucket 7: 100%\n Sorting block of length 368 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 369 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 371 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 329 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 166 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 204 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 6\nGetting block 8 of 58\n Reserving size (388) for bucket 8\n Calculating Z arrays for bucket 8\nGetting block 9 of 58\n Reserving size (388) for bucket 9\nGetting block 10 of 58\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 8:\n Reserving size (388) for bucket 10\n Entering block accumulator loop for bucket 9:\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 10:\n bucket 8: 10%\n bucket 9: 10%\n bucket 10: 10%\n bucket 8: 20%\n bucket 10: 20%\n bucket 8: 30%\n bucket 9: 20%\n bucket 10: 30%\n bucket 8: 40%\n bucket 9: 30%\n bucket 8: 50%\n bucket 10: 40%\n bucket 8: 60%\n bucket 9: 40%\n bucket 10: 50%\n bucket 8: 70%\n bucket 9: 50%\n bucket 10: 60%\n bucket 8: 80%\n bucket 9: 60%\n bucket 10: 70%\n bucket 8: 90%\n bucket 10: 80%\n bucket 9: 70%\n bucket 8: 100%\n Sorting block of length 171 for bucket 8\n (Using difference cover)\n bucket 10: 90%\n bucket 9: 80%\n bucket 9: 90%\n bucket 10: 100%\n Sorting block of length 357 for bucket 10\n (Using difference cover)\n bucket 9: 100%\n Sorting block of length 339 for bucket 9\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 172 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 358 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 9\nGetting block 11 of 58\n Reserving size (388) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\nGetting block 12 of 58\n Reserving size (388) for bucket 12\n Calculating Z arrays for bucket 12\n bucket 11: 10%\n Entering block accumulator loop for bucket 12:\n bucket 11: 20%\n bucket 12: 10%\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 12: 90%\n bucket 11: 100%\n Sorting block of length 305 for bucket 11\n (Using difference cover)\n bucket 12: 100%\n Sorting block of length 185 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 306 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 186 for bucket 12\nGetting block 13 of 58\n Reserving size (388) for bucket 13\nGetting block 14 of 58\n Calculating Z arrays for bucket 13\n Reserving size (388) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 14:\n Entering block accumulator loop for bucket 13:\n bucket 14: 10%\n bucket 13: 10%\n bucket 14: 20%\n bucket 13: 20%\n bucket 13: 30%\n bucket 14: 30%\n bucket 13: 40%\n bucket 14: 40%\n bucket 13: 50%\n bucket 13: 60%\n bucket 14: 50%\n bucket 13: 70%\n bucket 14: 60%\n bucket 13: 80%\n bucket 13: 90%\n bucket 14: 70%\n bucket 13: 100%\n bucket 14: 80%\n Sorting block of length 282 for bucket 13\n (Using difference cover)\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 339 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 283 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 14\nGetting block 15 of 58\n Reserving size (388) for bucket 15\nGetting block 16 of 58\n Calculating Z arrays for bucket 15\n Reserving size (388) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 15:\n Entering block accumulator loop for bucket 16:\n bucket 15: 10%\n bucket 16: 10%\n bucket 15: 20%\n bucket 16: 20%\n bucket 15: 30%\n bucket 15: 40%\n bucket 16: 30%\n bucket 15: 50%\n bucket 16: 40%\n bucket 15: 60%\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 241 for bucket 15\n (Using difference cover)\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block time: 00:00:00\n Sorting block of length 379 for bucket 16\n (Using difference cover)\nReturning block of 242 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 380 for bucket 16\nGetting block 17 of 58\n Reserving size (388) 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 215 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 216 for bucket 17\nGetting block 18 of 58\n Reserving size (388) for bucket 18\nGetting block 19 of 58\n Calculating Z arrays for bucket 18\n Reserving size (388) 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 19: 10%\n bucket 18: 10%\n bucket 19: 20%\n bucket 18: 20%\n bucket 19: 30%\n bucket 18: 30%\n bucket 19: 40%\n bucket 18: 40%\n bucket 19: 50%\n bucket 18: 50%\n bucket 19: 60%\n bucket 18: 60%\n bucket 19: 70%\n bucket 18: 70%\n bucket 19: 80%\n bucket 18: 80%\n bucket 19: 90%\n bucket 18: 90%\n bucket 19: 100%\n Sorting block of length 334 for bucket 19\n (Using difference cover)\n bucket 18: 100%\n Sorting block of length 378 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 335 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 379 for bucket 18\nGetting block 20 of 58\n Reserving size (388) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\nGetting block 21 of 58\n Reserving size (388) for bucket 21\n Calculating Z arrays for bucket 21\n bucket 20: 10%\n Entering block accumulator loop for bucket 21:\n bucket 20: 20%\n bucket 21: 10%\n bucket 20: 30%\n bucket 21: 20%\n bucket 21: 30%\n bucket 20: 40%\n bucket 21: 40%\n bucket 20: 50%\n bucket 21: 50%\n bucket 21: 60%\n bucket 20: 60%\n bucket 21: 70%\n bucket 21: 80%\n bucket 20: 70%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 210 for bucket 21\n (Using difference cover)\n bucket 20: 80%\n bucket 20: 90%\n Sorting block time: 00:00:00\nReturning block of 211 for bucket 21\n bucket 20: 100%\n Sorting block of length 313 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 314 for bucket 20\nGetting block 22 of 58\n Reserving size (388) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\nGetting block 23 of 58\n Reserving size (388) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 22: 10%\n bucket 22: 20%\n bucket 23: 10%\n bucket 22: 30%\n bucket 23: 20%\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 23: 70%\n bucket 22: 70%\n bucket 23: 80%\n bucket 22: 80%\n bucket 23: 90%\n bucket 22: 90%\n bucket 23: 100%\n Sorting block of length 238 for bucket 23\n (Using difference cover)\n bucket 22: 100%\n Sorting block of length 386 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 239 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 387 for bucket 22\nGetting block 24 of 58\n Reserving size (388) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\nGetting block 25 of 58\n Reserving size (388) for bucket 25\n Calculating Z arrays for bucket 25\nGetting block 26 of 58\n bucket 24: 10%\n Reserving size (388) 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 24: 20%\n bucket 26: 10%\n bucket 25: 10%\n bucket 26: 20%\n bucket 24: 30%\n bucket 25: 20%\n bucket 26: 30%\n bucket 24: 40%\n bucket 25: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 24: 50%\n bucket 25: 40%\n bucket 26: 60%\n bucket 25: 50%\n bucket 26: 70%\n bucket 24: 60%\n bucket 25: 60%\n bucket 26: 80%\n bucket 24: 70%\n bucket 26: 90%\n bucket 25: 70%\n bucket 26: 100%\n bucket 25: 80%\n Sorting block of length 354 for bucket 26\n (Using difference cover)\n bucket 24: 80%\n bucket 25: 90%\n bucket 24: 90%\n bucket 25: 100%\n Sorting block of length 105 for bucket 25\n (Using difference cover)\n bucket 24: 100%\n Sorting block of length 351 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 355 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 106 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 352 for bucket 24\nGetting block 27 of 58\n Reserving size (388) for bucket 27\n Calculating Z arrays for bucket 27\nGetting block 28 of 58\n Reserving size (388) for bucket 28\n Entering block accumulator loop for bucket 27:\n Calculating Z arrays for bucket 28\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 28: 30%\n bucket 27: 30%\n bucket 28: 40%\n bucket 27: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 27: 50%\n bucket 28: 70%\n bucket 27: 60%\n bucket 28: 80%\n bucket 27: 70%\n bucket 28: 90%\n bucket 27: 80%\n bucket 28: 100%\n Sorting block of length 253 for bucket 28\n (Using difference cover)\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 334 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 254 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 335 for bucket 27\nGetting block 29 of 58\n Reserving size (388) for bucket 29\n Calculating Z arrays for bucket 29\nGetting block 30 of 58\n Reserving size (388) 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 30: 70%\n bucket 29: 70%\n bucket 30: 80%\n bucket 29: 80%\n bucket 30: 90%\n bucket 29: 90%\n bucket 30: 100%\n Sorting block of length 345 for bucket 30\n (Using difference cover)\n bucket 29: 100%\n Sorting block of length 289 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 290 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 346 for bucket 30\nGetting block 31 of 58\n Reserving size (388) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 31:\n bucket 31: 10%\nGetting block 32 of 58\n Reserving size (388) for bucket 32\n Calculating Z arrays for bucket 32\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 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 32: 70%\n buc\n..\n0:00\nReturning block of 350 for bucket 23\nGetting block 24 of 57\n Reserving size (388) 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 245 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 246 for bucket 24\nGetting block 25 of 57\n Reserving size (388) for bucket 25\n Calculating Z arrays for bucket 25\nGetting block 26 of 57\n Entering block accumulator loop for bucket 25:\n Reserving size (388) for bucket 26\n Calculating Z arrays for bucket 26\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 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 286 for bucket 25\n (Using difference cover)\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 384 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 287 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 385 for bucket 26\nGetting block 27 of 57\n Reserving size (388) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\nGetting block 28 of 57\n Reserving size (388) for bucket 28\n bucket 27: 10%\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 27: 20%\n bucket 27: 30%\n bucket 28: 10%\n bucket 27: 40%\n bucket 28: 20%\n bucket 27: 50%\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 359 for bucket 27\n (Using difference cover)\n bucket 28: 70%\n bucket 28: 80%\n Sorting block time: 00:00:00\nReturning block of 360 for bucket 27\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 387 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 28\nGetting block 29 of 57\n Reserving size (388) for bucket 29\n Calculating Z arrays for bucket 29\nGetting block 30 of 57\n Reserving size (388) for bucket 30\n Calculating Z arrays for bucket 30\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 29: 20%\n bucket 30: 30%\n bucket 29: 30%\n bucket 30: 40%\n bucket 29: 40%\n bucket 30: 50%\n bucket 29: 50%\n bucket 30: 60%\n bucket 30: 70%\n bucket 29: 60%\n bucket 30: 80%\n bucket 29: 70%\n bucket 30: 90%\n bucket 29: 80%\n bucket 30: 100%\n bucket 29: 90%\n Sorting block of length 257 for bucket 30\n (Using difference cover)\n bucket 29: 100%\n Sorting block of length 195 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 258 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 29\nGetting block 31 of 57\n Reserving size (388) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 31:\nGetting block 32 of 57\n bucket 31: 10%\n Reserving size (388) for bucket 32\n Calculating Z arrays for bucket 32\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 32: 30%\n bucket 31: 60%\n bucket 31: 70%\n bucket 32: 40%\n bucket 31: 80%\n bucket 32: 50%\n bucket 31: 90%\n bucket 32: 60%\n bucket 31: 100%\n Sorting block of length 310 for bucket 31\n (Using difference cover)\n bucket 32: 70%\n bucket 32: 80%\n Sorting block time: 00:00:00\nReturning block of 311 for bucket 31\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 219 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 220 for bucket 32\nGetting block 33 of 57\n Reserving size (388) 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 387 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 33\nGetting block 34 of 57\n Reserving size (388) for bucket 34\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\nGetting block 35 of 57\n Reserving size (388) for bucket 35\n Calculating Z arrays for bucket 35\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 35: 30%\n bucket 34: 60%\n bucket 35: 40%\n bucket 35: 50%\n bucket 34: 70%\n bucket 35: 60%\n bucket 34: 80%\n bucket 35: 70%\n bucket 34: 90%\n bucket 35: 80%\n bucket 34: 100%\n Sorting block of length 275 for bucket 34\n (Using difference cover)\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 350 for bucket 35\n Sorting block time: 00:00:00\n (Using difference cover)\nReturning block of 276 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 351 for bucket 35\nGetting block 36 of 57\n Reserving size (388) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\nGetting block 37 of 57\n bucket 36: 10%\n Reserving size (388) for bucket 37\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 37:\n bucket 36: 20%\n bucket 36: 30%\n bucket 37: 10%\n bucket 36: 40%\n bucket 37: 20%\n bucket 36: 50%\n bucket 37: 30%\n bucket 36: 60%\n bucket 37: 40%\n bucket 36: 70%\n bucket 37: 50%\n bucket 36: 80%\n bucket 37: 60%\n bucket 36: 90%\n bucket 37: 70%\n bucket 36: 100%\n Sorting block of length 150 for bucket 36\n (Using difference cover)\n bucket 37: 80%\n bucket 37: 90%\n Sorting block time: 00:00:00\nReturning block of 151 for bucket 36\n bucket 37: 100%\n Sorting block of length 267 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 268 for bucket 37\nGetting block 38 of 57\n Reserving size (388) for bucket 38\nGetting block 39 of 57\n Calculating Z arrays for bucket 38\n Reserving size (388) 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 39: 10%\n bucket 38: 10%\n bucket 39: 20%\n bucket 38: 20%\n bucket 39: 30%\n bucket 39: 40%\n bucket 38: 30%\n bucket 39: 50%\n bucket 38: 40%\n bucket 39: 60%\n bucket 38: 50%\n bucket 39: 70%\n bucket 38: 60%\n bucket 39: 80%\n bucket 39: 90%\n bucket 38: 70%\n bucket 39: 100%\n Sorting block of length 387 for bucket 39\n (Using difference cover)\n bucket 38: 80%\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 337 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 39\n Sorting block time: 00:00:00\nReturning block of 338 for bucket 38\nGetting block 40 of 57\n Reserving size (388) for bucket 40\n Calculating Z arrays for bucket 40\nGetting block 41 of 57\n Reserving size (388) 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 41: 60%\n bucket 40: 60%\n bucket 41: 70%\n bucket 40: 70%\n bucket 41: 80%\n bucket 41: 90%\n bucket 40: 80%\n bucket 41: 100%\n Sorting block of length 330 for bucket 41\n (Using difference cover)\n bucket 40: 90%\n Sorting block time: 00:00:00\nReturning block of 331 for bucket 41\n bucket 40: 100%\n Sorting block of length 379 for bucket 40\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 380 for bucket 40\nGetting block 42 of 57\n Reserving size (388) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\nGetting block 43 of 57\n Reserving size (388) for bucket 43\n Calculating Z arrays for bucket 43\n bucket 42: 20%\n Entering block accumulator loop for bucket 43:\n bucket 42: 30%\n bucket 43: 10%\n bucket 42: 40%\n bucket 43: 20%\n bucket 42: 50%\n bucket 43: 30%\n bucket 43: 40%\n bucket 42: 60%\n bucket 43: 50%\n bucket 42: 70%\n bucket 43: 60%\n bucket 42: 80%\n bucket 43: 70%\n bucket 42: 90%\n bucket 43: 80%\n bucket 42: 100%\n Sorting block of length 188 for bucket 42\n (Using difference cover)\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 321 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 189 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 322 for bucket 43\nGetting block 44 of 57\n Reserving size (388) for bucket 44\n Calculating Z arrays for bucket 44\nGetting block 45 of 57\n Reserving size (388) for bucket 45\n Calculating Z arrays for bucket 45\n Entering block accumulator loop for bucket 44:\n Entering block accumulator loop for bucket 45:\n bucket 44: 10%\n bucket 45: 10%\n bucket 45: 20%\n bucket 44: 20%\n bucket 45: 30%\n bucket 44: 30%\n bucket 45: 40%\n bucket 44: 40%\n bucket 45: 50%\n bucket 44: 50%\n bucket 45: 60%\n bucket 44: 60%\n bucket 44: 70%\n bucket 45: 70%\n bucket 44: 80%\n bucket 45: 80%\n bucket 44: 90%\n bucket 45: 90%\n bucket 44: 100%\n Sorting block of length 366 for bucket 44\n (Using difference cover)\n bucket 45: 100%\n Sorting block of length 365 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 367 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 366 for bucket 45\nGetting block 46 of 57\n Reserving size (388) 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 253 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 254 for bucket 46\nGetting block 47 of 57\n Reserving size (388) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 47:\nGetting block 48 of 57\n Reserving size (388) 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 47: 70%\n bucket 48: 40%\n bucket 47: 80%\n bucket 48: 50%\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 217 for bucket 47\n (Using difference cover)\n bucket 48: 60%\n Sorting block time: 00:00:00\nReturning block of 218 for bucket 47\n bucket 48: 70%\n bucket 48: 80%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 384 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 385 for bucket 48\nGetting block 49 of 57\n Reserving size (388) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\nGetting block 50 of 57\n Reserving size (388) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 50:\n bucket 49: 10%\n bucket 50: 10%\n bucket 50: 20%\n bucket 49: 20%\n bucket 50: 30%\n bucket 50: 40%\n bucket 49: 30%\n bucket 50: 50%\n bucket 49: 40%\n bucket 50: 60%\n bucket 50: 70%\n bucket 49: 50%\n bucket 50: 80%\n bucket 49: 60%\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 275 for bucket 50\n (Using difference cover)\n bucket 49: 70%\n bucket 49: 80%\n bucket 49: 90%\n Sorting block time: 00:00:00\nReturning block of 276 for bucket 50\n bucket 49: 100%\n Sorting block of length 112 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 49\nGetting block 51 of 57\n Reserving size (388) 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 350 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 351 for bucket 51\nGetting block 52 of 57\n Reserving size (388) for bucket 52\nGetting block 53 of 57\n Calculating Z arrays for bucket 52\n Reserving size (388) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 52:\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\n bucket 52: 10%\n bucket 53: 20%\n bucket 52: 20%\n bucket 53: 30%\n bucket 52: 30%\n bucket 53: 40%\n bucket 52: 40%\n bucket 53: 50%\n bucket 53: 60%\n bucket 52: 50%\n bucket 53: 70%\n bucket 52: 60%\n bucket 52: 70%\n bucket 53: 80%\n bucket 53: 90%\n bucket 52: 80%\n bucket 53: 100%\n bucket 52: 90%\n Sorting block of length 370 for bucket 53\n (Using difference cover)\n bucket 52: 100%\n Sorting block of length 378 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 371 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 379 for bucket 52\nGetting block 54 of 57\n Reserving size (388) for bucket 54\n Calculating Z arrays for bucket 54\nGetting block 55 of 57\n Reserving size (388) for bucket 55\n Entering block accumulator loop for bucket 54:\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\n bucket 54: 10%\n bucket 54: 20%\n bucket 55: 10%\n bucket 54: 30%\n bucket 55: 20%\n bucket 54: 40%\n bucket 55: 30%\n bucket 54: 50%\n bucket 54: 60%\n bucket 55: 40%\n bucket 54: 70%\n bucket 55: 50%\n bucket 54: 80%\n bucket 55: 60%\n bucket 54: 90%\n bucket 55: 70%\n bucket 54: 100%\n Sorting block of length 237 for bucket 54\n (Using difference cover)\n bucket 55: 80%\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 344 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 238 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 345 for bucket 55\nGetting block 56 of 57\n Reserving size (388) for bucket 56\nGetting block 57 of 57\n Calculating Z arrays for bucket 56\n Reserving size (388) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 56:\n Entering block accumulator loop for bucket 57:\n bucket 56: 10%\n bucket 57: 10%\n bucket 56: 20%\n bucket 57: 20%\n bucket 57: 30%\n bucket 56: 30%\n bucket 57: 40%\n bucket 56: 40%\n bucket 57: 50%\n bucket 57: 60%\n bucket 57: 70%\n bucket 56: 50%\n bucket 57: 80%\n bucket 56: 60%\n bucket 57: 90%\n bucket 56: 70%\n bucket 57: 100%\n bucket 56: 80%\n Sorting block of length 132 for bucket 57\n (Using difference cover)\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 270 for bucket 56\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 133 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 271 for bucket 56\nExited Ebwt loop\nfchr[A]: 0\nfchr[C]: 5124\nfchr[G]: 10305\nfchr[T]: 12474\nfchr[$]: 16568\nExiting Ebwt::buildToDisk()\nReturning from initFromVector\nWrote 4200050 bytes to primary EBWT file: genome.rev.1.bt2.tmp\nWrote 4148 bytes to secondary EBWT file: genome.rev.2.bt2.tmp\nRe-opening _in1 and _in2 as input streams\nReturning from Ebwt constructor\nHeaders:\n len: 16568\n bwtLen: 16569\n sz: 4142\n bwtSz: 4143\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 20\n eftabSz: 80\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 1036\n offsSz: 4144\n lineSz: 64\n sideSz: 64\n sideBwtSz: 48\n sideBwtLen: 192\n numSides: 87\n numLines: 87\n ebwtTotLen: 5568\n ebwtTotSz: 5568\n color: 0\n reverse: 1\nTotal time for backward call to driver() for mirror index: 00:00:00\n", "tool_stderr": "Building a SMALL index\nRenaming genome.3.bt2.tmp to genome.3.bt2\nRenaming genome.4.bt2.tmp to genome.4.bt2\nRenaming genome.1.bt2.tmp to genome.1.bt2\nRenaming genome.2.bt2.tmp to genome.2.bt2\nRenaming genome.rev.1.bt2.tmp to genome.rev.1.bt2\nRenaming genome.rev.2.bt2.tmp to genome.rev.2.bt2\n100 reads; of these:\n 100 (100.00%) were paired; of these:\n 97 (97.00%) aligned concordantly 0 times\n 3 (3.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 97 pairs aligned concordantly 0 times; of these:\n 8 (8.25%) aligned discordantly 1 time\n ----\n 89 pairs aligned 0 times concordantly or discordantly; of these:\n 178 mates make up the pairs; of these:\n 153 (85.96%) aligned 0 times\n 25 (14.04%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n23.50% overall alignment rate\n", "job_stdout": "", "job_stderr": "", "stdout": "Settings:\n Output files: \"genome.*.bt2\"\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 Max bucket size: default\n Max bucket size, sqrt multiplier: default\n Max bucket size, len divisor: 32\n Difference-cover sample period: 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 /galaxy/server/database/objects/2/7/3/dataset_273eac40-e006-4876-bbd7-7aa74081e483.dat\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\nbmax according to bmaxDivN setting: 517\nUsing parameters --bmax 388 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 388 --dcv 1024\nConstructing suffix-array element generator\nBuilding DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 86 sample suffixes\nGenerating random suffixes\nQSorting 86 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 86 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 12, merged 41; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 6; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 284.672 (target: 387)\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering Ebwt loop\nGetting block 1 of 58\n Reserving size (388) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 2 of 58\nGetting block 3 of 58\n Entering block accumulator loop for bucket 1:\n Reserving size (388) for bucket 2\n Reserving size (388) for bucket 3\nGetting block 4 of 58\nGetting block 5 of 58\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 3\n Reserving size (388) for bucket 4\nGetting block 6 of 58\n Reserving size (388) for bucket 5\nGetting block 7 of 58\n bucket 1: 10%\n Calculating Z arrays for bucket 4\n Reserving size (388) for bucket 6\n Entering block accumulator loop for bucket 3:\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 2:\n Reserving size (388) for bucket 7\n bucket 1: 20%\n Entering block accumulator loop for bucket 4:\n Calculating Z arrays for bucket 6\n Calculating Z arrays for bucket 7\n bucket 1: 30%\n Entering block accumulator loop for bucket 5:\n bucket 3: 10%\n bucket 1: 40%\n Entering block accumulator loop for bucket 6:\n Entering block accumulator loop for bucket 7:\n bucket 5: 10%\n bucket 2: 10%\n bucket 4: 10%\n bucket 1: 50%\n bucket 3: 20%\n bucket 5: 20%\n bucket 1: 60%\n bucket 3: 30%\n bucket 2: 20%\n bucket 6: 10%\n bucket 5: 30%\n bucket 7: 10%\n bucket 4: 20%\n bucket 1: 70%\n bucket 3: 40%\n bucket 5: 40%\n bucket 2: 30%\n bucket 1: 80%\n bucket 6: 20%\n bucket 3: 50%\n bucket 4: 30%\n bucket 2: 40%\n bucket 5: 50%\n bucket 7: 20%\n bucket 1: 90%\n bucket 3: 60%\n bucket 6: 30%\n bucket 5: 60%\n bucket 2: 50%\n bucket 1: 100%\n bucket 4: 40%\n Sorting block of length 355 for bucket 1\n (Using difference cover)\n bucket 3: 70%\n bucket 7: 30%\n bucket 5: 70%\n bucket 2: 60%\n bucket 6: 40%\n bucket 3: 80%\n bucket 4: 50%\n bucket 5: 80%\n bucket 2: 70%\n bucket 7: 40%\n bucket 3: 90%\n bucket 2: 80%\n bucket 5: 90%\n bucket 6: 50%\n bucket 4: 60%\n bucket 3: 100%\n Sorting block of length 370 for bucket 3\n (Using difference cover)\n bucket 2: 90%\n bucket 5: 100%\n bucket 7: 50%\n Sorting block of length 203 for bucket 5\n (Using difference cover)\n bucket 6: 60%\n bucket 4: 70%\n bucket 2: 100%\n Sorting block of length 165 for bucket 2\n (Using difference cover)\n bucket 7: 60%\n bucket 6: 70%\n bucket 4: 80%\n Sorting block time: 00:00:00\nReturning block of 356 for bucket 1\n bucket 7: 70%\n bucket 6: 80%\n bucket 4: 90%\n bucket 7: 80%\n bucket 4: 100%\n bucket 6: 90%\n Sorting block of length 328 for bucket 4\n (Using difference cover)\n bucket 7: 90%\n bucket 6: 100%\n Sorting block of length 339 for bucket 6\n (Using difference cover)\n bucket 7: 100%\n Sorting block of length 368 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 369 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 371 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 329 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 166 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 204 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 6\nGetting block 8 of 58\n Reserving size (388) for bucket 8\n Calculating Z arrays for bucket 8\nGetting block 9 of 58\n Reserving size (388) for bucket 9\nGetting block 10 of 58\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 8:\n Reserving size (388) for bucket 10\n Entering block accumulator loop for bucket 9:\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 10:\n bucket 8: 10%\n bucket 9: 10%\n bucket 10: 10%\n bucket 8: 20%\n bucket 10: 20%\n bucket 8: 30%\n bucket 9: 20%\n bucket 10: 30%\n bucket 8: 40%\n bucket 9: 30%\n bucket 8: 50%\n bucket 10: 40%\n bucket 8: 60%\n bucket 9: 40%\n bucket 10: 50%\n bucket 8: 70%\n bucket 9: 50%\n bucket 10: 60%\n bucket 8: 80%\n bucket 9: 60%\n bucket 10: 70%\n bucket 8: 90%\n bucket 10: 80%\n bucket 9: 70%\n bucket 8: 100%\n Sorting block of length 171 for bucket 8\n (Using difference cover)\n bucket 10: 90%\n bucket 9: 80%\n bucket 9: 90%\n bucket 10: 100%\n Sorting block of length 357 for bucket 10\n (Using difference cover)\n bucket 9: 100%\n Sorting block of length 339 for bucket 9\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 172 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 358 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 9\nGetting block 11 of 58\n Reserving size (388) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\nGetting block 12 of 58\n Reserving size (388) for bucket 12\n Calculating Z arrays for bucket 12\n bucket 11: 10%\n Entering block accumulator loop for bucket 12:\n bucket 11: 20%\n bucket 12: 10%\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 12: 90%\n bucket 11: 100%\n Sorting block of length 305 for bucket 11\n (Using difference cover)\n bucket 12: 100%\n Sorting block of length 185 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 306 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 186 for bucket 12\nGetting block 13 of 58\n Reserving size (388) for bucket 13\nGetting block 14 of 58\n Calculating Z arrays for bucket 13\n Reserving size (388) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 14:\n Entering block accumulator loop for bucket 13:\n bucket 14: 10%\n bucket 13: 10%\n bucket 14: 20%\n bucket 13: 20%\n bucket 13: 30%\n bucket 14: 30%\n bucket 13: 40%\n bucket 14: 40%\n bucket 13: 50%\n bucket 13: 60%\n bucket 14: 50%\n bucket 13: 70%\n bucket 14: 60%\n bucket 13: 80%\n bucket 13: 90%\n bucket 14: 70%\n bucket 13: 100%\n bucket 14: 80%\n Sorting block of length 282 for bucket 13\n (Using difference cover)\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 339 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 283 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 14\nGetting block 15 of 58\n Reserving size (388) for bucket 15\nGetting block 16 of 58\n Calculating Z arrays for bucket 15\n Reserving size (388) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 15:\n Entering block accumulator loop for bucket 16:\n bucket 15: 10%\n bucket 16: 10%\n bucket 15: 20%\n bucket 16: 20%\n bucket 15: 30%\n bucket 15: 40%\n bucket 16: 30%\n bucket 15: 50%\n bucket 16: 40%\n bucket 15: 60%\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 241 for bucket 15\n (Using difference cover)\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block time: 00:00:00\n Sorting block of length 379 for bucket 16\n (Using difference cover)\nReturning block of 242 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 380 for bucket 16\nGetting block 17 of 58\n Reserving size (388) 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 215 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 216 for bucket 17\nGetting block 18 of 58\n Reserving size (388) for bucket 18\nGetting block 19 of 58\n Calculating Z arrays for bucket 18\n Reserving size (388) 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 19: 10%\n bucket 18: 10%\n bucket 19: 20%\n bucket 18: 20%\n bucket 19: 30%\n bucket 18: 30%\n bucket 19: 40%\n bucket 18: 40%\n bucket 19: 50%\n bucket 18: 50%\n bucket 19: 60%\n bucket 18: 60%\n bucket 19: 70%\n bucket 18: 70%\n bucket 19: 80%\n bucket 18: 80%\n bucket 19: 90%\n bucket 18: 90%\n bucket 19: 100%\n Sorting block of length 334 for bucket 19\n (Using difference cover)\n bucket 18: 100%\n Sorting block of length 378 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 335 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 379 for bucket 18\nGetting block 20 of 58\n Reserving size (388) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\nGetting block 21 of 58\n Reserving size (388) for bucket 21\n Calculating Z arrays for bucket 21\n bucket 20: 10%\n Entering block accumulator loop for bucket 21:\n bucket 20: 20%\n bucket 21: 10%\n bucket 20: 30%\n bucket 21: 20%\n bucket 21: 30%\n bucket 20: 40%\n bucket 21: 40%\n bucket 20: 50%\n bucket 21: 50%\n bucket 21: 60%\n bucket 20: 60%\n bucket 21: 70%\n bucket 21: 80%\n bucket 20: 70%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 210 for bucket 21\n (Using difference cover)\n bucket 20: 80%\n bucket 20: 90%\n Sorting block time: 00:00:00\nReturning block of 211 for bucket 21\n bucket 20: 100%\n Sorting block of length 313 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 314 for bucket 20\nGetting block 22 of 58\n Reserving size (388) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\nGetting block 23 of 58\n Reserving size (388) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 22: 10%\n bucket 22: 20%\n bucket 23: 10%\n bucket 22: 30%\n bucket 23: 20%\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 23: 70%\n bucket 22: 70%\n bucket 23: 80%\n bucket 22: 80%\n bucket 23: 90%\n bucket 22: 90%\n bucket 23: 100%\n Sorting block of length 238 for bucket 23\n (Using difference cover)\n bucket 22: 100%\n Sorting block of length 386 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 239 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 387 for bucket 22\nGetting block 24 of 58\n Reserving size (388) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\nGetting block 25 of 58\n Reserving size (388) for bucket 25\n Calculating Z arrays for bucket 25\nGetting block 26 of 58\n bucket 24: 10%\n Reserving size (388) 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 24: 20%\n bucket 26: 10%\n bucket 25: 10%\n bucket 26: 20%\n bucket 24: 30%\n bucket 25: 20%\n bucket 26: 30%\n bucket 24: 40%\n bucket 25: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 24: 50%\n bucket 25: 40%\n bucket 26: 60%\n bucket 25: 50%\n bucket 26: 70%\n bucket 24: 60%\n bucket 25: 60%\n bucket 26: 80%\n bucket 24: 70%\n bucket 26: 90%\n bucket 25: 70%\n bucket 26: 100%\n bucket 25: 80%\n Sorting block of length 354 for bucket 26\n (Using difference cover)\n bucket 24: 80%\n bucket 25: 90%\n bucket 24: 90%\n bucket 25: 100%\n Sorting block of length 105 for bucket 25\n (Using difference cover)\n bucket 24: 100%\n Sorting block of length 351 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 355 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 106 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 352 for bucket 24\nGetting block 27 of 58\n Reserving size (388) for bucket 27\n Calculating Z arrays for bucket 27\nGetting block 28 of 58\n Reserving size (388) for bucket 28\n Entering block accumulator loop for bucket 27:\n Calculating Z arrays for bucket 28\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 28: 30%\n bucket 27: 30%\n bucket 28: 40%\n bucket 27: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 27: 50%\n bucket 28: 70%\n bucket 27: 60%\n bucket 28: 80%\n bucket 27: 70%\n bucket 28: 90%\n bucket 27: 80%\n bucket 28: 100%\n Sorting block of length 253 for bucket 28\n (Using difference cover)\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 334 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 254 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 335 for bucket 27\nGetting block 29 of 58\n Reserving size (388) for bucket 29\n Calculating Z arrays for bucket 29\nGetting block 30 of 58\n Reserving size (388) 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 30: 70%\n bucket 29: 70%\n bucket 30: 80%\n bucket 29: 80%\n bucket 30: 90%\n bucket 29: 90%\n bucket 30: 100%\n Sorting block of length 345 for bucket 30\n (Using difference cover)\n bucket 29: 100%\n Sorting block of length 289 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 290 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 346 for bucket 30\nGetting block 31 of 58\n Reserving size (388) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 31:\n bucket 31: 10%\nGetting block 32 of 58\n Reserving size (388) for bucket 32\n Calculating Z arrays for bucket 32\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 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 32: 70%\n buc\n..\n0:00\nReturning block of 350 for bucket 23\nGetting block 24 of 57\n Reserving size (388) 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 245 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 246 for bucket 24\nGetting block 25 of 57\n Reserving size (388) for bucket 25\n Calculating Z arrays for bucket 25\nGetting block 26 of 57\n Entering block accumulator loop for bucket 25:\n Reserving size (388) for bucket 26\n Calculating Z arrays for bucket 26\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 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 286 for bucket 25\n (Using difference cover)\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 384 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 287 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 385 for bucket 26\nGetting block 27 of 57\n Reserving size (388) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\nGetting block 28 of 57\n Reserving size (388) for bucket 28\n bucket 27: 10%\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 27: 20%\n bucket 27: 30%\n bucket 28: 10%\n bucket 27: 40%\n bucket 28: 20%\n bucket 27: 50%\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 359 for bucket 27\n (Using difference cover)\n bucket 28: 70%\n bucket 28: 80%\n Sorting block time: 00:00:00\nReturning block of 360 for bucket 27\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 387 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 28\nGetting block 29 of 57\n Reserving size (388) for bucket 29\n Calculating Z arrays for bucket 29\nGetting block 30 of 57\n Reserving size (388) for bucket 30\n Calculating Z arrays for bucket 30\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 29: 20%\n bucket 30: 30%\n bucket 29: 30%\n bucket 30: 40%\n bucket 29: 40%\n bucket 30: 50%\n bucket 29: 50%\n bucket 30: 60%\n bucket 30: 70%\n bucket 29: 60%\n bucket 30: 80%\n bucket 29: 70%\n bucket 30: 90%\n bucket 29: 80%\n bucket 30: 100%\n bucket 29: 90%\n Sorting block of length 257 for bucket 30\n (Using difference cover)\n bucket 29: 100%\n Sorting block of length 195 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 258 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 29\nGetting block 31 of 57\n Reserving size (388) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 31:\nGetting block 32 of 57\n bucket 31: 10%\n Reserving size (388) for bucket 32\n Calculating Z arrays for bucket 32\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 32: 30%\n bucket 31: 60%\n bucket 31: 70%\n bucket 32: 40%\n bucket 31: 80%\n bucket 32: 50%\n bucket 31: 90%\n bucket 32: 60%\n bucket 31: 100%\n Sorting block of length 310 for bucket 31\n (Using difference cover)\n bucket 32: 70%\n bucket 32: 80%\n Sorting block time: 00:00:00\nReturning block of 311 for bucket 31\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 219 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 220 for bucket 32\nGetting block 33 of 57\n Reserving size (388) 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 387 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 33\nGetting block 34 of 57\n Reserving size (388) for bucket 34\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\nGetting block 35 of 57\n Reserving size (388) for bucket 35\n Calculating Z arrays for bucket 35\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 35: 30%\n bucket 34: 60%\n bucket 35: 40%\n bucket 35: 50%\n bucket 34: 70%\n bucket 35: 60%\n bucket 34: 80%\n bucket 35: 70%\n bucket 34: 90%\n bucket 35: 80%\n bucket 34: 100%\n Sorting block of length 275 for bucket 34\n (Using difference cover)\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 350 for bucket 35\n Sorting block time: 00:00:00\n (Using difference cover)\nReturning block of 276 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 351 for bucket 35\nGetting block 36 of 57\n Reserving size (388) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\nGetting block 37 of 57\n bucket 36: 10%\n Reserving size (388) for bucket 37\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 37:\n bucket 36: 20%\n bucket 36: 30%\n bucket 37: 10%\n bucket 36: 40%\n bucket 37: 20%\n bucket 36: 50%\n bucket 37: 30%\n bucket 36: 60%\n bucket 37: 40%\n bucket 36: 70%\n bucket 37: 50%\n bucket 36: 80%\n bucket 37: 60%\n bucket 36: 90%\n bucket 37: 70%\n bucket 36: 100%\n Sorting block of length 150 for bucket 36\n (Using difference cover)\n bucket 37: 80%\n bucket 37: 90%\n Sorting block time: 00:00:00\nReturning block of 151 for bucket 36\n bucket 37: 100%\n Sorting block of length 267 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 268 for bucket 37\nGetting block 38 of 57\n Reserving size (388) for bucket 38\nGetting block 39 of 57\n Calculating Z arrays for bucket 38\n Reserving size (388) 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 39: 10%\n bucket 38: 10%\n bucket 39: 20%\n bucket 38: 20%\n bucket 39: 30%\n bucket 39: 40%\n bucket 38: 30%\n bucket 39: 50%\n bucket 38: 40%\n bucket 39: 60%\n bucket 38: 50%\n bucket 39: 70%\n bucket 38: 60%\n bucket 39: 80%\n bucket 39: 90%\n bucket 38: 70%\n bucket 39: 100%\n Sorting block of length 387 for bucket 39\n (Using difference cover)\n bucket 38: 80%\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 337 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 39\n Sorting block time: 00:00:00\nReturning block of 338 for bucket 38\nGetting block 40 of 57\n Reserving size (388) for bucket 40\n Calculating Z arrays for bucket 40\nGetting block 41 of 57\n Reserving size (388) 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 41: 60%\n bucket 40: 60%\n bucket 41: 70%\n bucket 40: 70%\n bucket 41: 80%\n bucket 41: 90%\n bucket 40: 80%\n bucket 41: 100%\n Sorting block of length 330 for bucket 41\n (Using difference cover)\n bucket 40: 90%\n Sorting block time: 00:00:00\nReturning block of 331 for bucket 41\n bucket 40: 100%\n Sorting block of length 379 for bucket 40\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 380 for bucket 40\nGetting block 42 of 57\n Reserving size (388) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\nGetting block 43 of 57\n Reserving size (388) for bucket 43\n Calculating Z arrays for bucket 43\n bucket 42: 20%\n Entering block accumulator loop for bucket 43:\n bucket 42: 30%\n bucket 43: 10%\n bucket 42: 40%\n bucket 43: 20%\n bucket 42: 50%\n bucket 43: 30%\n bucket 43: 40%\n bucket 42: 60%\n bucket 43: 50%\n bucket 42: 70%\n bucket 43: 60%\n bucket 42: 80%\n bucket 43: 70%\n bucket 42: 90%\n bucket 43: 80%\n bucket 42: 100%\n Sorting block of length 188 for bucket 42\n (Using difference cover)\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 321 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 189 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 322 for bucket 43\nGetting block 44 of 57\n Reserving size (388) for bucket 44\n Calculating Z arrays for bucket 44\nGetting block 45 of 57\n Reserving size (388) for bucket 45\n Calculating Z arrays for bucket 45\n Entering block accumulator loop for bucket 44:\n Entering block accumulator loop for bucket 45:\n bucket 44: 10%\n bucket 45: 10%\n bucket 45: 20%\n bucket 44: 20%\n bucket 45: 30%\n bucket 44: 30%\n bucket 45: 40%\n bucket 44: 40%\n bucket 45: 50%\n bucket 44: 50%\n bucket 45: 60%\n bucket 44: 60%\n bucket 44: 70%\n bucket 45: 70%\n bucket 44: 80%\n bucket 45: 80%\n bucket 44: 90%\n bucket 45: 90%\n bucket 44: 100%\n Sorting block of length 366 for bucket 44\n (Using difference cover)\n bucket 45: 100%\n Sorting block of length 365 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 367 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 366 for bucket 45\nGetting block 46 of 57\n Reserving size (388) 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 253 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 254 for bucket 46\nGetting block 47 of 57\n Reserving size (388) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 47:\nGetting block 48 of 57\n Reserving size (388) 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 47: 70%\n bucket 48: 40%\n bucket 47: 80%\n bucket 48: 50%\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 217 for bucket 47\n (Using difference cover)\n bucket 48: 60%\n Sorting block time: 00:00:00\nReturning block of 218 for bucket 47\n bucket 48: 70%\n bucket 48: 80%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 384 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 385 for bucket 48\nGetting block 49 of 57\n Reserving size (388) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\nGetting block 50 of 57\n Reserving size (388) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 50:\n bucket 49: 10%\n bucket 50: 10%\n bucket 50: 20%\n bucket 49: 20%\n bucket 50: 30%\n bucket 50: 40%\n bucket 49: 30%\n bucket 50: 50%\n bucket 49: 40%\n bucket 50: 60%\n bucket 50: 70%\n bucket 49: 50%\n bucket 50: 80%\n bucket 49: 60%\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 275 for bucket 50\n (Using difference cover)\n bucket 49: 70%\n bucket 49: 80%\n bucket 49: 90%\n Sorting block time: 00:00:00\nReturning block of 276 for bucket 50\n bucket 49: 100%\n Sorting block of length 112 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 49\nGetting block 51 of 57\n Reserving size (388) 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 350 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 351 for bucket 51\nGetting block 52 of 57\n Reserving size (388) for bucket 52\nGetting block 53 of 57\n Calculating Z arrays for bucket 52\n Reserving size (388) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 52:\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\n bucket 52: 10%\n bucket 53: 20%\n bucket 52: 20%\n bucket 53: 30%\n bucket 52: 30%\n bucket 53: 40%\n bucket 52: 40%\n bucket 53: 50%\n bucket 53: 60%\n bucket 52: 50%\n bucket 53: 70%\n bucket 52: 60%\n bucket 52: 70%\n bucket 53: 80%\n bucket 53: 90%\n bucket 52: 80%\n bucket 53: 100%\n bucket 52: 90%\n Sorting block of length 370 for bucket 53\n (Using difference cover)\n bucket 52: 100%\n Sorting block of length 378 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 371 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 379 for bucket 52\nGetting block 54 of 57\n Reserving size (388) for bucket 54\n Calculating Z arrays for bucket 54\nGetting block 55 of 57\n Reserving size (388) for bucket 55\n Entering block accumulator loop for bucket 54:\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\n bucket 54: 10%\n bucket 54: 20%\n bucket 55: 10%\n bucket 54: 30%\n bucket 55: 20%\n bucket 54: 40%\n bucket 55: 30%\n bucket 54: 50%\n bucket 54: 60%\n bucket 55: 40%\n bucket 54: 70%\n bucket 55: 50%\n bucket 54: 80%\n bucket 55: 60%\n bucket 54: 90%\n bucket 55: 70%\n bucket 54: 100%\n Sorting block of length 237 for bucket 54\n (Using difference cover)\n bucket 55: 80%\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 344 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 238 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 345 for bucket 55\nGetting block 56 of 57\n Reserving size (388) for bucket 56\nGetting block 57 of 57\n Calculating Z arrays for bucket 56\n Reserving size (388) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 56:\n Entering block accumulator loop for bucket 57:\n bucket 56: 10%\n bucket 57: 10%\n bucket 56: 20%\n bucket 57: 20%\n bucket 57: 30%\n bucket 56: 30%\n bucket 57: 40%\n bucket 56: 40%\n bucket 57: 50%\n bucket 57: 60%\n bucket 57: 70%\n bucket 56: 50%\n bucket 57: 80%\n bucket 56: 60%\n bucket 57: 90%\n bucket 56: 70%\n bucket 57: 100%\n bucket 56: 80%\n Sorting block of length 132 for bucket 57\n (Using difference cover)\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 270 for bucket 56\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 133 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 271 for bucket 56\nExited Ebwt loop\nfchr[A]: 0\nfchr[C]: 5124\nfchr[G]: 10305\nfchr[T]: 12474\nfchr[$]: 16568\nExiting Ebwt::buildToDisk()\nReturning from initFromVector\nWrote 4200050 bytes to primary EBWT file: genome.rev.1.bt2.tmp\nWrote 4148 bytes to secondary EBWT file: genome.rev.2.bt2.tmp\nRe-opening _in1 and _in2 as input streams\nReturning from Ebwt constructor\nHeaders:\n len: 16568\n bwtLen: 16569\n sz: 4142\n bwtSz: 4143\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 20\n eftabSz: 80\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 1036\n offsSz: 4144\n lineSz: 64\n sideSz: 64\n sideBwtSz: 48\n sideBwtLen: 192\n numSides: 87\n numLines: 87\n ebwtTotLen: 5568\n ebwtTotSz: 5568\n color: 0\n reverse: 1\nTotal time for backward call to driver() for mirror index: 00:00:00\n", "stderr": "Building a SMALL index\nRenaming genome.3.bt2.tmp to genome.3.bt2\nRenaming genome.4.bt2.tmp to genome.4.bt2\nRenaming genome.1.bt2.tmp to genome.1.bt2\nRenaming genome.2.bt2.tmp to genome.2.bt2\nRenaming genome.rev.1.bt2.tmp to genome.rev.1.bt2\nRenaming genome.rev.2.bt2.tmp to genome.rev.2.bt2\n100 reads; of these:\n 100 (100.00%) were paired; of these:\n 97 (97.00%) aligned concordantly 0 times\n 3 (3.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 97 pairs aligned concordantly 0 times; of these:\n 8 (8.25%) aligned discordantly 1 time\n ----\n 89 pairs aligned 0 times concordantly or discordantly; of these:\n 178 mates make up the pairs; of these:\n 153 (85.96%) aligned 0 times\n 25 (14.04%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n23.50% overall alignment rate\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-08 18:51:28", "plugin": "core", "name": "end_epoch", "raw_value": "1731091888.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 18:51:27", "plugin": "core", "name": "start_epoch", "raw_value": "1731091887.0000000"}, {"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": "bowtie2/2.5.3+galaxy1-3", "has_data": true, "data": {"tool_id": "bowtie2", "tool_version": "2.5.3+galaxy1", "test_index": 3, "time_seconds": 44.13598442077637, "inputs": {"library|input_1": {"src": "hda", "id": "12f723b97d4a53c5"}, "library|input_2": {"src": "hda", "id": "2dae2f5e3e0f7ea7"}, "library|unaligned_file": false, "library|paired_options|paired_options_selector": "no", "library|type": "paired", "reference_genome|own_file": {"src": "hda", "id": "61add0d864102c44"}, "reference_genome|source": "history", "analysis_type|analysis_type_selector": "simple", "save_mapping_stats": true}, "job": {"model_class": "Job", "id": "61add0d864102c44", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T18:52:09.222395", "update_time": "2024-11-08T18:52:24.501831", "galaxy_version": "24.1", "external_id": "gxy-6rfjn", "handler": null, "job_runner_name": null, "command_line": "set -o | grep -q pipefail && set -o pipefail; bowtie2-build --threads ${GALAXY_SLOTS:-4} '/galaxy/server/database/objects/8/8/5/dataset_8858f956-b68e-498b-9fe6-4fdd63a567d0.dat' genome && ln -s -f '/galaxy/server/database/objects/8/8/5/dataset_8858f956-b68e-498b-9fe6-4fdd63a567d0.dat' genome.fa && ln -f -s '/galaxy/server/database/objects/2/4/9/dataset_24932b35-5f4f-46dc-9b62-d72b795ce5dc.dat' input_f.fastq && ln -f -s '/galaxy/server/database/objects/1/9/2/dataset_1925a707-e130-42eb-8d9c-e308ddc6cec1.dat' input_r.fastq && THREADS=${GALAXY_SLOTS:-4} && if [ \"$THREADS\" -gt 1 ]; then (( THREADS-- )); fi && bowtie2 -p \"$THREADS\" -x 'genome' -1 'input_f.fastq' -2 'input_r.fastq' 2> >(tee '/galaxy/server/database/objects/6/0/9/dataset_609194c0-0bf0-4170-ac6e-652731399cfd.dat' >&2) | samtools sort -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/7/5/9/dataset_759a2f3b-f634-4952-8bb5-477f54da0cba.dat'", "user_email": "tests@fake.org", "command_version": "/usr/local/bin/bowtie2-align-s version 2.5.3\n64-bit\nBuilt on fv-az365-785\nWed Jan 17 04:43:48 UTC 2024\nCompiler: gcc version 12.3.0 (conda-forge gcc 12.3.0-3) \nOptions: -O3 -msse2 -funroll-loops -g3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /usr/local/include -fdebug-prefix-map=/opt/conda/conda-bld/bowtie2_1705465427853/work=/usr/local/src/conda/bowtie2-2.5.3 -fdebug-prefix-map=/usr/local=/usr/local/src/conda-prefix -std=c++11 -Wall -Wno-unused-but-set-variable -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -DWITH_ZSTD\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "save_mapping_stats": "true", "sam_options": "{\"__current_case__\": 1, \"sam_options_selector\": \"no\"}", "analysis_type": "{\"__current_case__\": 0, \"analysis_type_selector\": \"simple\", \"presets\": \"no_presets\"}", "rg": "{\"__current_case__\": 3, \"rg_selector\": \"do_not_set\"}", "reference_genome": "{\"__current_case__\": 1, \"own_file\": {\"values\": [{\"id\": 61, \"src\": \"hda\"}]}, \"source\": \"history\"}", "library": "{\"__current_case__\": 1, \"aligned_file\": false, \"input_1\": {\"values\": [{\"id\": 59, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 60, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 1, \"paired_options_selector\": \"no\"}, \"type\": \"paired\", \"unaligned_file\": false}"}, "inputs": {"library|input_1": {"id": "12f723b97d4a53c5", "src": "hda", "uuid": "24932b35-5f4f-46dc-9b62-d72b795ce5dc"}, "library|input_2": {"id": "2dae2f5e3e0f7ea7", "src": "hda", "uuid": "1925a707-e130-42eb-8d9c-e308ddc6cec1"}, "reference_genome|own_file": {"id": "61add0d864102c44", "src": "hda", "uuid": "8858f956-b68e-498b-9fe6-4fdd63a567d0"}}, "outputs": {"output": {"id": "fb05b536cd69771d", "src": "hda", "uuid": "759a2f3b-f634-4952-8bb5-477f54da0cba"}, "mapping_stats": {"id": "c700bc1b046f6d9a", "src": "hda", "uuid": "609194c0-0bf0-4170-ac6e-652731399cfd"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Settings:\n Output files: \"genome.*.bt2\"\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 Max bucket size: default\n Max bucket size, sqrt multiplier: default\n Max bucket size, len divisor: 32\n Difference-cover sample period: 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 /galaxy/server/database/objects/8/8/5/dataset_8858f956-b68e-498b-9fe6-4fdd63a567d0.dat\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\nbmax according to bmaxDivN setting: 517\nUsing parameters --bmax 388 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 388 --dcv 1024\nConstructing suffix-array element generator\nBuilding DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 86 sample suffixes\nGenerating random suffixes\nQSorting 86 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 86 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 12, merged 41; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 6; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 284.672 (target: 387)\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering Ebwt loop\nGetting block 1 of 58\n Reserving size (388) for bucket 1\nGetting block 2 of 58\nGetting block 3 of 58\nGetting block 4 of 58\nGetting block 5 of 58\nGetting block 6 of 58\n Calculating Z arrays for bucket 1\n Reserving size (388) for bucket 2\n Reserving size (388) for bucket 3\n Reserving size (388) for bucket 4\n Reserving size (388) for bucket 5\n Reserving size (388) for bucket 6\nGetting block 7 of 58\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 3\n Entering block accumulator loop for bucket 1:\n Calculating Z arrays for bucket 4\n Calculating Z arrays for bucket 5\n Calculating Z arrays for bucket 6\n Reserving size (388) for bucket 7\n Entering block accumulator loop for bucket 2:\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 3:\n Entering block accumulator loop for bucket 4:\n Entering block accumulator loop for bucket 5:\n Entering block accumulator loop for bucket 6:\n Entering block accumulator loop for bucket 7:\n bucket 2: 10%\n bucket 1: 10%\n bucket 4: 10%\n bucket 5: 10%\n bucket 3: 10%\n bucket 6: 10%\n bucket 2: 20%\n bucket 7: 10%\n bucket 1: 20%\n bucket 2: 30%\n bucket 4: 20%\n bucket 1: 30%\n bucket 5: 20%\n bucket 3: 20%\n bucket 6: 20%\n bucket 7: 20%\n bucket 2: 40%\n bucket 1: 40%\n bucket 4: 30%\n bucket 5: 30%\n bucket 2: 50%\n bucket 1: 50%\n bucket 3: 30%\n bucket 6: 30%\n bucket 7: 30%\n bucket 4: 40%\n bucket 2: 60%\n bucket 1: 60%\n bucket 5: 40%\n bucket 2: 70%\n bucket 3: 40%\n bucket 1: 70%\n bucket 6: 40%\n bucket 4: 50%\n bucket 7: 40%\n bucket 2: 80%\n bucket 1: 80%\n bucket 5: 50%\n bucket 4: 60%\n bucket 3: 50%\n bucket 2: 90%\n bucket 1: 90%\n bucket 7: 50%\n bucket 4: 70%\n bucket 2: 100%\n bucket 6: 50%\n bucket 1: 100%\n bucket 5: 60%\n Sorting block of length 165 for bucket 2\n (Using difference cover)\n Sorting block of length 355 for bucket 1\n (Using difference cover)\n bucket 3: 60%\n bucket 4: 80%\n bucket 7: 60%\n bucket 6: 60%\n bucket 5: 70%\n bucket 4: 90%\n bucket 3: 70%\n bucket 4: 100%\n bucket 7: 70%\n bucket 5: 80%\n bucket 6: 70%\n Sorting block of length 328 for bucket 4\n (Using difference cover)\n bucket 3: 80%\n bucket 7: 80%\n bucket 5: 90%\n bucket 6: 80%\n bucket 3: 90%\n bucket 5: 100%\n bucket 7: 90%\n Sorting block of length 203 for bucket 5\n (Using difference cover)\n bucket 6: 90%\n bucket 3: 100%\n Sorting block of length 370 for bucket 3\n (Using difference cover)\n bucket 7: 100%\n Sorting block time: 00:00:00\n bucket 6: 100%\n Sorting block of length 368 for bucket 7\n (Using difference cover)\nReturning block of 166 for bucket 2\n Sorting block of length 339 for bucket 6\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 329 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 356 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 369 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 204 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 371 for bucket 3\nGetting block 8 of 58\n Reserving size (388) for bucket 8\n Calculating Z arrays for bucket 8\n Entering block accumulator loop for bucket 8:\n bucket 8: 10%\n bucket 8: 20%\nGetting block 9 of 58\n bucket 8: 30%\n Reserving size (388) for bucket 9\n Calculating Z arrays for bucket 9\n bucket 8: 40%\n Entering block accumulator loop for bucket 9:\n bucket 8: 50%\n bucket 9: 10%\n bucket 8: 60%\n bucket 9: 20%\n bucket 8: 70%\n bucket 9: 30%\n bucket 8: 80%\n bucket 9: 40%\n bucket 8: 90%\n bucket 9: 50%\n bucket 8: 100%\n Sorting block of length 171 for bucket 8\n (Using difference cover)\n bucket 9: 60%\n bucket 9: 70%\n bucket 9: 80%\n Sorting block time: 00:00:00\nReturning block of 172 for bucket 8\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 339 for bucket 9\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 9\nGetting block 10 of 58\n Reserving size (388) for bucket 10\n Calculating Z arrays for bucket 10\nGetting block 11 of 58\n Reserving size (388) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 10:\n Entering block accumulator loop for bucket 11:\n bucket 10: 10%\n bucket 11: 10%\n bucket 10: 20%\n bucket 11: 20%\n bucket 10: 30%\n bucket 10: 40%\n bucket 11: 30%\n bucket 10: 50%\n bucket 11: 40%\n bucket 10: 60%\n bucket 11: 50%\n bucket 10: 70%\n bucket 11: 60%\n bucket 10: 80%\n bucket 11: 70%\n bucket 11: 80%\n bucket 10: 90%\n bucket 10: 100%\n bucket 11: 90%\n Sorting block of length 357 for bucket 10\n (Using difference cover)\n bucket 11: 100%\n Sorting block of length 305 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 358 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 306 for bucket 11\nGetting block 12 of 58\n Reserving size (388) for bucket 12\n Calculating Z arrays for bucket 12\nGetting block 13 of 58\n Entering block accumulator loop for bucket 12:\n Reserving size (388) for bucket 13\n Calculating Z arrays for bucket 13\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 185 for bucket 12\n (Using difference cover)\n bucket 13: 80%\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 282 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 186 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 283 for bucket 13\nGetting block 14 of 58\n Reserving size (388) 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 339 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 14\nGetting block 15 of 58\n Reserving size (388) 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 241 for bucket 15\n (Using difference cover)\nGetting block 16 of 58\n Reserving size (388) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\nGetting block 17 of 58\n Reserving size (388) for bucket 17\n Calculating Z arrays for bucket 17\n bucket 16: 10%\n bucket 16: 20%\n Entering block accumulator loop for bucket 17:\n bucket 16: 30%\n bucket 16: 40%\n bucket 17: 10%\n bucket 16: 50%\n Sorting block time: 00:00:00\nReturning block of 242 for bucket 15\n bucket 17: 20%\n bucket 16: 60%\n bucket 16: 70%\n bucket 17: 30%\n bucket 16: 80%\n bucket 17: 40%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 379 for bucket 16\n (Using difference cover)\n bucket 17: 50%\n bucket 17: 60%\n Sorting block time: 00:00:00\nReturning block of 380 for bucket 16\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 215 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 216 for bucket 17\nGetting block 18 of 58\n Reserving size (388) for bucket 18\nGetting block 19 of 58\n Calculating Z arrays for bucket 18\n Reserving size (388) 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 19: 40%\n bucket 18: 40%\n bucket 19: 50%\n bucket 18: 50%\n bucket 19: 60%\n bucket 18: 60%\n bucket 19: 70%\n bucket 18: 70%\n bucket 19: 80%\n bucket 18: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 334 for bucket 19\n (Using difference cover)\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 378 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 335 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 379 for bucket 18\nGetting block 20 of 58\n Reserving size (388) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\nGetting block 21 of 58\n bucket 20: 10%\n Reserving size (388) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 20: 20%\n bucket 20: 30%\n bucket 21: 10%\n bucket 20: 40%\n bucket 21: 20%\n bucket 20: 50%\n bucket 20: 60%\n bucket 21: 30%\n bucket 20: 70%\n bucket 21: 40%\n bucket 20: 80%\n bucket 20: 90%\n bucket 21: 50%\n bucket 20: 100%\n Sorting block of length 313 for bucket 20\n (Using difference cover)\n bucket 21: 60%\n bucket 21: 70%\n bucket 21: 80%\n Sorting block time: 00:00:00\nReturning block of 314 for bucket 20\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 210 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 211 for bucket 21\nGetting block 22 of 58\n Reserving size (388) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\nGetting block 23 of 58\n Reserving size (388) for bucket 23\n bucket 22: 10%\n Calculating Z arrays for bucket 23\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 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 23: 70%\n bucket 22: 90%\n bucket 23: 80%\n bucket 22: 100%\n Sorting block of length 386 for bucket 22\n (Using difference cover)\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 238 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 239 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 387 for bucket 22\nGetting block 24 of 58\n Reserving size (388) 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 58\n bucket 24: 20%\n Reserving size (388) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 25:\n bucket 24: 30%\n bucket 25: 10%\n bucket 24: 40%\n bucket 25: 20%\n bucket 24: 50%\n bucket 25: 30%\n bucket 24: 60%\n bucket 24: 70%\n bucket 25: 40%\n bucket 25: 50%\n bucket 24: 80%\n bucket 24: 90%\n bucket 25: 60%\n bucket 25: 70%\n bucket 24: 100%\n Sorting block of length 351 for bucket 24\n (Using difference cover)\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 105 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 352 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 106 for bucket 25\nGetting block 26 of 58\n Reserving size (388) for bucket 26\n Calculating Z arrays for bucket 26\nGetting block 27 of 58\n Entering block accumulator loop for bucket 26:\n Reserving size (388) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n bucket 26: 10%\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 26: 80%\n bucket 27: 50%\n bucket 26: 90%\n bucket 27: 60%\n bucket 26: 100%\n Sorting block of length 354 for bucket 26\n (Using difference cover)\n bucket 27: 70%\n bucket 27: 80%\n Sorting block time: 00:00:00\nReturning block of 355 for bucket 26\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 334 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 335 for bucket 27\nGetting block 28 of 58\n Reserving size (388) 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 253 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 254 for bucket 28\nGetting block 29 of 58\n Reserving size (388) for bucket 29\nGetting block 30 of 58\n Calculating Z arrays for bucket 29\n Reserving size (388) 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 30: 80%\n bucket 29: 80%\n bucket 30: 90%\n bucket 29: 90%\n bucket 30: 100%\n Sorting block of length 345 for bucket 30\n (Using difference cover)\n bucket 29: 100%\n Sorting block of length 289 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 346 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 290 for bucket 29\nGetting block 31 of 58\n Reserving size (388) 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%\nGetting block 32 of 58\n Reserving size (388) for bucket 32\n Calculating Z arrays for bucket 32\n bucket 31: 40%\n Entering block accumulator loop for bucket 32:\n bucket 31: 50%\n bucket 32: 10%\n bucket 31: 60%\n bucket 31: 70%\n bucket 32: 20%\n bucket 31: 80%\n bucket 32: 30%\n bucket 31: 90%\n bucket 31: 100%\n bucket 32: 40%\n Sorting block of length 377 for buck\n..\n0:00\nReturning block of 372 for bucket 22\nGetting block 24 of 57\n Reserving size (388) for bucket 24\nGetting block 25 of 57\n Calculating Z arrays for bucket 24\n Reserving size (388) for bucket 25\n Calculating Z arrays for bucket 25\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 24: 30%\n bucket 25: 30%\n bucket 24: 40%\n bucket 25: 40%\n bucket 24: 50%\n bucket 25: 50%\n bucket 24: 60%\n bucket 25: 60%\n bucket 24: 70%\n bucket 25: 70%\n bucket 24: 80%\n bucket 25: 80%\n bucket 24: 90%\n bucket 25: 90%\n bucket 24: 100%\n bucket 25: 100%\n Sorting block of length 245 for bucket 24\n (Using difference cover)\n Sorting block of length 286 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 246 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 287 for bucket 25\nGetting block 26 of 57\n Reserving size (388) 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 384 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 385 for bucket 26\nGetting block 27 of 57\n Reserving size (388) 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 57\n bucket 27: 20%\n Reserving size (388) for bucket 28\n Calculating Z arrays for bucket 28\n bucket 27: 30%\n Entering block accumulator loop for bucket 28:\n bucket 27: 40%\n bucket 27: 50%\n bucket 28: 10%\n bucket 27: 60%\n bucket 27: 70%\n bucket 28: 20%\n bucket 27: 80%\n bucket 27: 90%\n bucket 28: 30%\n bucket 27: 100%\n Sorting block of length 359 for bucket 27\n (Using difference cover)\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n Sorting block time: 00:00:00\nReturning block of 360 for bucket 27\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 387 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 28\nGetting block 29 of 57\n Reserving size (388) for bucket 29\n Calculating Z arrays for bucket 29\nGetting block 30 of 57\n Reserving size (388) 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 30: 10%\n bucket 29: 10%\n bucket 30: 20%\n bucket 29: 20%\n bucket 30: 30%\n bucket 29: 30%\n bucket 30: 40%\n bucket 30: 50%\n bucket 29: 40%\n bucket 30: 60%\n bucket 29: 50%\n bucket 30: 70%\n bucket 30: 80%\n bucket 29: 60%\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 257 for bucket 30\n (Using difference cover)\n bucket 29: 70%\n bucket 29: 80%\n Sorting block time: 00:00:00\n bucket 29: 90%\nReturning block of 258 for bucket 30\n bucket 29: 100%\n Sorting block of length 195 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 29\nGetting block 31 of 57\n Reserving size (388) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 31:\n bucket 31: 10%\nGetting block 32 of 57\n Reserving size (388) for bucket 32\n Calculating Z arrays for bucket 32\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 31: 90%\n bucket 32: 60%\n bucket 31: 100%\n Sorting block of length 310 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 219 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 311 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 220 for bucket 32\nGetting block 33 of 57\n Reserving size (388) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 33:\n bucket 33: 10%\nGetting block 34 of 57\n Reserving size (388) for bucket 34\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 34:\n bucket 33: 20%\n bucket 33: 30%\n bucket 34: 10%\n bucket 33: 40%\n bucket 33: 50%\n bucket 34: 20%\n bucket 33: 60%\n bucket 34: 30%\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 387 for bucket 33\n (Using difference cover)\n bucket 34: 60%\n bucket 34: 70%\n bucket 34: 80%\n bucket 34: 90%\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 33\n bucket 34: 100%\n Sorting block of length 275 for bucket 34\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 276 for bucket 34\nGetting block 35 of 57\n Reserving size (388) 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 350 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 351 for bucket 35\nGetting block 36 of 57\n Reserving size (388) 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 57\n bucket 36: 20%\n Reserving size (388) for bucket 37\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 37:\n bucket 36: 30%\n bucket 37: 10%\n bucket 36: 40%\n bucket 37: 20%\n bucket 37: 30%\n bucket 36: 50%\n bucket 37: 40%\n bucket 36: 60%\n bucket 37: 50%\n bucket 36: 70%\n bucket 37: 60%\n bucket 36: 80%\n bucket 37: 70%\n bucket 37: 80%\n bucket 36: 90%\n bucket 37: 90%\n bucket 36: 100%\n Sorting block of length 150 for bucket 36\n (Using difference cover)\n bucket 37: 100%\n Sorting block of length 267 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 151 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 268 for bucket 37\nGetting block 38 of 57\n Reserving size (388) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 38:\nGetting block 39 of 57\n bucket 38: 10%\n Reserving size (388) for bucket 39\n Calculating Z arrays for bucket 39\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 38: 40%\n bucket 39: 40%\n bucket 38: 50%\n bucket 38: 60%\n bucket 39: 50%\n bucket 38: 70%\n bucket 39: 60%\n bucket 38: 80%\n bucket 38: 90%\n bucket 39: 70%\n bucket 38: 100%\n Sorting block of length 337 for bucket 38\n (Using difference cover)\n bucket 39: 80%\n bucket 39: 90%\n bucket 39: 100%\n Sorting block of length 387 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 338 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 39\nGetting block 40 of 57\n Reserving size (388) 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 57\n Reserving size (388) for bucket 41\n Calculating Z arrays for bucket 41\n bucket 40: 20%\n Entering block accumulator loop for bucket 41:\n bucket 40: 30%\n bucket 41: 10%\n bucket 40: 40%\n bucket 40: 50%\n bucket 41: 20%\n bucket 41: 30%\n bucket 40: 60%\n bucket 41: 40%\n bucket 40: 70%\n bucket 41: 50%\n bucket 40: 80%\n bucket 41: 60%\n bucket 41: 70%\n bucket 40: 90%\n bucket 41: 80%\n bucket 40: 100%\n Sorting block of length 379 for bucket 40\n (Using difference cover)\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 330 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 380 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 331 for bucket 41\nGetting block 42 of 57\n Reserving size (388) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\nGetting block 43 of 57\n bucket 42: 10%\n Reserving size (388) for bucket 43\n Calculating Z arrays for bucket 43\n Entering block accumulator loop for bucket 43:\n bucket 42: 20%\n bucket 42: 30%\n bucket 43: 10%\n bucket 42: 40%\n bucket 42: 50%\n bucket 43: 20%\n bucket 42: 60%\n bucket 43: 30%\n bucket 42: 70%\n bucket 42: 80%\n bucket 43: 40%\n bucket 42: 90%\n bucket 43: 50%\n bucket 43: 60%\n bucket 42: 100%\n Sorting block of length 188 for bucket 42\n (Using difference cover)\n bucket 43: 70%\n bucket 43: 80%\n Sorting block time: 00:00:00\n bucket 43: 90%\nReturning block of 189 for bucket 42\n bucket 43: 100%\n Sorting block of length 321 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 322 for bucket 43\nGetting block 44 of 57\n Reserving size (388) 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 366 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 367 for bucket 44\nGetting block 45 of 57\n Reserving size (388) 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 57\n Reserving size (388) for bucket 46\n Calculating Z arrays for bucket 46\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 46: 20%\n bucket 45: 50%\n bucket 46: 30%\n bucket 45: 60%\n bucket 46: 40%\n bucket 45: 70%\n bucket 45: 80%\n bucket 46: 50%\n bucket 45: 90%\n bucket 46: 60%\n bucket 45: 100%\n Sorting block of length 365 for bucket 45\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 253 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 366 for bucket 45\n Sorting block time: 00:00:00\nReturning block of 254 for bucket 46\nGetting block 47 of 57\n Reserving size (388) for bucket 47\nGetting block 48 of 57\n Calculating Z arrays for bucket 47\n Reserving size (388) 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 48: 10%\n bucket 47: 10%\n bucket 48: 20%\n bucket 47: 20%\n bucket 47: 30%\n bucket 48: 30%\n bucket 48: 40%\n bucket 47: 40%\n bucket 48: 50%\n bucket 47: 50%\n bucket 48: 60%\n bucket 48: 70%\n bucket 47: 60%\n bucket 48: 80%\n bucket 47: 70%\n bucket 48: 90%\n bucket 47: 80%\n bucket 48: 100%\n Sorting block of length 384 for bucket 48\n (Using difference cover)\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 217 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 385 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 218 for bucket 47\nGetting block 49 of 57\n Reserving size (388) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\nGetting block 50 of 57\n Reserving size (388) for bucket 50\n Calculating Z arrays for bucket 50\n bucket 49: 10%\n Entering block accumulator loop for bucket 50:\n bucket 49: 20%\n bucket 50: 10%\n bucket 49: 30%\n bucket 50: 20%\n bucket 49: 40%\n bucket 50: 30%\n bucket 49: 50%\n bucket 50: 40%\n bucket 49: 60%\n bucket 50: 50%\n bucket 50: 60%\n bucket 49: 70%\n bucket 50: 70%\n bucket 49: 80%\n bucket 50: 80%\n bucket 49: 90%\n bucket 50: 90%\n bucket 49: 100%\n Sorting block of length 112 for bucket 49\n (Using difference cover)\n bucket 50: 100%\n Sorting block of length 275 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 276 for bucket 50\nGetting block 51 of 57\n Reserving size (388) 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 350 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 351 for bucket 51\nGetting block 52 of 57\n Reserving size (388) for bucket 52\n Calculating Z arrays for bucket 52\nGetting block 53 of 57\n Reserving size (388) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 52:\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\n bucket 52: 10%\n bucket 53: 20%\n bucket 52: 20%\n bucket 52: 30%\n bucket 53: 30%\n bucket 52: 40%\n bucket 53: 40%\n bucket 53: 50%\n bucket 52: 50%\n bucket 53: 60%\n bucket 52: 60%\n bucket 53: 70%\n bucket 53: 80%\n bucket 52: 70%\n bucket 53: 90%\n bucket 53: 100%\n bucket 52: 80%\n Sorting block of length 370 for bucket 53\n (Using difference cover)\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 378 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 371 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 379 for bucket 52\nGetting block 54 of 57\n Reserving size (388) for bucket 54\n Calculating Z arrays for bucket 54\nGetting block 55 of 57\n Entering block accumulator loop for bucket 54:\n Reserving size (388) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\n bucket 54: 10%\n bucket 55: 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 54: 80%\n bucket 55: 80%\n bucket 54: 90%\n bucket 55: 90%\n bucket 54: 100%\n bucket 55: 100%\n Sorting block of length 237 for bucket 54\n (Using difference cover)\n Sorting block of length 344 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 345 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 238 for bucket 54\nGetting block 56 of 57\n Reserving size (388) for bucket 56\n Calculating Z arrays for bucket 56\nGetting block 57 of 57\n Reserving size (388) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 56:\n Entering block accumulator loop for bucket 57:\n bucket 57: 10%\n bucket 56: 10%\n bucket 57: 20%\n bucket 56: 20%\n bucket 57: 30%\n bucket 56: 30%\n bucket 57: 40%\n bucket 56: 40%\n bucket 57: 50%\n bucket 56: 50%\n bucket 57: 60%\n bucket 56: 60%\n bucket 57: 70%\n bucket 56: 70%\n bucket 57: 80%\n bucket 56: 80%\n bucket 57: 90%\n bucket 56: 90%\n bucket 57: 100%\n Sorting block of length 132 for bucket 57\n (Using difference cover)\n bucket 56: 100%\n Sorting block of length 270 for bucket 56\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 133 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 271 for bucket 56\nExited Ebwt loop\nfchr[A]: 0\nfchr[C]: 5124\nfchr[G]: 10305\nfchr[T]: 12474\nfchr[$]: 16568\nExiting Ebwt::buildToDisk()\nReturning from initFromVector\nWrote 4200050 bytes to primary EBWT file: genome.rev.1.bt2.tmp\nWrote 4148 bytes to secondary EBWT file: genome.rev.2.bt2.tmp\nRe-opening _in1 and _in2 as input streams\nReturning from Ebwt constructor\nHeaders:\n len: 16568\n bwtLen: 16569\n sz: 4142\n bwtSz: 4143\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 20\n eftabSz: 80\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 1036\n offsSz: 4144\n lineSz: 64\n sideSz: 64\n sideBwtSz: 48\n sideBwtLen: 192\n numSides: 87\n numLines: 87\n ebwtTotLen: 5568\n ebwtTotSz: 5568\n color: 0\n reverse: 1\nTotal time for backward call to driver() for mirror index: 00:00:01\n", "tool_stderr": "Building a SMALL index\nRenaming genome.3.bt2.tmp to genome.3.bt2\nRenaming genome.4.bt2.tmp to genome.4.bt2\nRenaming genome.1.bt2.tmp to genome.1.bt2\nRenaming genome.2.bt2.tmp to genome.2.bt2\nRenaming genome.rev.1.bt2.tmp to genome.rev.1.bt2\nRenaming genome.rev.2.bt2.tmp to genome.rev.2.bt2\n100 reads; of these:\n 100 (100.00%) were paired; of these:\n 97 (97.00%) aligned concordantly 0 times\n 3 (3.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 97 pairs aligned concordantly 0 times; of these:\n 8 (8.25%) aligned discordantly 1 time\n ----\n 89 pairs aligned 0 times concordantly or discordantly; of these:\n 178 mates make up the pairs; of these:\n 153 (85.96%) aligned 0 times\n 25 (14.04%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n23.50% overall alignment rate\n", "job_stdout": "", "job_stderr": "", "stdout": "Settings:\n Output files: \"genome.*.bt2\"\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 Max bucket size: default\n Max bucket size, sqrt multiplier: default\n Max bucket size, len divisor: 32\n Difference-cover sample period: 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 /galaxy/server/database/objects/8/8/5/dataset_8858f956-b68e-498b-9fe6-4fdd63a567d0.dat\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\nbmax according to bmaxDivN setting: 517\nUsing parameters --bmax 388 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 388 --dcv 1024\nConstructing suffix-array element generator\nBuilding DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 86 sample suffixes\nGenerating random suffixes\nQSorting 86 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 86 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 12, merged 41; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 6; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 284.672 (target: 387)\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering Ebwt loop\nGetting block 1 of 58\n Reserving size (388) for bucket 1\nGetting block 2 of 58\nGetting block 3 of 58\nGetting block 4 of 58\nGetting block 5 of 58\nGetting block 6 of 58\n Calculating Z arrays for bucket 1\n Reserving size (388) for bucket 2\n Reserving size (388) for bucket 3\n Reserving size (388) for bucket 4\n Reserving size (388) for bucket 5\n Reserving size (388) for bucket 6\nGetting block 7 of 58\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 3\n Entering block accumulator loop for bucket 1:\n Calculating Z arrays for bucket 4\n Calculating Z arrays for bucket 5\n Calculating Z arrays for bucket 6\n Reserving size (388) for bucket 7\n Entering block accumulator loop for bucket 2:\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 3:\n Entering block accumulator loop for bucket 4:\n Entering block accumulator loop for bucket 5:\n Entering block accumulator loop for bucket 6:\n Entering block accumulator loop for bucket 7:\n bucket 2: 10%\n bucket 1: 10%\n bucket 4: 10%\n bucket 5: 10%\n bucket 3: 10%\n bucket 6: 10%\n bucket 2: 20%\n bucket 7: 10%\n bucket 1: 20%\n bucket 2: 30%\n bucket 4: 20%\n bucket 1: 30%\n bucket 5: 20%\n bucket 3: 20%\n bucket 6: 20%\n bucket 7: 20%\n bucket 2: 40%\n bucket 1: 40%\n bucket 4: 30%\n bucket 5: 30%\n bucket 2: 50%\n bucket 1: 50%\n bucket 3: 30%\n bucket 6: 30%\n bucket 7: 30%\n bucket 4: 40%\n bucket 2: 60%\n bucket 1: 60%\n bucket 5: 40%\n bucket 2: 70%\n bucket 3: 40%\n bucket 1: 70%\n bucket 6: 40%\n bucket 4: 50%\n bucket 7: 40%\n bucket 2: 80%\n bucket 1: 80%\n bucket 5: 50%\n bucket 4: 60%\n bucket 3: 50%\n bucket 2: 90%\n bucket 1: 90%\n bucket 7: 50%\n bucket 4: 70%\n bucket 2: 100%\n bucket 6: 50%\n bucket 1: 100%\n bucket 5: 60%\n Sorting block of length 165 for bucket 2\n (Using difference cover)\n Sorting block of length 355 for bucket 1\n (Using difference cover)\n bucket 3: 60%\n bucket 4: 80%\n bucket 7: 60%\n bucket 6: 60%\n bucket 5: 70%\n bucket 4: 90%\n bucket 3: 70%\n bucket 4: 100%\n bucket 7: 70%\n bucket 5: 80%\n bucket 6: 70%\n Sorting block of length 328 for bucket 4\n (Using difference cover)\n bucket 3: 80%\n bucket 7: 80%\n bucket 5: 90%\n bucket 6: 80%\n bucket 3: 90%\n bucket 5: 100%\n bucket 7: 90%\n Sorting block of length 203 for bucket 5\n (Using difference cover)\n bucket 6: 90%\n bucket 3: 100%\n Sorting block of length 370 for bucket 3\n (Using difference cover)\n bucket 7: 100%\n Sorting block time: 00:00:00\n bucket 6: 100%\n Sorting block of length 368 for bucket 7\n (Using difference cover)\nReturning block of 166 for bucket 2\n Sorting block of length 339 for bucket 6\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 329 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 356 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 369 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 204 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 371 for bucket 3\nGetting block 8 of 58\n Reserving size (388) for bucket 8\n Calculating Z arrays for bucket 8\n Entering block accumulator loop for bucket 8:\n bucket 8: 10%\n bucket 8: 20%\nGetting block 9 of 58\n bucket 8: 30%\n Reserving size (388) for bucket 9\n Calculating Z arrays for bucket 9\n bucket 8: 40%\n Entering block accumulator loop for bucket 9:\n bucket 8: 50%\n bucket 9: 10%\n bucket 8: 60%\n bucket 9: 20%\n bucket 8: 70%\n bucket 9: 30%\n bucket 8: 80%\n bucket 9: 40%\n bucket 8: 90%\n bucket 9: 50%\n bucket 8: 100%\n Sorting block of length 171 for bucket 8\n (Using difference cover)\n bucket 9: 60%\n bucket 9: 70%\n bucket 9: 80%\n Sorting block time: 00:00:00\nReturning block of 172 for bucket 8\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 339 for bucket 9\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 9\nGetting block 10 of 58\n Reserving size (388) for bucket 10\n Calculating Z arrays for bucket 10\nGetting block 11 of 58\n Reserving size (388) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 10:\n Entering block accumulator loop for bucket 11:\n bucket 10: 10%\n bucket 11: 10%\n bucket 10: 20%\n bucket 11: 20%\n bucket 10: 30%\n bucket 10: 40%\n bucket 11: 30%\n bucket 10: 50%\n bucket 11: 40%\n bucket 10: 60%\n bucket 11: 50%\n bucket 10: 70%\n bucket 11: 60%\n bucket 10: 80%\n bucket 11: 70%\n bucket 11: 80%\n bucket 10: 90%\n bucket 10: 100%\n bucket 11: 90%\n Sorting block of length 357 for bucket 10\n (Using difference cover)\n bucket 11: 100%\n Sorting block of length 305 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 358 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 306 for bucket 11\nGetting block 12 of 58\n Reserving size (388) for bucket 12\n Calculating Z arrays for bucket 12\nGetting block 13 of 58\n Entering block accumulator loop for bucket 12:\n Reserving size (388) for bucket 13\n Calculating Z arrays for bucket 13\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 185 for bucket 12\n (Using difference cover)\n bucket 13: 80%\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 282 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 186 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 283 for bucket 13\nGetting block 14 of 58\n Reserving size (388) 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 339 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 14\nGetting block 15 of 58\n Reserving size (388) 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 241 for bucket 15\n (Using difference cover)\nGetting block 16 of 58\n Reserving size (388) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\nGetting block 17 of 58\n Reserving size (388) for bucket 17\n Calculating Z arrays for bucket 17\n bucket 16: 10%\n bucket 16: 20%\n Entering block accumulator loop for bucket 17:\n bucket 16: 30%\n bucket 16: 40%\n bucket 17: 10%\n bucket 16: 50%\n Sorting block time: 00:00:00\nReturning block of 242 for bucket 15\n bucket 17: 20%\n bucket 16: 60%\n bucket 16: 70%\n bucket 17: 30%\n bucket 16: 80%\n bucket 17: 40%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 379 for bucket 16\n (Using difference cover)\n bucket 17: 50%\n bucket 17: 60%\n Sorting block time: 00:00:00\nReturning block of 380 for bucket 16\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 215 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 216 for bucket 17\nGetting block 18 of 58\n Reserving size (388) for bucket 18\nGetting block 19 of 58\n Calculating Z arrays for bucket 18\n Reserving size (388) 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 19: 40%\n bucket 18: 40%\n bucket 19: 50%\n bucket 18: 50%\n bucket 19: 60%\n bucket 18: 60%\n bucket 19: 70%\n bucket 18: 70%\n bucket 19: 80%\n bucket 18: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 334 for bucket 19\n (Using difference cover)\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 378 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 335 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 379 for bucket 18\nGetting block 20 of 58\n Reserving size (388) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\nGetting block 21 of 58\n bucket 20: 10%\n Reserving size (388) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 20: 20%\n bucket 20: 30%\n bucket 21: 10%\n bucket 20: 40%\n bucket 21: 20%\n bucket 20: 50%\n bucket 20: 60%\n bucket 21: 30%\n bucket 20: 70%\n bucket 21: 40%\n bucket 20: 80%\n bucket 20: 90%\n bucket 21: 50%\n bucket 20: 100%\n Sorting block of length 313 for bucket 20\n (Using difference cover)\n bucket 21: 60%\n bucket 21: 70%\n bucket 21: 80%\n Sorting block time: 00:00:00\nReturning block of 314 for bucket 20\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 210 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 211 for bucket 21\nGetting block 22 of 58\n Reserving size (388) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\nGetting block 23 of 58\n Reserving size (388) for bucket 23\n bucket 22: 10%\n Calculating Z arrays for bucket 23\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 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 23: 70%\n bucket 22: 90%\n bucket 23: 80%\n bucket 22: 100%\n Sorting block of length 386 for bucket 22\n (Using difference cover)\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 238 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 239 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 387 for bucket 22\nGetting block 24 of 58\n Reserving size (388) 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 58\n bucket 24: 20%\n Reserving size (388) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 25:\n bucket 24: 30%\n bucket 25: 10%\n bucket 24: 40%\n bucket 25: 20%\n bucket 24: 50%\n bucket 25: 30%\n bucket 24: 60%\n bucket 24: 70%\n bucket 25: 40%\n bucket 25: 50%\n bucket 24: 80%\n bucket 24: 90%\n bucket 25: 60%\n bucket 25: 70%\n bucket 24: 100%\n Sorting block of length 351 for bucket 24\n (Using difference cover)\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 105 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 352 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 106 for bucket 25\nGetting block 26 of 58\n Reserving size (388) for bucket 26\n Calculating Z arrays for bucket 26\nGetting block 27 of 58\n Entering block accumulator loop for bucket 26:\n Reserving size (388) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n bucket 26: 10%\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 26: 80%\n bucket 27: 50%\n bucket 26: 90%\n bucket 27: 60%\n bucket 26: 100%\n Sorting block of length 354 for bucket 26\n (Using difference cover)\n bucket 27: 70%\n bucket 27: 80%\n Sorting block time: 00:00:00\nReturning block of 355 for bucket 26\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 334 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 335 for bucket 27\nGetting block 28 of 58\n Reserving size (388) 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 253 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 254 for bucket 28\nGetting block 29 of 58\n Reserving size (388) for bucket 29\nGetting block 30 of 58\n Calculating Z arrays for bucket 29\n Reserving size (388) 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 30: 80%\n bucket 29: 80%\n bucket 30: 90%\n bucket 29: 90%\n bucket 30: 100%\n Sorting block of length 345 for bucket 30\n (Using difference cover)\n bucket 29: 100%\n Sorting block of length 289 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 346 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 290 for bucket 29\nGetting block 31 of 58\n Reserving size (388) 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%\nGetting block 32 of 58\n Reserving size (388) for bucket 32\n Calculating Z arrays for bucket 32\n bucket 31: 40%\n Entering block accumulator loop for bucket 32:\n bucket 31: 50%\n bucket 32: 10%\n bucket 31: 60%\n bucket 31: 70%\n bucket 32: 20%\n bucket 31: 80%\n bucket 32: 30%\n bucket 31: 90%\n bucket 31: 100%\n bucket 32: 40%\n Sorting block of length 377 for buck\n..\n0:00\nReturning block of 372 for bucket 22\nGetting block 24 of 57\n Reserving size (388) for bucket 24\nGetting block 25 of 57\n Calculating Z arrays for bucket 24\n Reserving size (388) for bucket 25\n Calculating Z arrays for bucket 25\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 24: 30%\n bucket 25: 30%\n bucket 24: 40%\n bucket 25: 40%\n bucket 24: 50%\n bucket 25: 50%\n bucket 24: 60%\n bucket 25: 60%\n bucket 24: 70%\n bucket 25: 70%\n bucket 24: 80%\n bucket 25: 80%\n bucket 24: 90%\n bucket 25: 90%\n bucket 24: 100%\n bucket 25: 100%\n Sorting block of length 245 for bucket 24\n (Using difference cover)\n Sorting block of length 286 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 246 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 287 for bucket 25\nGetting block 26 of 57\n Reserving size (388) 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 384 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 385 for bucket 26\nGetting block 27 of 57\n Reserving size (388) 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 57\n bucket 27: 20%\n Reserving size (388) for bucket 28\n Calculating Z arrays for bucket 28\n bucket 27: 30%\n Entering block accumulator loop for bucket 28:\n bucket 27: 40%\n bucket 27: 50%\n bucket 28: 10%\n bucket 27: 60%\n bucket 27: 70%\n bucket 28: 20%\n bucket 27: 80%\n bucket 27: 90%\n bucket 28: 30%\n bucket 27: 100%\n Sorting block of length 359 for bucket 27\n (Using difference cover)\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n Sorting block time: 00:00:00\nReturning block of 360 for bucket 27\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 387 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 28\nGetting block 29 of 57\n Reserving size (388) for bucket 29\n Calculating Z arrays for bucket 29\nGetting block 30 of 57\n Reserving size (388) 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 30: 10%\n bucket 29: 10%\n bucket 30: 20%\n bucket 29: 20%\n bucket 30: 30%\n bucket 29: 30%\n bucket 30: 40%\n bucket 30: 50%\n bucket 29: 40%\n bucket 30: 60%\n bucket 29: 50%\n bucket 30: 70%\n bucket 30: 80%\n bucket 29: 60%\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 257 for bucket 30\n (Using difference cover)\n bucket 29: 70%\n bucket 29: 80%\n Sorting block time: 00:00:00\n bucket 29: 90%\nReturning block of 258 for bucket 30\n bucket 29: 100%\n Sorting block of length 195 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 29\nGetting block 31 of 57\n Reserving size (388) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 31:\n bucket 31: 10%\nGetting block 32 of 57\n Reserving size (388) for bucket 32\n Calculating Z arrays for bucket 32\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 31: 90%\n bucket 32: 60%\n bucket 31: 100%\n Sorting block of length 310 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 219 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 311 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 220 for bucket 32\nGetting block 33 of 57\n Reserving size (388) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 33:\n bucket 33: 10%\nGetting block 34 of 57\n Reserving size (388) for bucket 34\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 34:\n bucket 33: 20%\n bucket 33: 30%\n bucket 34: 10%\n bucket 33: 40%\n bucket 33: 50%\n bucket 34: 20%\n bucket 33: 60%\n bucket 34: 30%\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 387 for bucket 33\n (Using difference cover)\n bucket 34: 60%\n bucket 34: 70%\n bucket 34: 80%\n bucket 34: 90%\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 33\n bucket 34: 100%\n Sorting block of length 275 for bucket 34\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 276 for bucket 34\nGetting block 35 of 57\n Reserving size (388) 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 350 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 351 for bucket 35\nGetting block 36 of 57\n Reserving size (388) 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 57\n bucket 36: 20%\n Reserving size (388) for bucket 37\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 37:\n bucket 36: 30%\n bucket 37: 10%\n bucket 36: 40%\n bucket 37: 20%\n bucket 37: 30%\n bucket 36: 50%\n bucket 37: 40%\n bucket 36: 60%\n bucket 37: 50%\n bucket 36: 70%\n bucket 37: 60%\n bucket 36: 80%\n bucket 37: 70%\n bucket 37: 80%\n bucket 36: 90%\n bucket 37: 90%\n bucket 36: 100%\n Sorting block of length 150 for bucket 36\n (Using difference cover)\n bucket 37: 100%\n Sorting block of length 267 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 151 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 268 for bucket 37\nGetting block 38 of 57\n Reserving size (388) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 38:\nGetting block 39 of 57\n bucket 38: 10%\n Reserving size (388) for bucket 39\n Calculating Z arrays for bucket 39\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 38: 40%\n bucket 39: 40%\n bucket 38: 50%\n bucket 38: 60%\n bucket 39: 50%\n bucket 38: 70%\n bucket 39: 60%\n bucket 38: 80%\n bucket 38: 90%\n bucket 39: 70%\n bucket 38: 100%\n Sorting block of length 337 for bucket 38\n (Using difference cover)\n bucket 39: 80%\n bucket 39: 90%\n bucket 39: 100%\n Sorting block of length 387 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 338 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 39\nGetting block 40 of 57\n Reserving size (388) 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 57\n Reserving size (388) for bucket 41\n Calculating Z arrays for bucket 41\n bucket 40: 20%\n Entering block accumulator loop for bucket 41:\n bucket 40: 30%\n bucket 41: 10%\n bucket 40: 40%\n bucket 40: 50%\n bucket 41: 20%\n bucket 41: 30%\n bucket 40: 60%\n bucket 41: 40%\n bucket 40: 70%\n bucket 41: 50%\n bucket 40: 80%\n bucket 41: 60%\n bucket 41: 70%\n bucket 40: 90%\n bucket 41: 80%\n bucket 40: 100%\n Sorting block of length 379 for bucket 40\n (Using difference cover)\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 330 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 380 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 331 for bucket 41\nGetting block 42 of 57\n Reserving size (388) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\nGetting block 43 of 57\n bucket 42: 10%\n Reserving size (388) for bucket 43\n Calculating Z arrays for bucket 43\n Entering block accumulator loop for bucket 43:\n bucket 42: 20%\n bucket 42: 30%\n bucket 43: 10%\n bucket 42: 40%\n bucket 42: 50%\n bucket 43: 20%\n bucket 42: 60%\n bucket 43: 30%\n bucket 42: 70%\n bucket 42: 80%\n bucket 43: 40%\n bucket 42: 90%\n bucket 43: 50%\n bucket 43: 60%\n bucket 42: 100%\n Sorting block of length 188 for bucket 42\n (Using difference cover)\n bucket 43: 70%\n bucket 43: 80%\n Sorting block time: 00:00:00\n bucket 43: 90%\nReturning block of 189 for bucket 42\n bucket 43: 100%\n Sorting block of length 321 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 322 for bucket 43\nGetting block 44 of 57\n Reserving size (388) 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 366 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 367 for bucket 44\nGetting block 45 of 57\n Reserving size (388) 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 57\n Reserving size (388) for bucket 46\n Calculating Z arrays for bucket 46\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 46: 20%\n bucket 45: 50%\n bucket 46: 30%\n bucket 45: 60%\n bucket 46: 40%\n bucket 45: 70%\n bucket 45: 80%\n bucket 46: 50%\n bucket 45: 90%\n bucket 46: 60%\n bucket 45: 100%\n Sorting block of length 365 for bucket 45\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 253 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 366 for bucket 45\n Sorting block time: 00:00:00\nReturning block of 254 for bucket 46\nGetting block 47 of 57\n Reserving size (388) for bucket 47\nGetting block 48 of 57\n Calculating Z arrays for bucket 47\n Reserving size (388) 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 48: 10%\n bucket 47: 10%\n bucket 48: 20%\n bucket 47: 20%\n bucket 47: 30%\n bucket 48: 30%\n bucket 48: 40%\n bucket 47: 40%\n bucket 48: 50%\n bucket 47: 50%\n bucket 48: 60%\n bucket 48: 70%\n bucket 47: 60%\n bucket 48: 80%\n bucket 47: 70%\n bucket 48: 90%\n bucket 47: 80%\n bucket 48: 100%\n Sorting block of length 384 for bucket 48\n (Using difference cover)\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 217 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 385 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 218 for bucket 47\nGetting block 49 of 57\n Reserving size (388) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\nGetting block 50 of 57\n Reserving size (388) for bucket 50\n Calculating Z arrays for bucket 50\n bucket 49: 10%\n Entering block accumulator loop for bucket 50:\n bucket 49: 20%\n bucket 50: 10%\n bucket 49: 30%\n bucket 50: 20%\n bucket 49: 40%\n bucket 50: 30%\n bucket 49: 50%\n bucket 50: 40%\n bucket 49: 60%\n bucket 50: 50%\n bucket 50: 60%\n bucket 49: 70%\n bucket 50: 70%\n bucket 49: 80%\n bucket 50: 80%\n bucket 49: 90%\n bucket 50: 90%\n bucket 49: 100%\n Sorting block of length 112 for bucket 49\n (Using difference cover)\n bucket 50: 100%\n Sorting block of length 275 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 276 for bucket 50\nGetting block 51 of 57\n Reserving size (388) 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 350 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 351 for bucket 51\nGetting block 52 of 57\n Reserving size (388) for bucket 52\n Calculating Z arrays for bucket 52\nGetting block 53 of 57\n Reserving size (388) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 52:\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\n bucket 52: 10%\n bucket 53: 20%\n bucket 52: 20%\n bucket 52: 30%\n bucket 53: 30%\n bucket 52: 40%\n bucket 53: 40%\n bucket 53: 50%\n bucket 52: 50%\n bucket 53: 60%\n bucket 52: 60%\n bucket 53: 70%\n bucket 53: 80%\n bucket 52: 70%\n bucket 53: 90%\n bucket 53: 100%\n bucket 52: 80%\n Sorting block of length 370 for bucket 53\n (Using difference cover)\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 378 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 371 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 379 for bucket 52\nGetting block 54 of 57\n Reserving size (388) for bucket 54\n Calculating Z arrays for bucket 54\nGetting block 55 of 57\n Entering block accumulator loop for bucket 54:\n Reserving size (388) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\n bucket 54: 10%\n bucket 55: 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 54: 80%\n bucket 55: 80%\n bucket 54: 90%\n bucket 55: 90%\n bucket 54: 100%\n bucket 55: 100%\n Sorting block of length 237 for bucket 54\n (Using difference cover)\n Sorting block of length 344 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 345 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 238 for bucket 54\nGetting block 56 of 57\n Reserving size (388) for bucket 56\n Calculating Z arrays for bucket 56\nGetting block 57 of 57\n Reserving size (388) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 56:\n Entering block accumulator loop for bucket 57:\n bucket 57: 10%\n bucket 56: 10%\n bucket 57: 20%\n bucket 56: 20%\n bucket 57: 30%\n bucket 56: 30%\n bucket 57: 40%\n bucket 56: 40%\n bucket 57: 50%\n bucket 56: 50%\n bucket 57: 60%\n bucket 56: 60%\n bucket 57: 70%\n bucket 56: 70%\n bucket 57: 80%\n bucket 56: 80%\n bucket 57: 90%\n bucket 56: 90%\n bucket 57: 100%\n Sorting block of length 132 for bucket 57\n (Using difference cover)\n bucket 56: 100%\n Sorting block of length 270 for bucket 56\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 133 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 271 for bucket 56\nExited Ebwt loop\nfchr[A]: 0\nfchr[C]: 5124\nfchr[G]: 10305\nfchr[T]: 12474\nfchr[$]: 16568\nExiting Ebwt::buildToDisk()\nReturning from initFromVector\nWrote 4200050 bytes to primary EBWT file: genome.rev.1.bt2.tmp\nWrote 4148 bytes to secondary EBWT file: genome.rev.2.bt2.tmp\nRe-opening _in1 and _in2 as input streams\nReturning from Ebwt constructor\nHeaders:\n len: 16568\n bwtLen: 16569\n sz: 4142\n bwtSz: 4143\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 20\n eftabSz: 80\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 1036\n offsSz: 4144\n lineSz: 64\n sideSz: 64\n sideBwtSz: 48\n sideBwtLen: 192\n numSides: 87\n numLines: 87\n ebwtTotLen: 5568\n ebwtTotSz: 5568\n color: 0\n reverse: 1\nTotal time for backward call to driver() for mirror index: 00:00:01\n", "stderr": "Building a SMALL index\nRenaming genome.3.bt2.tmp to genome.3.bt2\nRenaming genome.4.bt2.tmp to genome.4.bt2\nRenaming genome.1.bt2.tmp to genome.1.bt2\nRenaming genome.2.bt2.tmp to genome.2.bt2\nRenaming genome.rev.1.bt2.tmp to genome.rev.1.bt2\nRenaming genome.rev.2.bt2.tmp to genome.rev.2.bt2\n100 reads; of these:\n 100 (100.00%) were paired; of these:\n 97 (97.00%) aligned concordantly 0 times\n 3 (3.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 97 pairs aligned concordantly 0 times; of these:\n 8 (8.25%) aligned discordantly 1 time\n ----\n 89 pairs aligned 0 times concordantly or discordantly; of these:\n 178 mates make up the pairs; of these:\n 153 (85.96%) aligned 0 times\n 25 (14.04%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n23.50% overall alignment rate\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-08 18:52:12", "plugin": "core", "name": "end_epoch", "raw_value": "1731091932.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 18:52:11", "plugin": "core", "name": "start_epoch", "raw_value": "1731091931.0000000"}, {"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": "bowtie2/2.5.3+galaxy1-4", "has_data": true, "data": {"tool_id": "bowtie2", "tool_version": "2.5.3+galaxy1", "test_index": 4, "time_seconds": 38.00878596305847, "inputs": {"library|input_1": {"src": "hda", "id": "d7119413a306e9b0"}, "library|unaligned_file": false, "library|type": "paired_interleaved", "reference_genome|own_file": {"src": "hda", "id": "933ce35b72edc64e"}, "reference_genome|source": "history", "rg|read_group_id_conditional|ID": "rg1", "rg|PL": "CAPILLARY", "rg|rg_selector": "set", "analysis_type|analysis_type_selector": "simple"}, "job": {"model_class": "Job", "id": "d7119413a306e9b0", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T18:52:47.596615", "update_time": "2024-11-08T18:53:02.933226", "galaxy_version": "24.1", "external_id": "gxy-6g7qx", "handler": null, "job_runner_name": null, "command_line": "set -o | grep -q pipefail && set -o pipefail; bowtie2-build --threads ${GALAXY_SLOTS:-4} '/galaxy/server/database/objects/b/d/3/dataset_bd3f902b-73d4-401c-880c-188fe9f0c258.dat' genome && ln -s -f '/galaxy/server/database/objects/b/d/3/dataset_bd3f902b-73d4-401c-880c-188fe9f0c258.dat' genome.fa && ln -f -s '/galaxy/server/database/objects/f/0/4/dataset_f0413610-649e-4eb2-9d63-c7a8ac8377d6.dat' input_il.fastq && THREADS=${GALAXY_SLOTS:-4} && if [ \"$THREADS\" -gt 1 ]; then (( THREADS-- )); fi && bowtie2 -p \"$THREADS\" -x 'genome' --interleaved 'input_il.fastq' --rg-id \"rg1\" --rg \"PL:CAPILLARY\" | samtools sort -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/a/a/1/dataset_aa14e3cc-c251-4f1d-acf1-a6cfe553ddf1.dat'", "user_email": "tests@fake.org", "command_version": "/usr/local/bin/bowtie2-align-s version 2.5.3\n64-bit\nBuilt on fv-az365-785\nWed Jan 17 04:43:48 UTC 2024\nCompiler: gcc version 12.3.0 (conda-forge gcc 12.3.0-3) \nOptions: -O3 -msse2 -funroll-loops -g3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /usr/local/include -fdebug-prefix-map=/opt/conda/conda-bld/bowtie2_1705465427853/work=/usr/local/src/conda/bowtie2-2.5.3 -fdebug-prefix-map=/usr/local=/usr/local/src/conda-prefix -std=c++11 -Wall -Wno-unused-but-set-variable -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -DWITH_ZSTD\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "save_mapping_stats": "false", "sam_options": "{\"__current_case__\": 1, \"sam_options_selector\": \"no\"}", "analysis_type": "{\"__current_case__\": 0, \"analysis_type_selector\": \"simple\", \"presets\": \"no_presets\"}", "rg": "{\"CN\": null, \"DS\": null, \"DT\": null, \"FO\": null, \"KS\": null, \"PG\": null, \"PI\": \"\", \"PL\": \"CAPILLARY\", \"PU\": null, \"__current_case__\": 1, \"read_group_id_conditional\": {\"ID\": \"rg1\", \"__current_case__\": 1, \"do_auto_name\": false}, \"read_group_lb_conditional\": {\"LB\": null, \"__current_case__\": 1, \"do_auto_name\": false}, \"read_group_sm_conditional\": {\"SM\": \"\", \"__current_case__\": 1, \"do_auto_name\": false}, \"rg_selector\": \"set\"}", "reference_genome": "{\"__current_case__\": 1, \"own_file\": {\"values\": [{\"id\": 65, \"src\": \"hda\"}]}, \"source\": \"history\"}", "library": "{\"__current_case__\": 3, \"aligned_file\": false, \"input_1\": {\"values\": [{\"id\": 64, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 1, \"paired_options_selector\": \"no\"}, \"type\": \"paired_interleaved\", \"unaligned_file\": false}"}, "inputs": {"library|input_1": {"id": "d7119413a306e9b0", "src": "hda", "uuid": "f0413610-649e-4eb2-9d63-c7a8ac8377d6"}, "reference_genome|own_file": {"id": "933ce35b72edc64e", "src": "hda", "uuid": "bd3f902b-73d4-401c-880c-188fe9f0c258"}}, "outputs": {"output": {"id": "b39762222150b9fa", "src": "hda", "uuid": "aa14e3cc-c251-4f1d-acf1-a6cfe553ddf1"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Settings:\n Output files: \"genome.*.bt2\"\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 Max bucket size: default\n Max bucket size, sqrt multiplier: default\n Max bucket size, len divisor: 32\n Difference-cover sample period: 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 /galaxy/server/database/objects/b/d/3/dataset_bd3f902b-73d4-401c-880c-188fe9f0c258.dat\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\nbmax according to bmaxDivN setting: 517\nUsing parameters --bmax 388 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 388 --dcv 1024\nConstructing suffix-array element generator\nBuilding DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 86 sample suffixes\nGenerating random suffixes\nQSorting 86 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 86 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 12, merged 41; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 6; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 284.672 (target: 387)\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering Ebwt loop\nGetting block 1 of 58\n Reserving size (388) for bucket 1\nGetting block 2 of 58\nGetting block 3 of 58\nGetting block 4 of 58\nGetting block 5 of 58\n Calculating Z arrays for bucket 1\n Reserving size (388) for bucket 2\n Reserving size (388) for bucket 3\n Reserving size (388) for bucket 4\n Reserving size (388) for bucket 5\nGetting block 6 of 58\nGetting block 7 of 58\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 3\n Entering block accumulator loop for bucket 1:\n Calculating Z arrays for bucket 4\n Calculating Z arrays for bucket 5\n Reserving size (388) for bucket 6\n Reserving size (388) for bucket 7\n Calculating Z arrays for bucket 6\n Entering block accumulator loop for bucket 2:\n Entering block accumulator loop for bucket 3:\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 4:\n Entering block accumulator loop for bucket 5:\n bucket 1: 10%\n Entering block accumulator loop for bucket 6:\n bucket 2: 10%\n Entering block accumulator loop for bucket 7:\n bucket 3: 10%\n bucket 1: 20%\n bucket 2: 20%\n bucket 3: 20%\n bucket 5: 10%\n bucket 1: 30%\n bucket 4: 10%\n bucket 6: 10%\n bucket 7: 10%\n bucket 2: 30%\n bucket 3: 30%\n bucket 1: 40%\n bucket 5: 20%\n bucket 2: 40%\n bucket 3: 40%\n bucket 1: 50%\n bucket 7: 20%\n bucket 4: 20%\n bucket 6: 20%\n bucket 2: 50%\n bucket 3: 50%\n bucket 5: 30%\n bucket 1: 60%\n bucket 2: 60%\n bucket 3: 60%\n bucket 7: 30%\n bucket 1: 70%\n bucket 4: 30%\n bucket 5: 40%\n bucket 6: 30%\n bucket 2: 70%\n bucket 3: 70%\n bucket 1: 80%\n bucket 7: 40%\n bucket 2: 80%\n bucket 5: 50%\n bucket 3: 80%\n bucket 4: 40%\n bucket 1: 90%\n bucket 6: 40%\n bucket 2: 90%\n bucket 3: 90%\n bucket 7: 50%\n bucket 5: 60%\n bucket 1: 100%\n bucket 2: 100%\n bucket 4: 50%\n Sorting block of length 355 for bucket 1\n (Using difference cover)\n Sorting block of length 165 for bucket 2\n (Using difference cover)\n bucket 3: 100%\n bucket 6: 50%\n Sorting block of length 370 for bucket 3\n (Using difference cover)\n bucket 5: 70%\n bucket 7: 60%\n bucket 4: 60%\n bucket 6: 60%\n bucket 5: 80%\n bucket 7: 70%\n bucket 4: 70%\n bucket 6: 70%\n bucket 5: 90%\n bucket 7: 80%\n bucket 4: 80%\n bucket 6: 80%\n bucket 5: 100%\n Sorting block of length 203 for bucket 5\n (Using difference cover)\n bucket 7: 90%\n bucket 4: 90%\n bucket 6: 90%\n bucket 7: 100%\n bucket 4: 100%\n bucket 6: 100%\n Sorting block of length 368 for bucket 7\n (Using difference cover)\n Sorting block of length 328 for bucket 4\n (Using difference cover)\n Sorting block of length 339 for bucket 6\n Sorting block time: 00:00:00\n (Using difference cover)\nReturning block of 356 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 166 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 371 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 204 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 369 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 329 for bucket 4\nGetting block 8 of 58\n Reserving size (388) for bucket 8\n Calculating Z arrays for bucket 8\nGetting block 9 of 58\n Reserving size (388) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 8:\n Entering block accumulator loop for bucket 9:\n bucket 8: 10%\n bucket 9: 10%\n bucket 8: 20%\n bucket 9: 20%\n bucket 8: 30%\n bucket 9: 30%\n bucket 8: 40%\n bucket 9: 40%\n bucket 8: 50%\n bucket 9: 50%\n bucket 8: 60%\n bucket 9: 60%\n bucket 8: 70%\n bucket 9: 70%\n bucket 8: 80%\n bucket 9: 80%\n bucket 8: 90%\n bucket 9: 90%\n bucket 8: 100%\n Sorting block of length 171 for bucket 8\n (Using difference cover)\n bucket 9: 100%\n Sorting block of length 339 for bucket 9\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 172 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 9\nGetting block 10 of 58\n Reserving size (388) for bucket 10\n Calculating Z arrays for bucket 10\nGetting block 11 of 58\n Reserving size (388) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 10:\nGetting block 12 of 58\n Reserving size (388) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 11:\n bucket 10: 10%\n Entering block accumulator loop for bucket 12:\n bucket 10: 20%\n bucket 10: 30%\n bucket 12: 10%\n bucket 11: 10%\n bucket 10: 40%\n bucket 10: 50%\n bucket 12: 20%\n bucket 11: 20%\n bucket 10: 60%\n bucket 10: 70%\n bucket 12: 30%\n bucket 11: 30%\n bucket 10: 80%\n bucket 11: 40%\n bucket 12: 40%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 357 for bucket 10\n (Using difference cover)\n bucket 11: 50%\n bucket 12: 50%\n bucket 11: 60%\n bucket 12: 60%\n bucket 11: 70%\n bucket 12: 70%\n Sorting block time: 00:00:00\nReturning block of 358 for bucket 10\n bucket 11: 80%\n bucket 12: 80%\n bucket 11: 90%\n bucket 12: 90%\n bucket 11: 100%\n bucket 12: 100%\n Sorting block of length 305 for bucket 11\n (Using difference cover)\n Sorting block of length 185 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 186 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 306 for bucket 11\nGetting block 13 of 58\n Reserving size (388) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 13:\nGetting block 14 of 58\n bucket 13: 10%\n Reserving size (388) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 14:\n bucket 13: 20%\n bucket 14: 10%\n bucket 13: 30%\n bucket 13: 40%\n bucket 14: 20%\n bucket 13: 50%\n bucket 14: 30%\n bucket 13: 60%\n bucket 14: 40%\n bucket 13: 70%\n bucket 14: 50%\n bucket 13: 80%\n bucket 14: 60%\n bucket 13: 90%\n bucket 14: 70%\n bucket 13: 100%\n bucket 14: 80%\n Sorting block of length 282 for bucket 13\n (Using difference cover)\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 339 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 283 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 14\nGetting block 15 of 58\n Reserving size (388) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\nGetting block 16 of 58\n Reserving size (388) for bucket 16\n Calculating Z arrays for bucket 16\n bucket 15: 10%\n Entering block accumulator loop for bucket 16:\n bucket 15: 20%\n bucket 16: 10%\n bucket 15: 30%\n bucket 16: 20%\n bucket 16: 30%\n bucket 15: 40%\n bucket 16: 40%\n bucket 15: 50%\n bucket 16: 50%\n bucket 16: 60%\n bucket 15: 60%\n bucket 16: 70%\n bucket 15: 70%\n bucket 16: 80%\n bucket 15: 80%\n bucket 16: 90%\n bucket 15: 90%\n bucket 16: 100%\n Sorting block of length 379 for bucket 16\n (Using difference cover)\n bucket 15: 100%\n Sorting block of length 241 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 242 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 380 for bucket 16\nGetting block 17 of 58\n Reserving size (388) 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 58\n bucket 17: 20%\n Reserving size (388) for bucket 18\n Calculating Z arrays for bucket 18\n bucket 17: 30%\n Entering block accumulator loop for bucket 18:\n bucket 17: 40%\n bucket 17: 50%\n bucket 18: 10%\n bucket 17: 60%\n bucket 17: 70%\n bucket 18: 20%\n bucket 17: 80%\n bucket 17: 90%\n bucket 18: 30%\n bucket 17: 100%\n Sorting block of length 215 for bucket 17\n (Using difference cover)\n bucket 18: 40%\n Sorting block time: 00:00:00\nReturning block of 216 for bucket 17\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 378 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 379 for bucket 18\nGetting block 19 of 58\n Reserving size (388) for bucket 19\n Calculating Z arrays for bucket 19\nGetting block 20 of 58\n Reserving size (388) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 19:\n Entering block accumulator loop for bucket 20:\n bucket 19: 10%\n bucket 20: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 20: 20%\n bucket 19: 40%\n bucket 20: 30%\n bucket 20: 40%\n bucket 19: 50%\n bucket 20: 50%\n bucket 19: 60%\n bucket 20: 60%\n bucket 19: 70%\n bucket 20: 70%\n bucket 19: 80%\n bucket 20: 80%\n bucket 20: 90%\n bucket 19: 90%\n bucket 20: 100%\n Sorting block of length 313 for bucket 20\n (Using difference cover)\n bucket 19: 100%\n Sorting block of length 334 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 314 for bucket 20\n Sorting block time: 00:00:00\nReturning block of 335 for bucket 19\nGetting block 21 of 58\n Reserving size (388) 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 210 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 211 for bucket 21\nGetting block 22 of 58\n Reserving size (388) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\nGetting block 23 of 58\n Reserving size (388) for bucket 23\n Calculating Z arrays for bucket 23\n bucket 22: 10%\n Entering block accumulator loop for bucket 23:\n bucket 22: 20%\n bucket 23: 10%\n bucket 22: 30%\n bucket 23: 20%\n bucket 22: 40%\n bucket 23: 30%\n bucket 23: 40%\n bucket 22: 50%\n bucket 23: 50%\n bucket 22: 60%\n bucket 23: 60%\n bucket 23: 70%\n bucket 22: 70%\n bucket 23: 80%\n bucket 22: 80%\n bucket 23: 90%\n bucket 22: 90%\n bucket 23: 100%\n Sorting block of length 238 for bucket 23\n (Using difference cover)\n bucket 22: 100%\n Sorting block of length 386 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 239 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 387 for bucket 22\nGetting block 24 of 58\n Reserving size (388) 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 351 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 352 for bucket 24\nGetting block 25 of 58\n Reserving size (388) 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 105 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 106 for bucket 25\nGetting block 26 of 58\n Reserving size (388) 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 354 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 355 for bucket 26\nGetting block 27 of 58\n Reserving size (388) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\nGetting block 28 of 58\n Reserving size (388) for bucket 28\n Calculating Z arrays for bucket 28\n bucket 27: 10%\n Entering block accumulator loop for bucket 28:\n bucket 27: 20%\n bucket 28: 10%\n bucket 27: 30%\n bucket 28: 20%\n bucket 27: 40%\n bucket 28: 30%\n bucket 27: 50%\n bucket 28: 40%\n bucket 28: 50%\n bucket 27: 60%\n bucket 28: 60%\n bucket 27: 70%\n bucket 28: 70%\n bucket 27: 80%\n bucket 28: 80%\n bucket 27: 90%\n bucket 28: 90%\n bucket 27: 100%\n Sorting block of length 334 for bucket 27\n (Using difference cover)\n bucket 28: 100%\n Sorting block of length 253 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 335 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 254 for bucket 28\nGetting block 29 of 58\n Reserving size (388) 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 289 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 290 for bucket 29\nGetting block 30 of 58\n Reserving size (388) 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 345 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 346 for bucket 30\nGetting block 31 of 58\n Reserving size (388) for bucket 31\n Calculating Z arrays for bucket 31\nGetting block 32 of 58\n Reserving size (388) for bucket 32\n Entering block accumulator loop for bucket 31:\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 32:\n bucket 31: 10%\n bucket 32: 10%\n bucket 31: 20%\n bucket 32: 20%\n bucket 31: 30%\n bucket 32: 30%\n bucket 32: 40%\n bucket 31: 40%\n bucket 32: 50%\n bucket 31: 50%\n bucket 32: 60%\n bucket 32: 70%\n bucket 31: 60%\n bucket 32: 80%\n bucket 31: 70%\n bucket 32: 90%\n buc\n..\ntor loop for bucket 25:\n bucket 23: 10%\n bucket 25: 10%\n bucket 24: 10%\n bucket 23: 20%\n bucket 25: 20%\n bucket 23: 30%\n bucket 24: 20%\n bucket 23: 40%\n bucket 25: 30%\n bucket 24: 30%\n bucket 23: 50%\n bucket 25: 40%\n bucket 23: 60%\n bucket 24: 40%\n bucket 23: 70%\n bucket 25: 50%\n bucket 23: 80%\n bucket 24: 50%\n bucket 25: 60%\n bucket 23: 90%\n bucket 23: 100%\n bucket 24: 60%\n bucket 25: 70%\n Sorting block of length 349 for bucket 23\n (Using difference cover)\n bucket 25: 80%\n bucket 24: 70%\n bucket 25: 90%\n bucket 24: 80%\n Sorting block time: 00:00:00\nReturning block of 350 for bucket 23\n bucket 24: 90%\n bucket 25: 100%\n Sorting block of length 286 for bucket 25\n (Using difference cover)\n bucket 24: 100%\n Sorting block of length 245 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 246 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 287 for bucket 25\nGetting block 26 of 57\n Reserving size (388) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\nGetting block 27 of 57\n Reserving size (388) for bucket 27\n Calculating Z arrays for bucket 27\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 27: 50%\n bucket 26: 60%\n bucket 27: 60%\n bucket 26: 70%\n bucket 27: 70%\n bucket 26: 80%\n bucket 27: 80%\n bucket 26: 90%\n bucket 27: 90%\n bucket 26: 100%\n Sorting block of length 384 for bucket 26\n (Using difference cover)\n bucket 27: 100%\n Sorting block of length 359 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 385 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 360 for bucket 27\nGetting block 28 of 57\n Reserving size (388) for bucket 28\nGetting block 29 of 57\n Calculating Z arrays for bucket 28\n Reserving size (388) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 28:\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 28: 10%\n bucket 29: 20%\n bucket 28: 20%\n bucket 29: 30%\n bucket 28: 30%\n bucket 29: 40%\n bucket 28: 40%\n bucket 29: 50%\n bucket 28: 50%\n bucket 29: 60%\n bucket 28: 60%\n bucket 29: 70%\n bucket 28: 70%\n bucket 29: 80%\n bucket 28: 80%\n bucket 29: 90%\n bucket 28: 90%\n bucket 29: 100%\n Sorting block of length 195 for bucket 29\n (Using difference cover)\n bucket 28: 100%\n Sorting block of length 387 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 28\nGetting block 30 of 57\n Reserving size (388) 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 257 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 258 for bucket 30\nGetting block 31 of 57\n Reserving size (388) 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 310 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 311 for bucket 31\nGetting block 32 of 57\n Reserving size (388) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 32:\nGetting block 33 of 57\n Reserving size (388) for bucket 33\n Calculating Z arrays for bucket 33\n bucket 32: 10%\n Entering block accumulator loop for bucket 33:\n bucket 32: 20%\n bucket 33: 10%\n bucket 32: 30%\n bucket 33: 20%\n bucket 32: 40%\n bucket 33: 30%\n bucket 32: 50%\n bucket 33: 40%\n bucket 32: 60%\n bucket 32: 70%\n bucket 33: 50%\n bucket 32: 80%\n bucket 33: 60%\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 219 for bucket 32\n (Using difference cover)\n bucket 33: 70%\n bucket 33: 80%\n Sorting block time: 00:00:00\nReturning block of 220 for bucket 32\n bucket 33: 90%\n bucket 33: 100%\n Sorting block of length 387 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 33\nGetting block 34 of 57\n Reserving size (388) for bucket 34\n Calculating Z arrays for bucket 34\nGetting block 35 of 57\n Reserving size (388) 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 35: 10%\n bucket 34: 20%\n bucket 35: 20%\n bucket 34: 30%\n bucket 35: 30%\n bucket 34: 40%\n bucket 35: 40%\n bucket 34: 50%\n bucket 34: 60%\n bucket 35: 50%\n bucket 34: 70%\n bucket 35: 60%\n bucket 34: 80%\n bucket 35: 70%\n bucket 34: 90%\n bucket 35: 80%\n bucket 34: 100%\n Sorting block of length 275 for bucket 34\n (Using difference cover)\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 350 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 276 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 351 for bucket 35\nGetting block 36 of 57\n Reserving size (388) 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 150 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 151 for bucket 36\nGetting block 37 of 57\n Reserving size (388) for bucket 37\n Calculating Z arrays for bucket 37\nGetting block 38 of 57\n Reserving size (388) 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 37: 30%\n bucket 38: 30%\n bucket 37: 40%\n bucket 38: 40%\n bucket 38: 50%\n bucket 37: 50%\n bucket 38: 60%\n bucket 37: 60%\n bucket 38: 70%\n bucket 37: 70%\n bucket 38: 80%\n bucket 37: 80%\n bucket 38: 90%\n bucket 38: 100%\n bucket 37: 90%\n Sorting block of length 337 for bucket 38\n (Using difference cover)\n bucket 37: 100%\n Sorting block of length 267 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 338 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 268 for bucket 37\nGetting block 39 of 57\n Reserving size (388) for bucket 39\nGetting block 40 of 57\n Calculating Z arrays for bucket 39\n Reserving size (388) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 40:\n Entering block accumulator loop for bucket 39:\n bucket 40: 10%\n bucket 39: 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 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 387 for bucket 39\n (Using difference cover)\n bucket 40: 80%\n bucket 40: 90%\n bucket 40: 100%\n Sorting block time: 00:00:00\n Sorting block of length 379 for bucket 40\n (Using difference cover)\nReturning block of 388 for bucket 39\n Sorting block time: 00:00:00\nReturning block of 380 for bucket 40\nGetting block 41 of 57\n Reserving size (388) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 41:\nGetting block 42 of 57\n Reserving size (388) 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 41: 50%\n bucket 42: 30%\n bucket 41: 60%\n bucket 42: 40%\n bucket 41: 70%\n bucket 41: 80%\n bucket 42: 50%\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 330 for bucket 41\n (Using difference cover)\n bucket 42: 60%\n bucket 42: 70%\n bucket 42: 80%\n Sorting block time: 00:00:00\nReturning block of 331 for bucket 41\n bucket 42: 90%\n bucket 42: 100%\n Sorting block of length 188 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 189 for bucket 42\nGetting block 43 of 57\n Reserving size (388) for bucket 43\nGetting block 44 of 57\n Calculating Z arrays for bucket 43\n Reserving size (388) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 43:\n Entering block accumulator loop for bucket 44:\n bucket 43: 10%\n bucket 44: 10%\n bucket 43: 20%\n bucket 43: 30%\n bucket 44: 20%\n bucket 43: 40%\n bucket 44: 30%\n bucket 43: 50%\n bucket 44: 40%\n bucket 43: 60%\n bucket 44: 50%\n bucket 43: 70%\n bucket 43: 80%\n bucket 44: 60%\n bucket 44: 70%\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 321 for bucket 43\n (Using difference cover)\n bucket 44: 80%\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 366 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 322 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 367 for bucket 44\nGetting block 45 of 57\n Reserving size (388) 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 365 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 366 for bucket 45\nGetting block 46 of 57\n Reserving size (388) for bucket 46\nGetting block 47 of 57\n Calculating Z arrays for bucket 46\n Reserving size (388) 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 47: 10%\n bucket 46: 20%\n bucket 47: 20%\n bucket 46: 30%\n bucket 47: 30%\n bucket 46: 40%\n bucket 47: 40%\n bucket 46: 50%\n bucket 47: 50%\n bucket 46: 60%\n bucket 47: 60%\n bucket 46: 70%\n bucket 47: 70%\n bucket 46: 80%\n bucket 47: 80%\n bucket 46: 90%\n bucket 47: 90%\n bucket 46: 100%\n bucket 47: 100%\n Sorting block of length 253 for bucket 46\n (Using difference cover)\n Sorting block of length 217 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 218 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 254 for bucket 46\nGetting block 48 of 57\n Reserving size (388) 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 384 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 385 for bucket 48\nGetting block 49 of 57\n Reserving size (388) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\nGetting block 50 of 57\n Reserving size (388) for bucket 50\n Calculating Z arrays for bucket 50\n bucket 49: 20%\n Entering block accumulator loop for bucket 50:\nGetting block 51 of 57\n Reserving size (388) for bucket 51\n Calculating Z arrays for bucket 51\n bucket 49: 30%\n bucket 50: 10%\n Entering block accumulator loop for bucket 51:\n bucket 49: 40%\n bucket 50: 20%\n bucket 51: 10%\n bucket 49: 50%\n bucket 50: 30%\n bucket 50: 40%\n bucket 49: 60%\n bucket 51: 20%\n bucket 50: 50%\n bucket 49: 70%\n bucket 50: 60%\n bucket 51: 30%\n bucket 50: 70%\n bucket 49: 80%\n bucket 51: 40%\n bucket 50: 80%\n bucket 49: 90%\n bucket 50: 90%\n bucket 49: 100%\n Sorting block of length 112 for bucket 49\n (Using difference cover)\n bucket 51: 50%\n bucket 50: 100%\n Sorting block of length 275 for bucket 50\n (Using difference cover)\n bucket 51: 60%\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 49\n bucket 51: 70%\n Sorting block time: 00:00:00\nReturning block of 276 for bucket 50\n bucket 51: 80%\n bucket 51: 90%\n bucket 51: 100%\n Sorting block of length 350 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 351 for bucket 51\nGetting block 52 of 57\n Reserving size (388) for bucket 52\nGetting block 53 of 57\n Calculating Z arrays for bucket 52\n Reserving size (388) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 52:\n Entering block accumulator loop for bucket 53:\n bucket 52: 10%\n bucket 53: 10%\n bucket 53: 20%\n bucket 52: 20%\n bucket 53: 30%\n bucket 52: 30%\n bucket 53: 40%\n bucket 52: 40%\n bucket 53: 50%\n bucket 52: 50%\n bucket 53: 60%\n bucket 52: 60%\n bucket 53: 70%\n bucket 52: 70%\n bucket 53: 80%\n bucket 52: 80%\n bucket 53: 90%\n bucket 52: 90%\n bucket 53: 100%\n Sorting block of length 370 for bucket 53\n (Using difference cover)\n bucket 52: 100%\n Sorting block of length 378 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 371 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 379 for bucket 52\nGetting block 54 of 57\n Reserving size (388) 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 237 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 238 for bucket 54\nGetting block 55 of 57\n Reserving size (388) for bucket 55\nGetting block 56 of 57\n Calculating Z arrays for bucket 55\n Reserving size (388) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 55:\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n bucket 55: 10%\n bucket 56: 20%\n bucket 55: 20%\n bucket 56: 30%\n bucket 55: 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 270 for bucket 56\n (Using difference cover)\n bucket 55: 100%\n Sorting block of length 344 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 271 for bucket 56\n Sorting block time: 00:00:00\nReturning block of 345 for bucket 55\nGetting block 57 of 57\n Reserving size (388) 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 132 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 133 for bucket 57\nExited Ebwt loop\nfchr[A]: 0\nfchr[C]: 5124\nfchr[G]: 10305\nfchr[T]: 12474\nfchr[$]: 16568\nExiting Ebwt::buildToDisk()\nReturning from initFromVector\nWrote 4200050 bytes to primary EBWT file: genome.rev.1.bt2.tmp\nWrote 4148 bytes to secondary EBWT file: genome.rev.2.bt2.tmp\nRe-opening _in1 and _in2 as input streams\nReturning from Ebwt constructor\nHeaders:\n len: 16568\n bwtLen: 16569\n sz: 4142\n bwtSz: 4143\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 20\n eftabSz: 80\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 1036\n offsSz: 4144\n lineSz: 64\n sideSz: 64\n sideBwtSz: 48\n sideBwtLen: 192\n numSides: 87\n numLines: 87\n ebwtTotLen: 5568\n ebwtTotSz: 5568\n color: 0\n reverse: 1\nTotal time for backward call to driver() for mirror index: 00:00:01\n", "tool_stderr": "Building a SMALL index\nRenaming genome.3.bt2.tmp to genome.3.bt2\nRenaming genome.4.bt2.tmp to genome.4.bt2\nRenaming genome.1.bt2.tmp to genome.1.bt2\nRenaming genome.2.bt2.tmp to genome.2.bt2\nRenaming genome.rev.1.bt2.tmp to genome.rev.1.bt2\nRenaming genome.rev.2.bt2.tmp to genome.rev.2.bt2\n3 reads; of these:\n 3 (100.00%) were paired; of these:\n 2 (66.67%) aligned concordantly 0 times\n 1 (33.33%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 2 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 2 pairs aligned 0 times concordantly or discordantly; of these:\n 4 mates make up the pairs; of these:\n 3 (75.00%) aligned 0 times\n 1 (25.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n50.00% overall alignment rate\n", "job_stdout": "", "job_stderr": "", "stdout": "Settings:\n Output files: \"genome.*.bt2\"\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 Max bucket size: default\n Max bucket size, sqrt multiplier: default\n Max bucket size, len divisor: 32\n Difference-cover sample period: 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 /galaxy/server/database/objects/b/d/3/dataset_bd3f902b-73d4-401c-880c-188fe9f0c258.dat\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\nbmax according to bmaxDivN setting: 517\nUsing parameters --bmax 388 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 388 --dcv 1024\nConstructing suffix-array element generator\nBuilding DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 86 sample suffixes\nGenerating random suffixes\nQSorting 86 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 86 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 12, merged 41; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 6; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 284.672 (target: 387)\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering Ebwt loop\nGetting block 1 of 58\n Reserving size (388) for bucket 1\nGetting block 2 of 58\nGetting block 3 of 58\nGetting block 4 of 58\nGetting block 5 of 58\n Calculating Z arrays for bucket 1\n Reserving size (388) for bucket 2\n Reserving size (388) for bucket 3\n Reserving size (388) for bucket 4\n Reserving size (388) for bucket 5\nGetting block 6 of 58\nGetting block 7 of 58\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 3\n Entering block accumulator loop for bucket 1:\n Calculating Z arrays for bucket 4\n Calculating Z arrays for bucket 5\n Reserving size (388) for bucket 6\n Reserving size (388) for bucket 7\n Calculating Z arrays for bucket 6\n Entering block accumulator loop for bucket 2:\n Entering block accumulator loop for bucket 3:\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 4:\n Entering block accumulator loop for bucket 5:\n bucket 1: 10%\n Entering block accumulator loop for bucket 6:\n bucket 2: 10%\n Entering block accumulator loop for bucket 7:\n bucket 3: 10%\n bucket 1: 20%\n bucket 2: 20%\n bucket 3: 20%\n bucket 5: 10%\n bucket 1: 30%\n bucket 4: 10%\n bucket 6: 10%\n bucket 7: 10%\n bucket 2: 30%\n bucket 3: 30%\n bucket 1: 40%\n bucket 5: 20%\n bucket 2: 40%\n bucket 3: 40%\n bucket 1: 50%\n bucket 7: 20%\n bucket 4: 20%\n bucket 6: 20%\n bucket 2: 50%\n bucket 3: 50%\n bucket 5: 30%\n bucket 1: 60%\n bucket 2: 60%\n bucket 3: 60%\n bucket 7: 30%\n bucket 1: 70%\n bucket 4: 30%\n bucket 5: 40%\n bucket 6: 30%\n bucket 2: 70%\n bucket 3: 70%\n bucket 1: 80%\n bucket 7: 40%\n bucket 2: 80%\n bucket 5: 50%\n bucket 3: 80%\n bucket 4: 40%\n bucket 1: 90%\n bucket 6: 40%\n bucket 2: 90%\n bucket 3: 90%\n bucket 7: 50%\n bucket 5: 60%\n bucket 1: 100%\n bucket 2: 100%\n bucket 4: 50%\n Sorting block of length 355 for bucket 1\n (Using difference cover)\n Sorting block of length 165 for bucket 2\n (Using difference cover)\n bucket 3: 100%\n bucket 6: 50%\n Sorting block of length 370 for bucket 3\n (Using difference cover)\n bucket 5: 70%\n bucket 7: 60%\n bucket 4: 60%\n bucket 6: 60%\n bucket 5: 80%\n bucket 7: 70%\n bucket 4: 70%\n bucket 6: 70%\n bucket 5: 90%\n bucket 7: 80%\n bucket 4: 80%\n bucket 6: 80%\n bucket 5: 100%\n Sorting block of length 203 for bucket 5\n (Using difference cover)\n bucket 7: 90%\n bucket 4: 90%\n bucket 6: 90%\n bucket 7: 100%\n bucket 4: 100%\n bucket 6: 100%\n Sorting block of length 368 for bucket 7\n (Using difference cover)\n Sorting block of length 328 for bucket 4\n (Using difference cover)\n Sorting block of length 339 for bucket 6\n Sorting block time: 00:00:00\n (Using difference cover)\nReturning block of 356 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 166 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 371 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 204 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 369 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 329 for bucket 4\nGetting block 8 of 58\n Reserving size (388) for bucket 8\n Calculating Z arrays for bucket 8\nGetting block 9 of 58\n Reserving size (388) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 8:\n Entering block accumulator loop for bucket 9:\n bucket 8: 10%\n bucket 9: 10%\n bucket 8: 20%\n bucket 9: 20%\n bucket 8: 30%\n bucket 9: 30%\n bucket 8: 40%\n bucket 9: 40%\n bucket 8: 50%\n bucket 9: 50%\n bucket 8: 60%\n bucket 9: 60%\n bucket 8: 70%\n bucket 9: 70%\n bucket 8: 80%\n bucket 9: 80%\n bucket 8: 90%\n bucket 9: 90%\n bucket 8: 100%\n Sorting block of length 171 for bucket 8\n (Using difference cover)\n bucket 9: 100%\n Sorting block of length 339 for bucket 9\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 172 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 9\nGetting block 10 of 58\n Reserving size (388) for bucket 10\n Calculating Z arrays for bucket 10\nGetting block 11 of 58\n Reserving size (388) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 10:\nGetting block 12 of 58\n Reserving size (388) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 11:\n bucket 10: 10%\n Entering block accumulator loop for bucket 12:\n bucket 10: 20%\n bucket 10: 30%\n bucket 12: 10%\n bucket 11: 10%\n bucket 10: 40%\n bucket 10: 50%\n bucket 12: 20%\n bucket 11: 20%\n bucket 10: 60%\n bucket 10: 70%\n bucket 12: 30%\n bucket 11: 30%\n bucket 10: 80%\n bucket 11: 40%\n bucket 12: 40%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 357 for bucket 10\n (Using difference cover)\n bucket 11: 50%\n bucket 12: 50%\n bucket 11: 60%\n bucket 12: 60%\n bucket 11: 70%\n bucket 12: 70%\n Sorting block time: 00:00:00\nReturning block of 358 for bucket 10\n bucket 11: 80%\n bucket 12: 80%\n bucket 11: 90%\n bucket 12: 90%\n bucket 11: 100%\n bucket 12: 100%\n Sorting block of length 305 for bucket 11\n (Using difference cover)\n Sorting block of length 185 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 186 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 306 for bucket 11\nGetting block 13 of 58\n Reserving size (388) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 13:\nGetting block 14 of 58\n bucket 13: 10%\n Reserving size (388) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 14:\n bucket 13: 20%\n bucket 14: 10%\n bucket 13: 30%\n bucket 13: 40%\n bucket 14: 20%\n bucket 13: 50%\n bucket 14: 30%\n bucket 13: 60%\n bucket 14: 40%\n bucket 13: 70%\n bucket 14: 50%\n bucket 13: 80%\n bucket 14: 60%\n bucket 13: 90%\n bucket 14: 70%\n bucket 13: 100%\n bucket 14: 80%\n Sorting block of length 282 for bucket 13\n (Using difference cover)\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 339 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 283 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 14\nGetting block 15 of 58\n Reserving size (388) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\nGetting block 16 of 58\n Reserving size (388) for bucket 16\n Calculating Z arrays for bucket 16\n bucket 15: 10%\n Entering block accumulator loop for bucket 16:\n bucket 15: 20%\n bucket 16: 10%\n bucket 15: 30%\n bucket 16: 20%\n bucket 16: 30%\n bucket 15: 40%\n bucket 16: 40%\n bucket 15: 50%\n bucket 16: 50%\n bucket 16: 60%\n bucket 15: 60%\n bucket 16: 70%\n bucket 15: 70%\n bucket 16: 80%\n bucket 15: 80%\n bucket 16: 90%\n bucket 15: 90%\n bucket 16: 100%\n Sorting block of length 379 for bucket 16\n (Using difference cover)\n bucket 15: 100%\n Sorting block of length 241 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 242 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 380 for bucket 16\nGetting block 17 of 58\n Reserving size (388) 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 58\n bucket 17: 20%\n Reserving size (388) for bucket 18\n Calculating Z arrays for bucket 18\n bucket 17: 30%\n Entering block accumulator loop for bucket 18:\n bucket 17: 40%\n bucket 17: 50%\n bucket 18: 10%\n bucket 17: 60%\n bucket 17: 70%\n bucket 18: 20%\n bucket 17: 80%\n bucket 17: 90%\n bucket 18: 30%\n bucket 17: 100%\n Sorting block of length 215 for bucket 17\n (Using difference cover)\n bucket 18: 40%\n Sorting block time: 00:00:00\nReturning block of 216 for bucket 17\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 378 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 379 for bucket 18\nGetting block 19 of 58\n Reserving size (388) for bucket 19\n Calculating Z arrays for bucket 19\nGetting block 20 of 58\n Reserving size (388) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 19:\n Entering block accumulator loop for bucket 20:\n bucket 19: 10%\n bucket 20: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 20: 20%\n bucket 19: 40%\n bucket 20: 30%\n bucket 20: 40%\n bucket 19: 50%\n bucket 20: 50%\n bucket 19: 60%\n bucket 20: 60%\n bucket 19: 70%\n bucket 20: 70%\n bucket 19: 80%\n bucket 20: 80%\n bucket 20: 90%\n bucket 19: 90%\n bucket 20: 100%\n Sorting block of length 313 for bucket 20\n (Using difference cover)\n bucket 19: 100%\n Sorting block of length 334 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 314 for bucket 20\n Sorting block time: 00:00:00\nReturning block of 335 for bucket 19\nGetting block 21 of 58\n Reserving size (388) 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 210 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 211 for bucket 21\nGetting block 22 of 58\n Reserving size (388) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\nGetting block 23 of 58\n Reserving size (388) for bucket 23\n Calculating Z arrays for bucket 23\n bucket 22: 10%\n Entering block accumulator loop for bucket 23:\n bucket 22: 20%\n bucket 23: 10%\n bucket 22: 30%\n bucket 23: 20%\n bucket 22: 40%\n bucket 23: 30%\n bucket 23: 40%\n bucket 22: 50%\n bucket 23: 50%\n bucket 22: 60%\n bucket 23: 60%\n bucket 23: 70%\n bucket 22: 70%\n bucket 23: 80%\n bucket 22: 80%\n bucket 23: 90%\n bucket 22: 90%\n bucket 23: 100%\n Sorting block of length 238 for bucket 23\n (Using difference cover)\n bucket 22: 100%\n Sorting block of length 386 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 239 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 387 for bucket 22\nGetting block 24 of 58\n Reserving size (388) 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 351 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 352 for bucket 24\nGetting block 25 of 58\n Reserving size (388) 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 105 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 106 for bucket 25\nGetting block 26 of 58\n Reserving size (388) 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 354 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 355 for bucket 26\nGetting block 27 of 58\n Reserving size (388) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\nGetting block 28 of 58\n Reserving size (388) for bucket 28\n Calculating Z arrays for bucket 28\n bucket 27: 10%\n Entering block accumulator loop for bucket 28:\n bucket 27: 20%\n bucket 28: 10%\n bucket 27: 30%\n bucket 28: 20%\n bucket 27: 40%\n bucket 28: 30%\n bucket 27: 50%\n bucket 28: 40%\n bucket 28: 50%\n bucket 27: 60%\n bucket 28: 60%\n bucket 27: 70%\n bucket 28: 70%\n bucket 27: 80%\n bucket 28: 80%\n bucket 27: 90%\n bucket 28: 90%\n bucket 27: 100%\n Sorting block of length 334 for bucket 27\n (Using difference cover)\n bucket 28: 100%\n Sorting block of length 253 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 335 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 254 for bucket 28\nGetting block 29 of 58\n Reserving size (388) 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 289 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 290 for bucket 29\nGetting block 30 of 58\n Reserving size (388) 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 345 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 346 for bucket 30\nGetting block 31 of 58\n Reserving size (388) for bucket 31\n Calculating Z arrays for bucket 31\nGetting block 32 of 58\n Reserving size (388) for bucket 32\n Entering block accumulator loop for bucket 31:\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 32:\n bucket 31: 10%\n bucket 32: 10%\n bucket 31: 20%\n bucket 32: 20%\n bucket 31: 30%\n bucket 32: 30%\n bucket 32: 40%\n bucket 31: 40%\n bucket 32: 50%\n bucket 31: 50%\n bucket 32: 60%\n bucket 32: 70%\n bucket 31: 60%\n bucket 32: 80%\n bucket 31: 70%\n bucket 32: 90%\n buc\n..\ntor loop for bucket 25:\n bucket 23: 10%\n bucket 25: 10%\n bucket 24: 10%\n bucket 23: 20%\n bucket 25: 20%\n bucket 23: 30%\n bucket 24: 20%\n bucket 23: 40%\n bucket 25: 30%\n bucket 24: 30%\n bucket 23: 50%\n bucket 25: 40%\n bucket 23: 60%\n bucket 24: 40%\n bucket 23: 70%\n bucket 25: 50%\n bucket 23: 80%\n bucket 24: 50%\n bucket 25: 60%\n bucket 23: 90%\n bucket 23: 100%\n bucket 24: 60%\n bucket 25: 70%\n Sorting block of length 349 for bucket 23\n (Using difference cover)\n bucket 25: 80%\n bucket 24: 70%\n bucket 25: 90%\n bucket 24: 80%\n Sorting block time: 00:00:00\nReturning block of 350 for bucket 23\n bucket 24: 90%\n bucket 25: 100%\n Sorting block of length 286 for bucket 25\n (Using difference cover)\n bucket 24: 100%\n Sorting block of length 245 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 246 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 287 for bucket 25\nGetting block 26 of 57\n Reserving size (388) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\nGetting block 27 of 57\n Reserving size (388) for bucket 27\n Calculating Z arrays for bucket 27\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 27: 50%\n bucket 26: 60%\n bucket 27: 60%\n bucket 26: 70%\n bucket 27: 70%\n bucket 26: 80%\n bucket 27: 80%\n bucket 26: 90%\n bucket 27: 90%\n bucket 26: 100%\n Sorting block of length 384 for bucket 26\n (Using difference cover)\n bucket 27: 100%\n Sorting block of length 359 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 385 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 360 for bucket 27\nGetting block 28 of 57\n Reserving size (388) for bucket 28\nGetting block 29 of 57\n Calculating Z arrays for bucket 28\n Reserving size (388) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 28:\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 28: 10%\n bucket 29: 20%\n bucket 28: 20%\n bucket 29: 30%\n bucket 28: 30%\n bucket 29: 40%\n bucket 28: 40%\n bucket 29: 50%\n bucket 28: 50%\n bucket 29: 60%\n bucket 28: 60%\n bucket 29: 70%\n bucket 28: 70%\n bucket 29: 80%\n bucket 28: 80%\n bucket 29: 90%\n bucket 28: 90%\n bucket 29: 100%\n Sorting block of length 195 for bucket 29\n (Using difference cover)\n bucket 28: 100%\n Sorting block of length 387 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 28\nGetting block 30 of 57\n Reserving size (388) 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 257 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 258 for bucket 30\nGetting block 31 of 57\n Reserving size (388) 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 310 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 311 for bucket 31\nGetting block 32 of 57\n Reserving size (388) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 32:\nGetting block 33 of 57\n Reserving size (388) for bucket 33\n Calculating Z arrays for bucket 33\n bucket 32: 10%\n Entering block accumulator loop for bucket 33:\n bucket 32: 20%\n bucket 33: 10%\n bucket 32: 30%\n bucket 33: 20%\n bucket 32: 40%\n bucket 33: 30%\n bucket 32: 50%\n bucket 33: 40%\n bucket 32: 60%\n bucket 32: 70%\n bucket 33: 50%\n bucket 32: 80%\n bucket 33: 60%\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 219 for bucket 32\n (Using difference cover)\n bucket 33: 70%\n bucket 33: 80%\n Sorting block time: 00:00:00\nReturning block of 220 for bucket 32\n bucket 33: 90%\n bucket 33: 100%\n Sorting block of length 387 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 33\nGetting block 34 of 57\n Reserving size (388) for bucket 34\n Calculating Z arrays for bucket 34\nGetting block 35 of 57\n Reserving size (388) 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 35: 10%\n bucket 34: 20%\n bucket 35: 20%\n bucket 34: 30%\n bucket 35: 30%\n bucket 34: 40%\n bucket 35: 40%\n bucket 34: 50%\n bucket 34: 60%\n bucket 35: 50%\n bucket 34: 70%\n bucket 35: 60%\n bucket 34: 80%\n bucket 35: 70%\n bucket 34: 90%\n bucket 35: 80%\n bucket 34: 100%\n Sorting block of length 275 for bucket 34\n (Using difference cover)\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 350 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 276 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 351 for bucket 35\nGetting block 36 of 57\n Reserving size (388) 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 150 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 151 for bucket 36\nGetting block 37 of 57\n Reserving size (388) for bucket 37\n Calculating Z arrays for bucket 37\nGetting block 38 of 57\n Reserving size (388) 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 37: 30%\n bucket 38: 30%\n bucket 37: 40%\n bucket 38: 40%\n bucket 38: 50%\n bucket 37: 50%\n bucket 38: 60%\n bucket 37: 60%\n bucket 38: 70%\n bucket 37: 70%\n bucket 38: 80%\n bucket 37: 80%\n bucket 38: 90%\n bucket 38: 100%\n bucket 37: 90%\n Sorting block of length 337 for bucket 38\n (Using difference cover)\n bucket 37: 100%\n Sorting block of length 267 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 338 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 268 for bucket 37\nGetting block 39 of 57\n Reserving size (388) for bucket 39\nGetting block 40 of 57\n Calculating Z arrays for bucket 39\n Reserving size (388) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 40:\n Entering block accumulator loop for bucket 39:\n bucket 40: 10%\n bucket 39: 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 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 387 for bucket 39\n (Using difference cover)\n bucket 40: 80%\n bucket 40: 90%\n bucket 40: 100%\n Sorting block time: 00:00:00\n Sorting block of length 379 for bucket 40\n (Using difference cover)\nReturning block of 388 for bucket 39\n Sorting block time: 00:00:00\nReturning block of 380 for bucket 40\nGetting block 41 of 57\n Reserving size (388) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 41:\nGetting block 42 of 57\n Reserving size (388) 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 41: 50%\n bucket 42: 30%\n bucket 41: 60%\n bucket 42: 40%\n bucket 41: 70%\n bucket 41: 80%\n bucket 42: 50%\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 330 for bucket 41\n (Using difference cover)\n bucket 42: 60%\n bucket 42: 70%\n bucket 42: 80%\n Sorting block time: 00:00:00\nReturning block of 331 for bucket 41\n bucket 42: 90%\n bucket 42: 100%\n Sorting block of length 188 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 189 for bucket 42\nGetting block 43 of 57\n Reserving size (388) for bucket 43\nGetting block 44 of 57\n Calculating Z arrays for bucket 43\n Reserving size (388) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 43:\n Entering block accumulator loop for bucket 44:\n bucket 43: 10%\n bucket 44: 10%\n bucket 43: 20%\n bucket 43: 30%\n bucket 44: 20%\n bucket 43: 40%\n bucket 44: 30%\n bucket 43: 50%\n bucket 44: 40%\n bucket 43: 60%\n bucket 44: 50%\n bucket 43: 70%\n bucket 43: 80%\n bucket 44: 60%\n bucket 44: 70%\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 321 for bucket 43\n (Using difference cover)\n bucket 44: 80%\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 366 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 322 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 367 for bucket 44\nGetting block 45 of 57\n Reserving size (388) 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 365 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 366 for bucket 45\nGetting block 46 of 57\n Reserving size (388) for bucket 46\nGetting block 47 of 57\n Calculating Z arrays for bucket 46\n Reserving size (388) 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 47: 10%\n bucket 46: 20%\n bucket 47: 20%\n bucket 46: 30%\n bucket 47: 30%\n bucket 46: 40%\n bucket 47: 40%\n bucket 46: 50%\n bucket 47: 50%\n bucket 46: 60%\n bucket 47: 60%\n bucket 46: 70%\n bucket 47: 70%\n bucket 46: 80%\n bucket 47: 80%\n bucket 46: 90%\n bucket 47: 90%\n bucket 46: 100%\n bucket 47: 100%\n Sorting block of length 253 for bucket 46\n (Using difference cover)\n Sorting block of length 217 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 218 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 254 for bucket 46\nGetting block 48 of 57\n Reserving size (388) 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 384 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 385 for bucket 48\nGetting block 49 of 57\n Reserving size (388) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\nGetting block 50 of 57\n Reserving size (388) for bucket 50\n Calculating Z arrays for bucket 50\n bucket 49: 20%\n Entering block accumulator loop for bucket 50:\nGetting block 51 of 57\n Reserving size (388) for bucket 51\n Calculating Z arrays for bucket 51\n bucket 49: 30%\n bucket 50: 10%\n Entering block accumulator loop for bucket 51:\n bucket 49: 40%\n bucket 50: 20%\n bucket 51: 10%\n bucket 49: 50%\n bucket 50: 30%\n bucket 50: 40%\n bucket 49: 60%\n bucket 51: 20%\n bucket 50: 50%\n bucket 49: 70%\n bucket 50: 60%\n bucket 51: 30%\n bucket 50: 70%\n bucket 49: 80%\n bucket 51: 40%\n bucket 50: 80%\n bucket 49: 90%\n bucket 50: 90%\n bucket 49: 100%\n Sorting block of length 112 for bucket 49\n (Using difference cover)\n bucket 51: 50%\n bucket 50: 100%\n Sorting block of length 275 for bucket 50\n (Using difference cover)\n bucket 51: 60%\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 49\n bucket 51: 70%\n Sorting block time: 00:00:00\nReturning block of 276 for bucket 50\n bucket 51: 80%\n bucket 51: 90%\n bucket 51: 100%\n Sorting block of length 350 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 351 for bucket 51\nGetting block 52 of 57\n Reserving size (388) for bucket 52\nGetting block 53 of 57\n Calculating Z arrays for bucket 52\n Reserving size (388) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 52:\n Entering block accumulator loop for bucket 53:\n bucket 52: 10%\n bucket 53: 10%\n bucket 53: 20%\n bucket 52: 20%\n bucket 53: 30%\n bucket 52: 30%\n bucket 53: 40%\n bucket 52: 40%\n bucket 53: 50%\n bucket 52: 50%\n bucket 53: 60%\n bucket 52: 60%\n bucket 53: 70%\n bucket 52: 70%\n bucket 53: 80%\n bucket 52: 80%\n bucket 53: 90%\n bucket 52: 90%\n bucket 53: 100%\n Sorting block of length 370 for bucket 53\n (Using difference cover)\n bucket 52: 100%\n Sorting block of length 378 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 371 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 379 for bucket 52\nGetting block 54 of 57\n Reserving size (388) 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 237 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 238 for bucket 54\nGetting block 55 of 57\n Reserving size (388) for bucket 55\nGetting block 56 of 57\n Calculating Z arrays for bucket 55\n Reserving size (388) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 55:\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n bucket 55: 10%\n bucket 56: 20%\n bucket 55: 20%\n bucket 56: 30%\n bucket 55: 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 270 for bucket 56\n (Using difference cover)\n bucket 55: 100%\n Sorting block of length 344 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 271 for bucket 56\n Sorting block time: 00:00:00\nReturning block of 345 for bucket 55\nGetting block 57 of 57\n Reserving size (388) 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 132 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 133 for bucket 57\nExited Ebwt loop\nfchr[A]: 0\nfchr[C]: 5124\nfchr[G]: 10305\nfchr[T]: 12474\nfchr[$]: 16568\nExiting Ebwt::buildToDisk()\nReturning from initFromVector\nWrote 4200050 bytes to primary EBWT file: genome.rev.1.bt2.tmp\nWrote 4148 bytes to secondary EBWT file: genome.rev.2.bt2.tmp\nRe-opening _in1 and _in2 as input streams\nReturning from Ebwt constructor\nHeaders:\n len: 16568\n bwtLen: 16569\n sz: 4142\n bwtSz: 4143\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 20\n eftabSz: 80\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 1036\n offsSz: 4144\n lineSz: 64\n sideSz: 64\n sideBwtSz: 48\n sideBwtLen: 192\n numSides: 87\n numLines: 87\n ebwtTotLen: 5568\n ebwtTotSz: 5568\n color: 0\n reverse: 1\nTotal time for backward call to driver() for mirror index: 00:00:01\n", "stderr": "Building a SMALL index\nRenaming genome.3.bt2.tmp to genome.3.bt2\nRenaming genome.4.bt2.tmp to genome.4.bt2\nRenaming genome.1.bt2.tmp to genome.1.bt2\nRenaming genome.2.bt2.tmp to genome.2.bt2\nRenaming genome.rev.1.bt2.tmp to genome.rev.1.bt2\nRenaming genome.rev.2.bt2.tmp to genome.rev.2.bt2\n3 reads; of these:\n 3 (100.00%) were paired; of these:\n 2 (66.67%) aligned concordantly 0 times\n 1 (33.33%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 2 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 2 pairs aligned 0 times concordantly or discordantly; of these:\n 4 mates make up the pairs; of these:\n 3 (75.00%) aligned 0 times\n 1 (25.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n50.00% overall alignment rate\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-08 18:52:50", "plugin": "core", "name": "end_epoch", "raw_value": "1731091970.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 18:52:49", "plugin": "core", "name": "start_epoch", "raw_value": "1731091969.0000000"}, {"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": "bowtie2/2.5.3+galaxy1-5", "has_data": true, "data": {"tool_id": "bowtie2", "tool_version": "2.5.3+galaxy1", "test_index": 5, "time_seconds": 42.86958718299866, "inputs": {"library|input_1": {"src": "hda", "id": "48d443965fb79661"}, "library|input_2": {"src": "hda", "id": "3efd9b08baf135dc"}, "library|unaligned_file": false, "library|paired_options|paired_options_selector": "no", "library|type": "paired", "reference_genome|own_file": {"src": "hda", "id": "b290ad1616cef64a"}, "reference_genome|source": "history", "analysis_type|analysis_type_selector": "simple"}, "job": {"model_class": "Job", "id": "3efd9b08baf135dc", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T18:53:31.109000", "update_time": "2024-11-08T18:53:45.817293", "galaxy_version": "24.1", "external_id": "gxy-crcx4", "handler": null, "job_runner_name": null, "command_line": "set -o | grep -q pipefail && set -o pipefail; bowtie2-build --threads ${GALAXY_SLOTS:-4} '/galaxy/server/database/objects/1/8/c/dataset_18cea05d-389e-4888-9714-2faa6a33420f.dat' genome && ln -s -f '/galaxy/server/database/objects/1/8/c/dataset_18cea05d-389e-4888-9714-2faa6a33420f.dat' genome.fa && ln -f -s '/galaxy/server/database/objects/1/9/c/dataset_19cad22a-10ec-4f23-85f0-540d07b60bb9.dat' input_f.fastq.gz && ln -f -s '/galaxy/server/database/objects/7/7/5/dataset_77515113-69a9-4915-b45c-897e0b4e6221.dat' input_r.fastq.gz && THREADS=${GALAXY_SLOTS:-4} && if [ \"$THREADS\" -gt 1 ]; then (( THREADS-- )); fi && bowtie2 -p \"$THREADS\" -x 'genome' -1 'input_f.fastq.gz' -2 'input_r.fastq.gz' | samtools sort -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/9/e/a/dataset_9eaf20fc-94ec-4fe4-bd32-f0d76134ac5f.dat'", "user_email": "tests@fake.org", "command_version": "/usr/local/bin/bowtie2-align-s version 2.5.3\n64-bit\nBuilt on fv-az365-785\nWed Jan 17 04:43:48 UTC 2024\nCompiler: gcc version 12.3.0 (conda-forge gcc 12.3.0-3) \nOptions: -O3 -msse2 -funroll-loops -g3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /usr/local/include -fdebug-prefix-map=/opt/conda/conda-bld/bowtie2_1705465427853/work=/usr/local/src/conda/bowtie2-2.5.3 -fdebug-prefix-map=/usr/local=/usr/local/src/conda-prefix -std=c++11 -Wall -Wno-unused-but-set-variable -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -DWITH_ZSTD\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "save_mapping_stats": "false", "sam_options": "{\"__current_case__\": 1, \"sam_options_selector\": \"no\"}", "analysis_type": "{\"__current_case__\": 0, \"analysis_type_selector\": \"simple\", \"presets\": \"no_presets\"}", "rg": "{\"__current_case__\": 3, \"rg_selector\": \"do_not_set\"}", "reference_genome": "{\"__current_case__\": 1, \"own_file\": {\"values\": [{\"id\": 69, \"src\": \"hda\"}]}, \"source\": \"history\"}", "library": "{\"__current_case__\": 1, \"aligned_file\": false, \"input_1\": {\"values\": [{\"id\": 67, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 68, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 1, \"paired_options_selector\": \"no\"}, \"type\": \"paired\", \"unaligned_file\": false}"}, "inputs": {"library|input_1": {"id": "48d443965fb79661", "src": "hda", "uuid": "19cad22a-10ec-4f23-85f0-540d07b60bb9"}, "library|input_2": {"id": "3efd9b08baf135dc", "src": "hda", "uuid": "77515113-69a9-4915-b45c-897e0b4e6221"}, "reference_genome|own_file": {"id": "b290ad1616cef64a", "src": "hda", "uuid": "18cea05d-389e-4888-9714-2faa6a33420f"}}, "outputs": {"output": {"id": "72a54035b8840356", "src": "hda", "uuid": "9eaf20fc-94ec-4fe4-bd32-f0d76134ac5f"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Settings:\n Output files: \"genome.*.bt2\"\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 Max bucket size: default\n Max bucket size, sqrt multiplier: default\n Max bucket size, len divisor: 32\n Difference-cover sample period: 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 /galaxy/server/database/objects/1/8/c/dataset_18cea05d-389e-4888-9714-2faa6a33420f.dat\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\nbmax according to bmaxDivN setting: 517\nUsing parameters --bmax 388 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 388 --dcv 1024\nConstructing suffix-array element generator\nBuilding DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 86 sample suffixes\nGenerating random suffixes\nQSorting 86 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 86 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 12, merged 41; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 6; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 284.672 (target: 387)\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering Ebwt loop\nGetting block 1 of 58\n Reserving size (388) for bucket 1\nGetting block 2 of 58\nGetting block 3 of 58\nGetting block 4 of 58\nGetting block 5 of 58\n Calculating Z arrays for bucket 1\n Reserving size (388) for bucket 2\n Reserving size (388) for bucket 3\n Reserving size (388) for bucket 4\n Reserving size (388) for bucket 5\nGetting block 6 of 58\nGetting block 7 of 58\n Entering block accumulator loop for bucket 1:\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 3\n Calculating Z arrays for bucket 4\n Calculating Z arrays for bucket 5\n Reserving size (388) for bucket 6\n Reserving size (388) for bucket 7\n Entering block accumulator loop for bucket 2:\n Entering block accumulator loop for bucket 4:\n Calculating Z arrays for bucket 6\n Entering block accumulator loop for bucket 5:\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 3:\n bucket 1: 10%\n Entering block accumulator loop for bucket 6:\n Entering block accumulator loop for bucket 7:\n bucket 5: 10%\n bucket 1: 20%\n bucket 4: 10%\n bucket 2: 10%\n bucket 3: 10%\n bucket 1: 30%\n bucket 5: 20%\n bucket 4: 20%\n bucket 2: 20%\n bucket 6: 10%\n bucket 1: 40%\n bucket 5: 30%\n bucket 3: 20%\n bucket 4: 30%\n bucket 7: 10%\n bucket 1: 50%\n bucket 5: 40%\n bucket 2: 30%\n bucket 4: 40%\n bucket 3: 30%\n bucket 1: 60%\n bucket 7: 20%\n bucket 5: 50%\n bucket 4: 50%\n bucket 1: 70%\n bucket 6: 20%\n bucket 3: 40%\n bucket 2: 40%\n bucket 5: 60%\n bucket 4: 60%\n bucket 1: 80%\n bucket 7: 30%\n bucket 3: 50%\n bucket 5: 70%\n bucket 4: 70%\n bucket 1: 90%\n bucket 6: 30%\n bucket 2: 50%\n bucket 5: 80%\n bucket 7: 40%\n bucket 1: 100%\n bucket 4: 80%\n bucket 3: 60%\n Sorting block of length 355 for bucket 1\n (Using difference cover)\n bucket 2: 60%\n bucket 6: 40%\n bucket 5: 90%\n bucket 4: 90%\n bucket 3: 70%\n bucket 7: 50%\n bucket 5: 100%\n Sorting block of length 203 for bucket 5\n (Using difference cover)\n bucket 2: 70%\n bucket 4: 100%\n Sorting block of length 328 for bucket 4\n (Using difference cover)\n bucket 6: 50%\n bucket 3: 80%\n bucket 2: 80%\n bucket 7: 60%\n bucket 6: 60%\n bucket 3: 90%\n bucket 2: 90%\n bucket 7: 70%\n bucket 6: 70%\n bucket 3: 100%\n bucket 2: 100%\n Sorting block of length 370 for bucket 3\n (Using difference cover)\n Sorting block of length 165 for bucket 2\n (Using difference cover)\n bucket 7: 80%\n bucket 6: 80%\n bucket 7: 90%\n bucket 6: 90%\n Sorting block time: 00:00:00\nReturning block of 356 for bucket 1\n bucket 7: 100%\n bucket 6: 100%\n Sorting block of length 368 for bucket 7\n (Using difference cover)\n Sorting block of length 339 for bucket 6\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 369 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 204 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 371 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 329 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 166 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 6\nGetting block 8 of 58\n Reserving size (388) for bucket 8\n Calculating Z arrays for bucket 8\n Entering block accumulator loop for bucket 8:\nGetting block 9 of 58\n bucket 8: 10%\n Reserving size (388) for bucket 9\n Calculating Z arrays for bucket 9\nGetting block 10 of 58\n Reserving size (388) for bucket 10\n Calculating Z arrays for bucket 10\n bucket 8: 20%\n Entering block accumulator loop for bucket 9:\n Entering block accumulator loop for bucket 10:\n bucket 8: 30%\n bucket 9: 10%\n bucket 8: 40%\n bucket 10: 10%\n bucket 9: 20%\n bucket 8: 50%\n bucket 10: 20%\n bucket 9: 30%\n bucket 10: 30%\n bucket 8: 60%\n bucket 9: 40%\n bucket 10: 40%\n bucket 8: 70%\n bucket 9: 50%\n bucket 10: 50%\n bucket 8: 80%\n bucket 9: 60%\n bucket 10: 60%\n bucket 9: 70%\n bucket 8: 90%\n bucket 10: 70%\n bucket 9: 80%\n bucket 10: 80%\n bucket 8: 100%\n Sorting block of length 171 for bucket 8\n (Using difference cover)\n bucket 9: 90%\n bucket 10: 90%\n bucket 9: 100%\n Sorting block of length 339 for bucket 9\n (Using difference cover)\n bucket 10: 100%\n Sorting block of length 357 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 358 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 172 for bucket 8\nGetting block 11 of 58\n Reserving size (388) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\n bucket 11: 10%\nGetting block 12 of 58\n Reserving size (388) for bucket 12\n Calculating Z arrays for bucket 12\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 11: 70%\n bucket 12: 40%\n bucket 11: 80%\n bucket 12: 50%\n bucket 11: 90%\n bucket 12: 60%\n bucket 11: 100%\n Sorting block of length 305 for bucket 11\n (Using difference cover)\n bucket 12: 70%\n bucket 12: 80%\n bucket 12: 90%\n Sorting block time: 00:00:00\nReturning block of 306 for bucket 11\n bucket 12: 100%\n Sorting block of length 185 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 186 for bucket 12\nGetting block 13 of 58\n Reserving size (388) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\nGetting block 14 of 58\n Reserving size (388) for bucket 14\n Calculating Z arrays for bucket 14\n bucket 13: 20%\n Entering block accumulator loop for bucket 14:\n bucket 13: 30%\n bucket 14: 10%\n bucket 13: 40%\n bucket 14: 20%\n bucket 13: 50%\n bucket 14: 30%\n bucket 13: 60%\n bucket 14: 40%\n bucket 13: 70%\n bucket 14: 50%\n bucket 13: 80%\n bucket 13: 90%\n bucket 14: 60%\n bucket 13: 100%\n Sorting block of length 282 for bucket 13\n (Using difference cover)\n bucket 14: 70%\n bucket 14: 80%\n bucket 14: 90%\n Sorting block time: 00:00:00\nReturning block of 283 for bucket 13\n bucket 14: 100%\n Sorting block of length 339 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 14\nGetting block 15 of 58\n Reserving size (388) 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 58\n Reserving size (388) 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 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 241 for bucket 15\n (Using difference cover)\n bucket 16: 50%\n bucket 16: 60%\n Sorting block time: 00:00:00\nReturning block of 242 for bucket 15\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 379 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 380 for bucket 16\nGetting block 17 of 58\n Reserving size (388) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\nGetting block 18 of 58\n Reserving size (388) for bucket 18\n Calculating Z arrays for bucket 18\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 17: 60%\n bucket 18: 30%\n bucket 17: 70%\n bucket 18: 40%\n bucket 17: 80%\n bucket 18: 50%\n bucket 17: 90%\n bucket 18: 60%\n bucket 17: 100%\n Sorting block of length 215 for bucket 17\n (Using difference cover)\n bucket 18: 70%\n bucket 18: 80%\n Sorting block time: 00:00:00\nReturning block of 216 for bucket 17\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 378 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 379 for bucket 18\nGetting block 19 of 58\n Reserving size (388) for bucket 19\nGetting block 20 of 58\n Calculating Z arrays for bucket 19\n Reserving size (388) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 19:\n Entering block accumulator loop for bucket 20:\n bucket 19: 10%\n bucket 20: 10%\n bucket 19: 20%\n bucket 20: 20%\n bucket 19: 30%\n bucket 20: 30%\n bucket 19: 40%\n bucket 20: 40%\n bucket 19: 50%\n bucket 20: 50%\n bucket 19: 60%\n bucket 20: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 20: 70%\n bucket 19: 90%\n bucket 20: 80%\n bucket 19: 100%\n Sorting block of length 334 for bucket 19\n (Using difference cover)\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 313 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 335 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 314 for bucket 20\nGetting block 21 of 58\n Reserving size (388) for bucket 21\nGetting block 22 of 58\n Calculating Z arrays for bucket 21\n Reserving size (388) 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 22: 10%\n bucket 21: 10%\n bucket 22: 20%\n bucket 21: 20%\n bucket 22: 30%\n bucket 21: 30%\n bucket 22: 40%\n bucket 21: 40%\n bucket 22: 50%\n bucket 21: 50%\n bucket 22: 60%\n bucket 22: 70%\n bucket 21: 60%\n bucket 22: 80%\n bucket 21: 70%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 386 for bucket 22\n (Using difference cover)\n bucket 21: 80%\n bucket 21: 90%\n Sorting block time: 00:00:00\n bucket 21: 100%\nReturning block of 387 for bucket 22\n Sorting block of length 210 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 211 for bucket 21\nGetting block 23 of 58\n Reserving size (388) 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 238 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 239 for bucket 23\nGetting block 24 of 58\n Reserving size (388) 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 58\n Reserving size (388) for bucket 25\n Calculating Z arrays for bucket 25\n bucket 24: 20%\n Entering block accumulator loop for bucket 25:\n bucket 24: 30%\n bucket 25: 10%\n bucket 24: 40%\n bucket 25: 20%\n bucket 24: 50%\n bucket 25: 30%\n bucket 25: 40%\n bucket 24: 60%\n bucket 25: 50%\n bucket 24: 70%\n bucket 24: 80%\n bucket 25: 60%\n bucket 24: 90%\n bucket 25: 70%\n bucket 24: 100%\n Sorting block of length 351 for bucket 24\n (Using difference cover)\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 105 for bucket 25\n Sorting block time: 00:00:00\n (Using difference cover)\nReturning block of 352 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 106 for bucket 25\nGetting block 26 of 58\n Reserving size (388) 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%\nGetting block 27 of 58\n bucket 26: 40%\n Reserving size (388) for bucket 27\n bucket 26: 50%\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n bucket 26: 60%\n bucket 26: 70%\n bucket 27: 10%\n bucket 26: 80%\n bucket 27: 20%\n bucket 26: 90%\n bucket 27: 30%\n bucket 26: 100%\n Sorting block of length 354 for bucket 26\n (Using difference cover)\n bucket 27: 40%\n bucket 27: 50%\n bucket 27: 60%\n Sorting block time: 00:00:00\nReturning block of 355 for bucket 26\n bucket 27: 70%\n bucket 27: 80%\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 334 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 335 for bucket 27\nGetting block 28 of 58\n Reserving size (388) 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%\nGetting block 29 of 58\n Reserving size (388) for bucket 29\n Calculating Z arrays for bucket 29\n bucket 28: 30%\n Entering block accumulator loop for bucket 29:\n bucket 28: 40%\n bucket 28: 50%\n bucket 29: 10%\n bucket 28: 60%\n bucket 28: 70%\n bucket 29: 20%\n bucket 28: 80%\n bucket 28: 90%\n bucket 29: 30%\n bucket 28: 100%\n Sorting block of length 253 for bucket 28\n (Using difference cover)\n bucket 29: 40%\n bucket 29: 50%\n Sorting block time: 00:00:00\nReturning block of 254 for bucket 28\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 289 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 290 for bucket 29\nGetting block 30 of 58\n Reserving size (388) for bucket 30\nGetting block 31 of 58\n Calculating Z arrays for bucket 30\n Reserving size (388) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 31:\n Entering block accumulator loop for bucket 30:\n bucket 31: 10%\n bucket 30: 10%\n bucket 30: 20%\n bucket 31: 20%\n bucket 30: 30%\n bucket 31: 30%\n bucket 30: 40%\n bucket 31: 40%\n bucket 30: 50%\n bucket 31: 50%\n bucket 30: 60%\n bucket 31: 60%\n bucket 30: 70%\n bucket 31: 70%\n bucket 30: 80%\n bucket 31: 80%\n bucket 30: 90%\n bucket 31: 90%\n bucket 30: 100%\n Sorting block of length 345 for bucket 30\n (Using difference cover)\n bucket 31: 100%\n Sorting block of length 377 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 346 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 378 for bucket 31\nGetting block 32 of 58\n Reserving size (388) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block\n..\n0:00\nReturning block of 350 for bucket 23\nGetting block 24 of 57\n Reserving size (388) 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 245 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 246 for bucket 24\nGetting block 25 of 57\n Reserving size (388) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 25:\nGetting block 26 of 57\n bucket 25: 10%\n Reserving size (388) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\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 26: 30%\n bucket 25: 60%\n bucket 26: 40%\n bucket 26: 50%\n bucket 25: 70%\n bucket 26: 60%\n bucket 25: 80%\n bucket 26: 70%\n bucket 26: 80%\n bucket 25: 90%\n bucket 26: 90%\n bucket 25: 100%\n Sorting block of length 286 for bucket 25\n (Using difference cover)\n bucket 26: 100%\n Sorting block of length 384 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 287 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 385 for bucket 26\nGetting block 27 of 57\n Reserving size (388) for bucket 27\nGetting block 28 of 57\n Calculating Z arrays for bucket 27\n Reserving size (388) for bucket 28\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 28: 30%\n bucket 27: 30%\n bucket 28: 40%\n bucket 27: 40%\n bucket 28: 50%\n bucket 27: 50%\n bucket 28: 60%\n bucket 27: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 27: 70%\n bucket 28: 90%\n bucket 27: 80%\n bucket 28: 100%\n Sorting block of length 387 for bucket 28\n (Using difference cover)\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 359 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 360 for bucket 27\nGetting block 29 of 57\n Reserving size (388) 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 195 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 29\nGetting block 30 of 57\n Reserving size (388) for bucket 30\nGetting block 31 of 57\n Calculating Z arrays for bucket 30\n Reserving size (388) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 31:\n Entering block accumulator loop for bucket 30:\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 30: 40%\n bucket 31: 50%\n bucket 30: 50%\n bucket 31: 60%\n bucket 30: 60%\n bucket 31: 70%\n bucket 30: 70%\n bucket 31: 80%\n bucket 30: 80%\n bucket 31: 90%\n bucket 30: 90%\n bucket 31: 100%\n Sorting block of length 310 for bucket 31\n (Using difference cover)\n bucket 30: 100%\n Sorting block of length 257 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 311 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 258 for bucket 30\nGetting block 32 of 57\n Reserving size (388) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 32:\nGetting block 33 of 57\n bucket 32: 10%\n Reserving size (388) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 33:\n bucket 32: 20%\n bucket 33: 10%\n bucket 32: 30%\n bucket 33: 20%\n bucket 32: 40%\n bucket 33: 30%\n bucket 32: 50%\n bucket 33: 40%\n bucket 32: 60%\n bucket 32: 70%\n bucket 33: 50%\n bucket 32: 80%\n bucket 33: 60%\n bucket 32: 90%\n bucket 33: 70%\n bucket 32: 100%\n Sorting block of length 219 for bucket 32\n (Using difference cover)\n bucket 33: 80%\n bucket 33: 90%\n bucket 33: 100%\n Sorting block time: 00:00:00\n Sorting block of length 387 for bucket 33\n (Using difference cover)\nReturning block of 220 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 33\nGetting block 34 of 57\n Reserving size (388) for bucket 34\nGetting block 35 of 57\n Calculating Z arrays for bucket 34\n Reserving size (388) 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 35: 10%\n bucket 34: 20%\n bucket 34: 30%\n bucket 35: 20%\n bucket 34: 40%\n bucket 35: 30%\n bucket 34: 50%\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 275 for bucket 34\n (Using difference cover)\n bucket 35: 80%\n bucket 35: 90%\n Sorting block time: 00:00:00\nReturning block of 276 for bucket 34\n bucket 35: 100%\n Sorting block of length 350 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 351 for bucket 35\nGetting block 36 of 57\n Reserving size (388) 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 150 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 151 for bucket 36\nGetting block 37 of 57\n Reserving size (388) for bucket 37\n Calculating Z arrays for bucket 37\nGetting block 38 of 57\n Entering block accumulator loop for bucket 37:\n Reserving size (388) for bucket 38\n Calculating Z arrays for bucket 38\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 37: 40%\n bucket 38: 50%\n bucket 37: 50%\n bucket 38: 60%\n bucket 38: 70%\n bucket 37: 60%\n bucket 38: 80%\n bucket 38: 90%\n bucket 37: 70%\n bucket 38: 100%\n Sorting block of length 337 for bucket 38\n (Using difference cover)\n bucket 37: 80%\n Sorting block time: 00:00:00\nReturning block of 338 for bucket 38\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 267 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 268 for bucket 37\nGetting block 39 of 57\n Reserving size (388) for bucket 39\n Calculating Z arrays for bucket 39\n Entering block accumulator loop for bucket 39:\nGetting block 40 of 57\n Reserving size (388) for bucket 40\n Calculating Z arrays for bucket 40\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 40: 30%\n bucket 39: 30%\n bucket 40: 40%\n bucket 39: 40%\n bucket 40: 50%\n bucket 39: 50%\n bucket 40: 60%\n bucket 40: 70%\n bucket 39: 60%\n bucket 40: 80%\n bucket 39: 70%\n bucket 40: 90%\n bucket 40: 100%\n bucket 39: 80%\n Sorting block of length 379 for bucket 40\n (Using difference cover)\n bucket 39: 90%\n bucket 39: 100%\n Sorting block of length 387 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 380 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 39\nGetting block 41 of 57\n Reserving size (388) for bucket 41\n Calculating Z arrays for bucket 41\nGetting block 42 of 57\n Entering block accumulator loop for bucket 41:\n Reserving size (388) for bucket 42\n Calculating Z arrays for bucket 42\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 41: 70%\n bucket 42: 50%\n bucket 41: 80%\n bucket 42: 60%\n bucket 41: 90%\n bucket 41: 100%\n bucket 42: 70%\n Sorting block of length 330 for bucket 41\n (Using difference cover)\n bucket 42: 80%\n bucket 42: 90%\n Sorting block time: 00:00:00\nReturning block of 331 for bucket 41\n bucket 42: 100%\n Sorting block of length 188 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 189 for bucket 42\nGetting block 43 of 57\n Reserving size (388) for bucket 43\n Calculating Z arrays for bucket 43\n Entering block accumulator loop for bucket 43:\n bucket 43: 10%\nGetting block 44 of 57\n Reserving size (388) for bucket 44\n Calculating Z arrays for bucket 44\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 44: 40%\n bucket 43: 60%\n bucket 44: 50%\n bucket 43: 70%\n bucket 44: 60%\n bucket 43: 80%\n bucket 43: 90%\n bucket 44: 70%\n bucket 43: 100%\n Sorting block of length 321 for bucket 43\n (Using difference cover)\n bucket 44: 80%\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 366 for bucket 44\n Sorting block time: 00:00:00\n (Using difference cover)\nReturning block of 322 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 367 for bucket 44\nGetting block 45 of 57\n Reserving size (388) 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 365 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 366 for bucket 45\nGetting block 46 of 57\n Reserving size (388) for bucket 46\nGetting block 47 of 57\n Calculating Z arrays for bucket 46\n Reserving size (388) 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 47: 10%\n bucket 46: 20%\n bucket 47: 20%\n bucket 46: 30%\n bucket 47: 30%\n bucket 46: 40%\n bucket 46: 50%\n bucket 47: 40%\n bucket 46: 60%\n bucket 47: 50%\n bucket 46: 70%\n bucket 47: 60%\n bucket 46: 80%\n bucket 47: 70%\n bucket 46: 90%\n bucket 47: 80%\n bucket 46: 100%\n Sorting block of length 253 for bucket 46\n (Using difference cover)\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 217 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 254 for bucket 46\n Sorting block time: 00:00:00\nReturning block of 218 for bucket 47\nGetting block 48 of 57\n Reserving size (388) for bucket 48\nGetting block 49 of 57\n Calculating Z arrays for bucket 48\n Reserving size (388) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 48:\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\n bucket 48: 10%\n bucket 48: 20%\n bucket 49: 20%\n bucket 48: 30%\n bucket 49: 30%\n bucket 49: 40%\n bucket 48: 40%\n bucket 49: 50%\n bucket 48: 50%\n bucket 49: 60%\n bucket 48: 60%\n bucket 49: 70%\n bucket 48: 70%\n bucket 49: 80%\n bucket 48: 80%\n bucket 49: 90%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 384 for bucket 48\n (Using difference cover)\n bucket 49: 100%\n Sorting block of length 112 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 385 for bucket 48\nGetting block 50 of 57\n Reserving size (388) 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 57\n bucket 50: 20%\n Reserving size (388) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 51:\n bucket 50: 30%\n bucket 51: 10%\n bucket 50: 40%\n bucket 51: 20%\n bucket 50: 50%\n bucket 51: 30%\n bucket 50: 60%\n bucket 51: 40%\n bucket 50: 70%\n bucket 51: 50%\n bucket 50: 80%\n bucket 51: 60%\n bucket 50: 90%\n bucket 51: 70%\n bucket 50: 100%\n bucket 51: 80%\n Sorting block of length 275 for bucket 50\n (Using difference cover)\n bucket 51: 90%\n bucket 51: 100%\n Sorting block of length 350 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 276 for bucket 50\n Sorting block time: 00:00:00\nReturning block of 351 for bucket 51\nGetting block 52 of 57\n Reserving size (388) for bucket 52\n Calculating Z arrays for bucket 52\nGetting block 53 of 57\n Reserving size (388) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 52:\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\n bucket 52: 10%\n bucket 53: 20%\n bucket 52: 20%\n bucket 53: 30%\n bucket 53: 40%\n bucket 52: 30%\n bucket 53: 50%\n bucket 53: 60%\n bucket 52: 40%\n bucket 53: 70%\n bucket 52: 50%\n bucket 53: 80%\n bucket 52: 60%\n bucket 53: 90%\n bucket 52: 70%\n bucket 53: 100%\n Sorting block of length 370 for bucket 53\n (Using difference cover)\n bucket 52: 80%\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 378 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 371 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 379 for bucket 52\nGetting block 54 of 57\n Reserving size (388) 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 237 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 238 for bucket 54\nGetting block 55 of 57\n Reserving size (388) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\nGetting block 56 of 57\n Reserving size (388) for bucket 56\n bucket 55: 10%\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 56:\n bucket 55: 20%\n bucket 56: 10%\n bucket 56: 20%\n bucket 56: 30%\n bucket 55: 30%\n bucket 56: 40%\n bucket 56: 50%\n bucket 56: 60%\n bucket 55: 40%\n bucket 56: 70%\n bucket 55: 50%\n bucket 56: 80%\n bucket 55: 60%\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 270 for bucket 56\n (Using difference cover)\n bucket 55: 70%\n bucket 55: 80%\n bucket 55: 90%\n Sorting block time: 00:00:00\nReturning block of 271 for bucket 56\n bucket 55: 100%\n Sorting block of length 344 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 345 for bucket 55\nGetting block 57 of 57\n Reserving size (388) 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 132 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 133 for bucket 57\nExited Ebwt loop\nfchr[A]: 0\nfchr[C]: 5124\nfchr[G]: 10305\nfchr[T]: 12474\nfchr[$]: 16568\nExiting Ebwt::buildToDisk()\nReturning from initFromVector\nWrote 4200050 bytes to primary EBWT file: genome.rev.1.bt2.tmp\nWrote 4148 bytes to secondary EBWT file: genome.rev.2.bt2.tmp\nRe-opening _in1 and _in2 as input streams\nReturning from Ebwt constructor\nHeaders:\n len: 16568\n bwtLen: 16569\n sz: 4142\n bwtSz: 4143\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 20\n eftabSz: 80\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 1036\n offsSz: 4144\n lineSz: 64\n sideSz: 64\n sideBwtSz: 48\n sideBwtLen: 192\n numSides: 87\n numLines: 87\n ebwtTotLen: 5568\n ebwtTotSz: 5568\n color: 0\n reverse: 1\nTotal time for backward call to driver() for mirror index: 00:00:01\n", "tool_stderr": "Building a SMALL index\nRenaming genome.3.bt2.tmp to genome.3.bt2\nRenaming genome.4.bt2.tmp to genome.4.bt2\nRenaming genome.1.bt2.tmp to genome.1.bt2\nRenaming genome.2.bt2.tmp to genome.2.bt2\nRenaming genome.rev.1.bt2.tmp to genome.rev.1.bt2\nRenaming genome.rev.2.bt2.tmp to genome.rev.2.bt2\n100 reads; of these:\n 100 (100.00%) were paired; of these:\n 97 (97.00%) aligned concordantly 0 times\n 3 (3.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 97 pairs aligned concordantly 0 times; of these:\n 8 (8.25%) aligned discordantly 1 time\n ----\n 89 pairs aligned 0 times concordantly or discordantly; of these:\n 178 mates make up the pairs; of these:\n 153 (85.96%) aligned 0 times\n 25 (14.04%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n23.50% overall alignment rate\n", "job_stdout": "", "job_stderr": "", "stdout": "Settings:\n Output files: \"genome.*.bt2\"\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 Max bucket size: default\n Max bucket size, sqrt multiplier: default\n Max bucket size, len divisor: 32\n Difference-cover sample period: 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 /galaxy/server/database/objects/1/8/c/dataset_18cea05d-389e-4888-9714-2faa6a33420f.dat\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\nbmax according to bmaxDivN setting: 517\nUsing parameters --bmax 388 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 388 --dcv 1024\nConstructing suffix-array element generator\nBuilding DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 86 sample suffixes\nGenerating random suffixes\nQSorting 86 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 86 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 12, merged 41; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 6; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 284.672 (target: 387)\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering Ebwt loop\nGetting block 1 of 58\n Reserving size (388) for bucket 1\nGetting block 2 of 58\nGetting block 3 of 58\nGetting block 4 of 58\nGetting block 5 of 58\n Calculating Z arrays for bucket 1\n Reserving size (388) for bucket 2\n Reserving size (388) for bucket 3\n Reserving size (388) for bucket 4\n Reserving size (388) for bucket 5\nGetting block 6 of 58\nGetting block 7 of 58\n Entering block accumulator loop for bucket 1:\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 3\n Calculating Z arrays for bucket 4\n Calculating Z arrays for bucket 5\n Reserving size (388) for bucket 6\n Reserving size (388) for bucket 7\n Entering block accumulator loop for bucket 2:\n Entering block accumulator loop for bucket 4:\n Calculating Z arrays for bucket 6\n Entering block accumulator loop for bucket 5:\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 3:\n bucket 1: 10%\n Entering block accumulator loop for bucket 6:\n Entering block accumulator loop for bucket 7:\n bucket 5: 10%\n bucket 1: 20%\n bucket 4: 10%\n bucket 2: 10%\n bucket 3: 10%\n bucket 1: 30%\n bucket 5: 20%\n bucket 4: 20%\n bucket 2: 20%\n bucket 6: 10%\n bucket 1: 40%\n bucket 5: 30%\n bucket 3: 20%\n bucket 4: 30%\n bucket 7: 10%\n bucket 1: 50%\n bucket 5: 40%\n bucket 2: 30%\n bucket 4: 40%\n bucket 3: 30%\n bucket 1: 60%\n bucket 7: 20%\n bucket 5: 50%\n bucket 4: 50%\n bucket 1: 70%\n bucket 6: 20%\n bucket 3: 40%\n bucket 2: 40%\n bucket 5: 60%\n bucket 4: 60%\n bucket 1: 80%\n bucket 7: 30%\n bucket 3: 50%\n bucket 5: 70%\n bucket 4: 70%\n bucket 1: 90%\n bucket 6: 30%\n bucket 2: 50%\n bucket 5: 80%\n bucket 7: 40%\n bucket 1: 100%\n bucket 4: 80%\n bucket 3: 60%\n Sorting block of length 355 for bucket 1\n (Using difference cover)\n bucket 2: 60%\n bucket 6: 40%\n bucket 5: 90%\n bucket 4: 90%\n bucket 3: 70%\n bucket 7: 50%\n bucket 5: 100%\n Sorting block of length 203 for bucket 5\n (Using difference cover)\n bucket 2: 70%\n bucket 4: 100%\n Sorting block of length 328 for bucket 4\n (Using difference cover)\n bucket 6: 50%\n bucket 3: 80%\n bucket 2: 80%\n bucket 7: 60%\n bucket 6: 60%\n bucket 3: 90%\n bucket 2: 90%\n bucket 7: 70%\n bucket 6: 70%\n bucket 3: 100%\n bucket 2: 100%\n Sorting block of length 370 for bucket 3\n (Using difference cover)\n Sorting block of length 165 for bucket 2\n (Using difference cover)\n bucket 7: 80%\n bucket 6: 80%\n bucket 7: 90%\n bucket 6: 90%\n Sorting block time: 00:00:00\nReturning block of 356 for bucket 1\n bucket 7: 100%\n bucket 6: 100%\n Sorting block of length 368 for bucket 7\n (Using difference cover)\n Sorting block of length 339 for bucket 6\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 369 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 204 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 371 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 329 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 166 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 6\nGetting block 8 of 58\n Reserving size (388) for bucket 8\n Calculating Z arrays for bucket 8\n Entering block accumulator loop for bucket 8:\nGetting block 9 of 58\n bucket 8: 10%\n Reserving size (388) for bucket 9\n Calculating Z arrays for bucket 9\nGetting block 10 of 58\n Reserving size (388) for bucket 10\n Calculating Z arrays for bucket 10\n bucket 8: 20%\n Entering block accumulator loop for bucket 9:\n Entering block accumulator loop for bucket 10:\n bucket 8: 30%\n bucket 9: 10%\n bucket 8: 40%\n bucket 10: 10%\n bucket 9: 20%\n bucket 8: 50%\n bucket 10: 20%\n bucket 9: 30%\n bucket 10: 30%\n bucket 8: 60%\n bucket 9: 40%\n bucket 10: 40%\n bucket 8: 70%\n bucket 9: 50%\n bucket 10: 50%\n bucket 8: 80%\n bucket 9: 60%\n bucket 10: 60%\n bucket 9: 70%\n bucket 8: 90%\n bucket 10: 70%\n bucket 9: 80%\n bucket 10: 80%\n bucket 8: 100%\n Sorting block of length 171 for bucket 8\n (Using difference cover)\n bucket 9: 90%\n bucket 10: 90%\n bucket 9: 100%\n Sorting block of length 339 for bucket 9\n (Using difference cover)\n bucket 10: 100%\n Sorting block of length 357 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 358 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 172 for bucket 8\nGetting block 11 of 58\n Reserving size (388) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\n bucket 11: 10%\nGetting block 12 of 58\n Reserving size (388) for bucket 12\n Calculating Z arrays for bucket 12\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 11: 70%\n bucket 12: 40%\n bucket 11: 80%\n bucket 12: 50%\n bucket 11: 90%\n bucket 12: 60%\n bucket 11: 100%\n Sorting block of length 305 for bucket 11\n (Using difference cover)\n bucket 12: 70%\n bucket 12: 80%\n bucket 12: 90%\n Sorting block time: 00:00:00\nReturning block of 306 for bucket 11\n bucket 12: 100%\n Sorting block of length 185 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 186 for bucket 12\nGetting block 13 of 58\n Reserving size (388) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\nGetting block 14 of 58\n Reserving size (388) for bucket 14\n Calculating Z arrays for bucket 14\n bucket 13: 20%\n Entering block accumulator loop for bucket 14:\n bucket 13: 30%\n bucket 14: 10%\n bucket 13: 40%\n bucket 14: 20%\n bucket 13: 50%\n bucket 14: 30%\n bucket 13: 60%\n bucket 14: 40%\n bucket 13: 70%\n bucket 14: 50%\n bucket 13: 80%\n bucket 13: 90%\n bucket 14: 60%\n bucket 13: 100%\n Sorting block of length 282 for bucket 13\n (Using difference cover)\n bucket 14: 70%\n bucket 14: 80%\n bucket 14: 90%\n Sorting block time: 00:00:00\nReturning block of 283 for bucket 13\n bucket 14: 100%\n Sorting block of length 339 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 14\nGetting block 15 of 58\n Reserving size (388) 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 58\n Reserving size (388) 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 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 241 for bucket 15\n (Using difference cover)\n bucket 16: 50%\n bucket 16: 60%\n Sorting block time: 00:00:00\nReturning block of 242 for bucket 15\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 379 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 380 for bucket 16\nGetting block 17 of 58\n Reserving size (388) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\nGetting block 18 of 58\n Reserving size (388) for bucket 18\n Calculating Z arrays for bucket 18\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 17: 60%\n bucket 18: 30%\n bucket 17: 70%\n bucket 18: 40%\n bucket 17: 80%\n bucket 18: 50%\n bucket 17: 90%\n bucket 18: 60%\n bucket 17: 100%\n Sorting block of length 215 for bucket 17\n (Using difference cover)\n bucket 18: 70%\n bucket 18: 80%\n Sorting block time: 00:00:00\nReturning block of 216 for bucket 17\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 378 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 379 for bucket 18\nGetting block 19 of 58\n Reserving size (388) for bucket 19\nGetting block 20 of 58\n Calculating Z arrays for bucket 19\n Reserving size (388) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 19:\n Entering block accumulator loop for bucket 20:\n bucket 19: 10%\n bucket 20: 10%\n bucket 19: 20%\n bucket 20: 20%\n bucket 19: 30%\n bucket 20: 30%\n bucket 19: 40%\n bucket 20: 40%\n bucket 19: 50%\n bucket 20: 50%\n bucket 19: 60%\n bucket 20: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 20: 70%\n bucket 19: 90%\n bucket 20: 80%\n bucket 19: 100%\n Sorting block of length 334 for bucket 19\n (Using difference cover)\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 313 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 335 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 314 for bucket 20\nGetting block 21 of 58\n Reserving size (388) for bucket 21\nGetting block 22 of 58\n Calculating Z arrays for bucket 21\n Reserving size (388) 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 22: 10%\n bucket 21: 10%\n bucket 22: 20%\n bucket 21: 20%\n bucket 22: 30%\n bucket 21: 30%\n bucket 22: 40%\n bucket 21: 40%\n bucket 22: 50%\n bucket 21: 50%\n bucket 22: 60%\n bucket 22: 70%\n bucket 21: 60%\n bucket 22: 80%\n bucket 21: 70%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 386 for bucket 22\n (Using difference cover)\n bucket 21: 80%\n bucket 21: 90%\n Sorting block time: 00:00:00\n bucket 21: 100%\nReturning block of 387 for bucket 22\n Sorting block of length 210 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 211 for bucket 21\nGetting block 23 of 58\n Reserving size (388) 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 238 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 239 for bucket 23\nGetting block 24 of 58\n Reserving size (388) 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 58\n Reserving size (388) for bucket 25\n Calculating Z arrays for bucket 25\n bucket 24: 20%\n Entering block accumulator loop for bucket 25:\n bucket 24: 30%\n bucket 25: 10%\n bucket 24: 40%\n bucket 25: 20%\n bucket 24: 50%\n bucket 25: 30%\n bucket 25: 40%\n bucket 24: 60%\n bucket 25: 50%\n bucket 24: 70%\n bucket 24: 80%\n bucket 25: 60%\n bucket 24: 90%\n bucket 25: 70%\n bucket 24: 100%\n Sorting block of length 351 for bucket 24\n (Using difference cover)\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 105 for bucket 25\n Sorting block time: 00:00:00\n (Using difference cover)\nReturning block of 352 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 106 for bucket 25\nGetting block 26 of 58\n Reserving size (388) 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%\nGetting block 27 of 58\n bucket 26: 40%\n Reserving size (388) for bucket 27\n bucket 26: 50%\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n bucket 26: 60%\n bucket 26: 70%\n bucket 27: 10%\n bucket 26: 80%\n bucket 27: 20%\n bucket 26: 90%\n bucket 27: 30%\n bucket 26: 100%\n Sorting block of length 354 for bucket 26\n (Using difference cover)\n bucket 27: 40%\n bucket 27: 50%\n bucket 27: 60%\n Sorting block time: 00:00:00\nReturning block of 355 for bucket 26\n bucket 27: 70%\n bucket 27: 80%\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 334 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 335 for bucket 27\nGetting block 28 of 58\n Reserving size (388) 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%\nGetting block 29 of 58\n Reserving size (388) for bucket 29\n Calculating Z arrays for bucket 29\n bucket 28: 30%\n Entering block accumulator loop for bucket 29:\n bucket 28: 40%\n bucket 28: 50%\n bucket 29: 10%\n bucket 28: 60%\n bucket 28: 70%\n bucket 29: 20%\n bucket 28: 80%\n bucket 28: 90%\n bucket 29: 30%\n bucket 28: 100%\n Sorting block of length 253 for bucket 28\n (Using difference cover)\n bucket 29: 40%\n bucket 29: 50%\n Sorting block time: 00:00:00\nReturning block of 254 for bucket 28\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 289 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 290 for bucket 29\nGetting block 30 of 58\n Reserving size (388) for bucket 30\nGetting block 31 of 58\n Calculating Z arrays for bucket 30\n Reserving size (388) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 31:\n Entering block accumulator loop for bucket 30:\n bucket 31: 10%\n bucket 30: 10%\n bucket 30: 20%\n bucket 31: 20%\n bucket 30: 30%\n bucket 31: 30%\n bucket 30: 40%\n bucket 31: 40%\n bucket 30: 50%\n bucket 31: 50%\n bucket 30: 60%\n bucket 31: 60%\n bucket 30: 70%\n bucket 31: 70%\n bucket 30: 80%\n bucket 31: 80%\n bucket 30: 90%\n bucket 31: 90%\n bucket 30: 100%\n Sorting block of length 345 for bucket 30\n (Using difference cover)\n bucket 31: 100%\n Sorting block of length 377 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 346 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 378 for bucket 31\nGetting block 32 of 58\n Reserving size (388) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block\n..\n0:00\nReturning block of 350 for bucket 23\nGetting block 24 of 57\n Reserving size (388) 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 245 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 246 for bucket 24\nGetting block 25 of 57\n Reserving size (388) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 25:\nGetting block 26 of 57\n bucket 25: 10%\n Reserving size (388) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\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 26: 30%\n bucket 25: 60%\n bucket 26: 40%\n bucket 26: 50%\n bucket 25: 70%\n bucket 26: 60%\n bucket 25: 80%\n bucket 26: 70%\n bucket 26: 80%\n bucket 25: 90%\n bucket 26: 90%\n bucket 25: 100%\n Sorting block of length 286 for bucket 25\n (Using difference cover)\n bucket 26: 100%\n Sorting block of length 384 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 287 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 385 for bucket 26\nGetting block 27 of 57\n Reserving size (388) for bucket 27\nGetting block 28 of 57\n Calculating Z arrays for bucket 27\n Reserving size (388) for bucket 28\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 28: 30%\n bucket 27: 30%\n bucket 28: 40%\n bucket 27: 40%\n bucket 28: 50%\n bucket 27: 50%\n bucket 28: 60%\n bucket 27: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 27: 70%\n bucket 28: 90%\n bucket 27: 80%\n bucket 28: 100%\n Sorting block of length 387 for bucket 28\n (Using difference cover)\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 359 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 360 for bucket 27\nGetting block 29 of 57\n Reserving size (388) 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 195 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 29\nGetting block 30 of 57\n Reserving size (388) for bucket 30\nGetting block 31 of 57\n Calculating Z arrays for bucket 30\n Reserving size (388) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 31:\n Entering block accumulator loop for bucket 30:\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 30: 40%\n bucket 31: 50%\n bucket 30: 50%\n bucket 31: 60%\n bucket 30: 60%\n bucket 31: 70%\n bucket 30: 70%\n bucket 31: 80%\n bucket 30: 80%\n bucket 31: 90%\n bucket 30: 90%\n bucket 31: 100%\n Sorting block of length 310 for bucket 31\n (Using difference cover)\n bucket 30: 100%\n Sorting block of length 257 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 311 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 258 for bucket 30\nGetting block 32 of 57\n Reserving size (388) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 32:\nGetting block 33 of 57\n bucket 32: 10%\n Reserving size (388) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 33:\n bucket 32: 20%\n bucket 33: 10%\n bucket 32: 30%\n bucket 33: 20%\n bucket 32: 40%\n bucket 33: 30%\n bucket 32: 50%\n bucket 33: 40%\n bucket 32: 60%\n bucket 32: 70%\n bucket 33: 50%\n bucket 32: 80%\n bucket 33: 60%\n bucket 32: 90%\n bucket 33: 70%\n bucket 32: 100%\n Sorting block of length 219 for bucket 32\n (Using difference cover)\n bucket 33: 80%\n bucket 33: 90%\n bucket 33: 100%\n Sorting block time: 00:00:00\n Sorting block of length 387 for bucket 33\n (Using difference cover)\nReturning block of 220 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 33\nGetting block 34 of 57\n Reserving size (388) for bucket 34\nGetting block 35 of 57\n Calculating Z arrays for bucket 34\n Reserving size (388) 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 35: 10%\n bucket 34: 20%\n bucket 34: 30%\n bucket 35: 20%\n bucket 34: 40%\n bucket 35: 30%\n bucket 34: 50%\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 275 for bucket 34\n (Using difference cover)\n bucket 35: 80%\n bucket 35: 90%\n Sorting block time: 00:00:00\nReturning block of 276 for bucket 34\n bucket 35: 100%\n Sorting block of length 350 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 351 for bucket 35\nGetting block 36 of 57\n Reserving size (388) 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 150 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 151 for bucket 36\nGetting block 37 of 57\n Reserving size (388) for bucket 37\n Calculating Z arrays for bucket 37\nGetting block 38 of 57\n Entering block accumulator loop for bucket 37:\n Reserving size (388) for bucket 38\n Calculating Z arrays for bucket 38\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 37: 40%\n bucket 38: 50%\n bucket 37: 50%\n bucket 38: 60%\n bucket 38: 70%\n bucket 37: 60%\n bucket 38: 80%\n bucket 38: 90%\n bucket 37: 70%\n bucket 38: 100%\n Sorting block of length 337 for bucket 38\n (Using difference cover)\n bucket 37: 80%\n Sorting block time: 00:00:00\nReturning block of 338 for bucket 38\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 267 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 268 for bucket 37\nGetting block 39 of 57\n Reserving size (388) for bucket 39\n Calculating Z arrays for bucket 39\n Entering block accumulator loop for bucket 39:\nGetting block 40 of 57\n Reserving size (388) for bucket 40\n Calculating Z arrays for bucket 40\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 40: 30%\n bucket 39: 30%\n bucket 40: 40%\n bucket 39: 40%\n bucket 40: 50%\n bucket 39: 50%\n bucket 40: 60%\n bucket 40: 70%\n bucket 39: 60%\n bucket 40: 80%\n bucket 39: 70%\n bucket 40: 90%\n bucket 40: 100%\n bucket 39: 80%\n Sorting block of length 379 for bucket 40\n (Using difference cover)\n bucket 39: 90%\n bucket 39: 100%\n Sorting block of length 387 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 380 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 39\nGetting block 41 of 57\n Reserving size (388) for bucket 41\n Calculating Z arrays for bucket 41\nGetting block 42 of 57\n Entering block accumulator loop for bucket 41:\n Reserving size (388) for bucket 42\n Calculating Z arrays for bucket 42\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 41: 70%\n bucket 42: 50%\n bucket 41: 80%\n bucket 42: 60%\n bucket 41: 90%\n bucket 41: 100%\n bucket 42: 70%\n Sorting block of length 330 for bucket 41\n (Using difference cover)\n bucket 42: 80%\n bucket 42: 90%\n Sorting block time: 00:00:00\nReturning block of 331 for bucket 41\n bucket 42: 100%\n Sorting block of length 188 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 189 for bucket 42\nGetting block 43 of 57\n Reserving size (388) for bucket 43\n Calculating Z arrays for bucket 43\n Entering block accumulator loop for bucket 43:\n bucket 43: 10%\nGetting block 44 of 57\n Reserving size (388) for bucket 44\n Calculating Z arrays for bucket 44\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 44: 40%\n bucket 43: 60%\n bucket 44: 50%\n bucket 43: 70%\n bucket 44: 60%\n bucket 43: 80%\n bucket 43: 90%\n bucket 44: 70%\n bucket 43: 100%\n Sorting block of length 321 for bucket 43\n (Using difference cover)\n bucket 44: 80%\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 366 for bucket 44\n Sorting block time: 00:00:00\n (Using difference cover)\nReturning block of 322 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 367 for bucket 44\nGetting block 45 of 57\n Reserving size (388) 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 365 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 366 for bucket 45\nGetting block 46 of 57\n Reserving size (388) for bucket 46\nGetting block 47 of 57\n Calculating Z arrays for bucket 46\n Reserving size (388) 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 47: 10%\n bucket 46: 20%\n bucket 47: 20%\n bucket 46: 30%\n bucket 47: 30%\n bucket 46: 40%\n bucket 46: 50%\n bucket 47: 40%\n bucket 46: 60%\n bucket 47: 50%\n bucket 46: 70%\n bucket 47: 60%\n bucket 46: 80%\n bucket 47: 70%\n bucket 46: 90%\n bucket 47: 80%\n bucket 46: 100%\n Sorting block of length 253 for bucket 46\n (Using difference cover)\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 217 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 254 for bucket 46\n Sorting block time: 00:00:00\nReturning block of 218 for bucket 47\nGetting block 48 of 57\n Reserving size (388) for bucket 48\nGetting block 49 of 57\n Calculating Z arrays for bucket 48\n Reserving size (388) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 48:\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\n bucket 48: 10%\n bucket 48: 20%\n bucket 49: 20%\n bucket 48: 30%\n bucket 49: 30%\n bucket 49: 40%\n bucket 48: 40%\n bucket 49: 50%\n bucket 48: 50%\n bucket 49: 60%\n bucket 48: 60%\n bucket 49: 70%\n bucket 48: 70%\n bucket 49: 80%\n bucket 48: 80%\n bucket 49: 90%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 384 for bucket 48\n (Using difference cover)\n bucket 49: 100%\n Sorting block of length 112 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 385 for bucket 48\nGetting block 50 of 57\n Reserving size (388) 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 57\n bucket 50: 20%\n Reserving size (388) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 51:\n bucket 50: 30%\n bucket 51: 10%\n bucket 50: 40%\n bucket 51: 20%\n bucket 50: 50%\n bucket 51: 30%\n bucket 50: 60%\n bucket 51: 40%\n bucket 50: 70%\n bucket 51: 50%\n bucket 50: 80%\n bucket 51: 60%\n bucket 50: 90%\n bucket 51: 70%\n bucket 50: 100%\n bucket 51: 80%\n Sorting block of length 275 for bucket 50\n (Using difference cover)\n bucket 51: 90%\n bucket 51: 100%\n Sorting block of length 350 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 276 for bucket 50\n Sorting block time: 00:00:00\nReturning block of 351 for bucket 51\nGetting block 52 of 57\n Reserving size (388) for bucket 52\n Calculating Z arrays for bucket 52\nGetting block 53 of 57\n Reserving size (388) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 52:\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\n bucket 52: 10%\n bucket 53: 20%\n bucket 52: 20%\n bucket 53: 30%\n bucket 53: 40%\n bucket 52: 30%\n bucket 53: 50%\n bucket 53: 60%\n bucket 52: 40%\n bucket 53: 70%\n bucket 52: 50%\n bucket 53: 80%\n bucket 52: 60%\n bucket 53: 90%\n bucket 52: 70%\n bucket 53: 100%\n Sorting block of length 370 for bucket 53\n (Using difference cover)\n bucket 52: 80%\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 378 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 371 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 379 for bucket 52\nGetting block 54 of 57\n Reserving size (388) 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 237 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 238 for bucket 54\nGetting block 55 of 57\n Reserving size (388) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\nGetting block 56 of 57\n Reserving size (388) for bucket 56\n bucket 55: 10%\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 56:\n bucket 55: 20%\n bucket 56: 10%\n bucket 56: 20%\n bucket 56: 30%\n bucket 55: 30%\n bucket 56: 40%\n bucket 56: 50%\n bucket 56: 60%\n bucket 55: 40%\n bucket 56: 70%\n bucket 55: 50%\n bucket 56: 80%\n bucket 55: 60%\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 270 for bucket 56\n (Using difference cover)\n bucket 55: 70%\n bucket 55: 80%\n bucket 55: 90%\n Sorting block time: 00:00:00\nReturning block of 271 for bucket 56\n bucket 55: 100%\n Sorting block of length 344 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 345 for bucket 55\nGetting block 57 of 57\n Reserving size (388) 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 132 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 133 for bucket 57\nExited Ebwt loop\nfchr[A]: 0\nfchr[C]: 5124\nfchr[G]: 10305\nfchr[T]: 12474\nfchr[$]: 16568\nExiting Ebwt::buildToDisk()\nReturning from initFromVector\nWrote 4200050 bytes to primary EBWT file: genome.rev.1.bt2.tmp\nWrote 4148 bytes to secondary EBWT file: genome.rev.2.bt2.tmp\nRe-opening _in1 and _in2 as input streams\nReturning from Ebwt constructor\nHeaders:\n len: 16568\n bwtLen: 16569\n sz: 4142\n bwtSz: 4143\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 20\n eftabSz: 80\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 1036\n offsSz: 4144\n lineSz: 64\n sideSz: 64\n sideBwtSz: 48\n sideBwtLen: 192\n numSides: 87\n numLines: 87\n ebwtTotLen: 5568\n ebwtTotSz: 5568\n color: 0\n reverse: 1\nTotal time for backward call to driver() for mirror index: 00:00:01\n", "stderr": "Building a SMALL index\nRenaming genome.3.bt2.tmp to genome.3.bt2\nRenaming genome.4.bt2.tmp to genome.4.bt2\nRenaming genome.1.bt2.tmp to genome.1.bt2\nRenaming genome.2.bt2.tmp to genome.2.bt2\nRenaming genome.rev.1.bt2.tmp to genome.rev.1.bt2\nRenaming genome.rev.2.bt2.tmp to genome.rev.2.bt2\n100 reads; of these:\n 100 (100.00%) were paired; of these:\n 97 (97.00%) aligned concordantly 0 times\n 3 (3.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 97 pairs aligned concordantly 0 times; of these:\n 8 (8.25%) aligned discordantly 1 time\n ----\n 89 pairs aligned 0 times concordantly or discordantly; of these:\n 178 mates make up the pairs; of these:\n 153 (85.96%) aligned 0 times\n 25 (14.04%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n23.50% overall alignment rate\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-08 18:53:33", "plugin": "core", "name": "end_epoch", "raw_value": "1731092013.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 18:53:32", "plugin": "core", "name": "start_epoch", "raw_value": "1731092012.0000000"}, {"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": "bowtie2/2.5.3+galaxy1-6", "has_data": true, "data": {"tool_id": "bowtie2", "tool_version": "2.5.3+galaxy1", "test_index": 6, "time_seconds": 43.469274282455444, "inputs": {"library|input_1": {"src": "hda", "id": "fcfbfc0cad7773e1"}, "library|input_2": {"src": "hda", "id": "d49b9c201a58b5b5"}, "library|unaligned_file": false, "library|paired_options|paired_options_selector": "no", "library|type": "paired", "reference_genome|own_file": {"src": "hda", "id": "5eb0676f0cd5a893"}, "reference_genome|source": "history", "analysis_type|analysis_type_selector": "simple"}, "job": {"model_class": "Job", "id": "d49b9c201a58b5b5", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T18:54:14.617434", "update_time": "2024-11-08T18:54:29.454644", "galaxy_version": "24.1", "external_id": "gxy-pwnps", "handler": null, "job_runner_name": null, "command_line": "set -o | grep -q pipefail && set -o pipefail; bowtie2-build --threads ${GALAXY_SLOTS:-4} '/galaxy/server/database/objects/a/c/9/dataset_ac9afe33-2307-41bc-a570-a82d482916b9.dat' genome && ln -s -f '/galaxy/server/database/objects/a/c/9/dataset_ac9afe33-2307-41bc-a570-a82d482916b9.dat' genome.fa && ln -f -s '/galaxy/server/database/objects/a/d/3/dataset_ad337d5c-3dee-4652-ab22-b495a3753ebd.dat' input_f.fastq.bz2 && ln -f -s '/galaxy/server/database/objects/8/d/2/dataset_8d2b18c3-c1a1-4d59-b94b-1f793df46a5d.dat' input_r.fastq.bz2 && THREADS=${GALAXY_SLOTS:-4} && if [ \"$THREADS\" -gt 1 ]; then (( THREADS-- )); fi && bowtie2 -p \"$THREADS\" -x 'genome' -1 'input_f.fastq.bz2' -2 'input_r.fastq.bz2' | samtools sort -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/b/6/3/dataset_b636da42-4031-45de-a4e6-bc8e189f26dd.dat'", "user_email": "tests@fake.org", "command_version": "/usr/local/bin/bowtie2-align-s version 2.5.3\n64-bit\nBuilt on fv-az365-785\nWed Jan 17 04:43:48 UTC 2024\nCompiler: gcc version 12.3.0 (conda-forge gcc 12.3.0-3) \nOptions: -O3 -msse2 -funroll-loops -g3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /usr/local/include -fdebug-prefix-map=/opt/conda/conda-bld/bowtie2_1705465427853/work=/usr/local/src/conda/bowtie2-2.5.3 -fdebug-prefix-map=/usr/local=/usr/local/src/conda-prefix -std=c++11 -Wall -Wno-unused-but-set-variable -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -DWITH_ZSTD\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "save_mapping_stats": "false", "sam_options": "{\"__current_case__\": 1, \"sam_options_selector\": \"no\"}", "analysis_type": "{\"__current_case__\": 0, \"analysis_type_selector\": \"simple\", \"presets\": \"no_presets\"}", "rg": "{\"__current_case__\": 3, \"rg_selector\": \"do_not_set\"}", "reference_genome": "{\"__current_case__\": 1, \"own_file\": {\"values\": [{\"id\": 73, \"src\": \"hda\"}]}, \"source\": \"history\"}", "library": "{\"__current_case__\": 1, \"aligned_file\": false, \"input_1\": {\"values\": [{\"id\": 71, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 72, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 1, \"paired_options_selector\": \"no\"}, \"type\": \"paired\", \"unaligned_file\": false}"}, "inputs": {"library|input_1": {"id": "fcfbfc0cad7773e1", "src": "hda", "uuid": "ad337d5c-3dee-4652-ab22-b495a3753ebd"}, "library|input_2": {"id": "d49b9c201a58b5b5", "src": "hda", "uuid": "8d2b18c3-c1a1-4d59-b94b-1f793df46a5d"}, "reference_genome|own_file": {"id": "5eb0676f0cd5a893", "src": "hda", "uuid": "ac9afe33-2307-41bc-a570-a82d482916b9"}}, "outputs": {"output": {"id": "bb9b2610222c1c3b", "src": "hda", "uuid": "b636da42-4031-45de-a4e6-bc8e189f26dd"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Settings:\n Output files: \"genome.*.bt2\"\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 Max bucket size: default\n Max bucket size, sqrt multiplier: default\n Max bucket size, len divisor: 32\n Difference-cover sample period: 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 /galaxy/server/database/objects/a/c/9/dataset_ac9afe33-2307-41bc-a570-a82d482916b9.dat\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\nbmax according to bmaxDivN setting: 517\nUsing parameters --bmax 388 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 388 --dcv 1024\nConstructing suffix-array element generator\nBuilding DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 86 sample suffixes\nGenerating random suffixes\nQSorting 86 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 86 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 12, merged 41; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 6; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 284.672 (target: 387)\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering Ebwt loop\nGetting block 1 of 58\nGetting block 2 of 58\n Reserving size (388) for bucket 1\n Reserving size (388) for bucket 2\nGetting block 3 of 58\nGetting block 4 of 58\nGetting block 5 of 58\nGetting block 6 of 58\nGetting block 7 of 58\n Calculating Z arrays for bucket 1\n Calculating Z arrays for bucket 2\n Reserving size (388) for bucket 3\n Reserving size (388) for bucket 4\n Reserving size (388) for bucket 5\n Reserving size (388) for bucket 6\n Reserving size (388) for bucket 7\n Calculating Z arrays for bucket 3\n Entering block accumulator loop for bucket 1:\n Calculating Z arrays for bucket 4\n Calculating Z arrays for bucket 5\n Calculating Z arrays for bucket 6\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 2:\n Entering block accumulator loop for bucket 3:\n Entering block accumulator loop for bucket 4:\n Entering block accumulator loop for bucket 6:\n bucket 1: 10%\n Entering block accumulator loop for bucket 5:\n Entering block accumulator loop for bucket 7:\n bucket 3: 10%\n bucket 4: 10%\n bucket 2: 10%\n bucket 1: 20%\n bucket 6: 10%\n bucket 3: 20%\n bucket 5: 10%\n bucket 1: 30%\n bucket 4: 20%\n bucket 6: 20%\n bucket 2: 20%\n bucket 7: 10%\n bucket 3: 30%\n bucket 1: 40%\n bucket 4: 30%\n bucket 6: 30%\n bucket 5: 20%\n bucket 3: 40%\n bucket 1: 50%\n bucket 2: 30%\n bucket 4: 40%\n bucket 6: 40%\n bucket 7: 20%\n bucket 3: 50%\n bucket 1: 60%\n bucket 5: 30%\n bucket 4: 50%\n bucket 6: 50%\n bucket 2: 40%\n bucket 3: 60%\n bucket 1: 70%\n bucket 4: 60%\n bucket 7: 30%\n bucket 6: 60%\n bucket 5: 40%\n bucket 3: 70%\n bucket 1: 80%\n bucket 2: 50%\n bucket 4: 70%\n bucket 6: 70%\n bucket 3: 80%\n bucket 1: 90%\n bucket 7: 40%\n bucket 5: 50%\n bucket 4: 80%\n bucket 2: 60%\n bucket 1: 100%\n bucket 3: 90%\n bucket 6: 80%\n Sorting block of length 355 for bucket 1\n (Using difference cover)\n bucket 4: 90%\n bucket 7: 50%\n bucket 5: 60%\n bucket 3: 100%\n bucket 6: 90%\n Sorting block of length 370 for bucket 3\n (Using difference cover)\n bucket 2: 70%\n bucket 4: 100%\n Sorting block of length 328 for bucket 4\n (Using difference cover)\n bucket 6: 100%\n Sorting block of length 339 for bucket 6\n (Using difference cover)\n bucket 5: 70%\n bucket 7: 60%\n bucket 2: 80%\n bucket 5: 80%\n bucket 7: 70%\n bucket 2: 90%\n bucket 2: 100%\n bucket 5: 90%\n Sorting block of length 165 for bucket 2\n (Using difference cover)\n bucket 7: 80%\n bucket 5: 100%\n Sorting block of length 203 for bucket 5\n (Using difference cover)\n bucket 7: 90%\n bucket 7: 100%\n Sorting block of length 368 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 371 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 166 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 204 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 356 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 329 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 369 for bucket 7\nGetting block 8 of 58\n Reserving size (388) for bucket 8\n Calculating Z arrays for bucket 8\n Entering block accumulator loop for bucket 8:\nGetting block 9 of 58\n bucket 8: 10%\n Reserving size (388) for bucket 9\nGetting block 10 of 58\n Calculating Z arrays for bucket 9\n Reserving size (388) for bucket 10\n Calculating Z arrays for bucket 10\n bucket 8: 20%\n Entering block accumulator loop for bucket 9:\n Entering block accumulator loop for bucket 10:\n bucket 8: 30%\n bucket 9: 10%\n bucket 10: 10%\n bucket 9: 20%\n bucket 8: 40%\n bucket 10: 20%\n bucket 9: 30%\n bucket 8: 50%\n bucket 10: 30%\n bucket 9: 40%\n bucket 8: 60%\n bucket 10: 40%\n bucket 9: 50%\n bucket 8: 70%\n bucket 10: 50%\n bucket 9: 60%\n bucket 8: 80%\n bucket 10: 60%\n bucket 9: 70%\n bucket 8: 90%\n bucket 10: 70%\n bucket 9: 80%\n bucket 8: 100%\n Sorting block of length 171 for bucket 8\n (Using difference cover)\n bucket 10: 80%\n bucket 9: 90%\n bucket 10: 90%\n bucket 9: 100%\n Sorting block of length 339 for bucket 9\n (Using difference cover)\n bucket 10: 100%\n Sorting block of length 357 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 172 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 358 for bucket 10\nGetting block 11 of 58\n Reserving size (388) for bucket 11\nGetting block 12 of 58\n Calculating Z arrays for bucket 11\n Reserving size (388) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n Entering block accumulator loop for bucket 11:\n bucket 12: 10%\n bucket 11: 10%\n bucket 12: 20%\n bucket 12: 30%\n bucket 11: 20%\n bucket 12: 40%\n bucket 11: 30%\n bucket 12: 50%\n bucket 12: 60%\n bucket 11: 40%\n bucket 12: 70%\n bucket 11: 50%\n bucket 12: 80%\n bucket 12: 90%\n bucket 11: 60%\n bucket 12: 100%\n Sorting block of length 185 for bucket 12\n (Using difference cover)\n bucket 11: 70%\n bucket 11: 80%\n Sorting block time: 00:00:00\nReturning block of 186 for bucket 12\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 305 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 306 for bucket 11\nGetting block 13 of 58\n Reserving size (388) for bucket 13\n Calculating Z arrays for bucket 13\nGetting block 14 of 58\n Entering block accumulator loop for bucket 13:\n Reserving size (388) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 14:\n bucket 13: 10%\n bucket 13: 20%\n bucket 14: 10%\n bucket 14: 20%\n bucket 13: 30%\n bucket 14: 30%\n bucket 13: 40%\n bucket 14: 40%\n bucket 14: 50%\n bucket 13: 50%\n bucket 14: 60%\n bucket 13: 60%\n bucket 14: 70%\n bucket 13: 70%\n bucket 14: 80%\n bucket 14: 90%\n bucket 13: 80%\n bucket 14: 100%\n bucket 13: 90%\n Sorting block of length 339 for bucket 14\n (Using difference cover)\n bucket 13: 100%\n Sorting block of length 282 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 283 for bucket 13\nGetting block 15 of 58\n Reserving size (388) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\nGetting block 16 of 58\n Reserving size (388) for bucket 16\n bucket 15: 10%\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\n bucket 15: 20%\n bucket 15: 30%\n bucket 16: 10%\n bucket 15: 40%\n bucket 16: 20%\n bucket 15: 50%\n bucket 15: 60%\n bucket 16: 30%\n bucket 15: 70%\n bucket 16: 40%\n bucket 15: 80%\n bucket 16: 50%\n bucket 15: 90%\n bucket 16: 60%\n bucket 15: 100%\n bucket 16: 70%\n Sorting block of length 241 for bucket 15\n (Using difference cover)\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block time: 00:00:00\nReturning block of 242 for bucket 15\n Sorting block of length 379 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 380 for bucket 16\nGetting block 17 of 58\n Reserving size (388) for bucket 17\n Calculating Z arrays for bucket 17\nGetting block 18 of 58\n Entering block accumulator loop for bucket 17:\n Reserving size (388) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 17: 10%\n bucket 18: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 18: 20%\n bucket 17: 40%\n bucket 18: 30%\n bucket 18: 40%\n bucket 17: 50%\n bucket 18: 50%\n bucket 17: 60%\n bucket 18: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 18: 70%\n bucket 17: 90%\n bucket 18: 80%\n bucket 18: 90%\n bucket 17: 100%\n Sorting block of length 215 for bucket 17\n (Using difference cover)\n bucket 18: 100%\n Sorting block of length 378 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 216 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 379 for bucket 18\nGetting block 19 of 58\n Reserving size (388) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\nGetting block 20 of 58\n Reserving size (388) for bucket 20\n bucket 19: 10%\n Calculating Z arrays for bucket 20\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 20: 30%\n bucket 19: 40%\n bucket 20: 40%\n bucket 19: 50%\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 19: 100%\n bucket 20: 80%\n Sorting block of length 334 for bucket 19\n (Using difference cover)\n bucket 20: 90%\n Sorting block time: 00:00:00\n bucket 20: 100%\nReturning block of 335 for bucket 19\n Sorting block of length 313 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 314 for bucket 20\nGetting block 21 of 58\n Reserving size (388) for bucket 21\n Calculating Z arrays for bucket 21\nGetting block 22 of 58\n Reserving size (388) for bucket 22\n Entering block accumulator loop for bucket 21:\n Calculating Z arrays for bucket 22\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 21: 90%\n bucket 22: 80%\n bucket 21: 100%\n bucket 22: 90%\n Sorting block of length 210 for bucket 21\n (Using difference cover)\n bucket 22: 100%\n Sorting block of length 386 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 211 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 387 for bucket 22\nGetting block 23 of 58\n Reserving size (388) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n bucket 23: 20%\nGetting block 24 of 58\n bucket 23: 30%\n Reserving size (388) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\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 238 for bucket 23\n (Using difference cover)\n bucket 24: 70%\n bucket 24: 80%\n Sorting block time: 00:00:00\nReturning block of 239 for bucket 23\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 351 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 352 for bucket 24\nGetting block 25 of 58\n Reserving size (388) 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 105 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 106 for bucket 25\nGetting block 26 of 58\n Reserving size (388) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\nGetting block 27 of 58\n Reserving size (388) 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 27: 70%\n bucket 26: 80%\n bucket 27: 80%\n bucket 27: 90%\n bucket 26: 90%\n bucket 27: 100%\n bucket 26: 100%\n Sorting block of length 334 for bucket 27\n (Using difference cover)\n Sorting block of length 354 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 355 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 335 for bucket 27\nGetting block 28 of 58\n Reserving size (388) for bucket 28\nGetting block 29 of 58\n Calculating Z arrays for bucket 28\n Reserving size (388) for bucket 29\n Calculating Z arrays for bucket 29\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 28: 30%\n bucket 28: 40%\n bucket 29: 40%\n bucket 28: 50%\n bucket 29: 50%\n bucket 28: 60%\n bucket 29: 60%\n bucket 28: 70%\n bucket 29: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 29: 80%\n bucket 28: 100%\n Sorting block of length 253 for bucket 28\n (Using difference cover)\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 289 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 254 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 290 for bucket 29\nGetting block 30 of 58\n Reserving size (388) for bucket 30\n Calculating Z arrays for bucket 30\nGetting block 31 of 58\n Entering block accumulator loop for bucket 30:\n Reserving size (388) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 31:\n bucket 30: 10%\n bucket 31: 10%\n bucket 30: 20%\n bucket 31: 20%\n bucket 30: 30%\n bucket 31: 30%\n bucket 30: 40%\n bucket 31: 40%\n bucket 30: 50%\n bucket 31: 50%\n bucket 30: 60%\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 345 for bucket 30\n (Using difference cover)\n bucket 31: 90%\n bucket 31: 100%\n Sorting block of length 377 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 346 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 378 for bucket 31\nGetting block 32 of 58\n Reserving size (388) for bucket 32\nGetting block 33 of 58\n Calculating Z arrays for buc\n..\n0:00\nReturning block of 350 for bucket 23\nGetting block 24 of 57\n Reserving size (388) for bucket 24\n Calculating Z arrays for bucket 24\nGetting block 25 of 57\n Reserving size (388) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 24:\n Entering block accumulator loop for bucket 25:\n bucket 24: 10%\n bucket 25: 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 286 for bucket 25\n (Using difference cover)\n bucket 24: 100%\n Sorting block of length 245 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 287 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 246 for bucket 24\nGetting block 26 of 57\n Reserving size (388) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\nGetting block 27 of 57\n Reserving size (388) for bucket 27\n Calculating Z arrays for bucket 27\n bucket 26: 10%\n Entering block accumulator loop for bucket 27:\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 27: 60%\n bucket 26: 70%\n bucket 27: 70%\n bucket 26: 80%\n bucket 27: 80%\n bucket 26: 90%\n bucket 27: 90%\n bucket 26: 100%\n bucket 27: 100%\n Sorting block of length 384 for bucket 26\n (Using difference cover)\n Sorting block of length 359 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 385 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 360 for bucket 27\nGetting block 28 of 57\n Reserving size (388) for bucket 28\nGetting block 29 of 57\n Calculating Z arrays for bucket 28\n Reserving size (388) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 28:\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 28: 10%\n bucket 29: 20%\n bucket 28: 20%\n bucket 29: 30%\n bucket 28: 30%\n bucket 29: 40%\n bucket 28: 40%\n bucket 29: 50%\n bucket 28: 50%\n bucket 29: 60%\n bucket 28: 60%\n bucket 29: 70%\n bucket 28: 70%\n bucket 29: 80%\n bucket 28: 80%\n bucket 29: 90%\n bucket 28: 90%\n bucket 29: 100%\n Sorting block of length 195 for bucket 29\n (Using difference cover)\n bucket 28: 100%\n Sorting block of length 387 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 28\nGetting block 30 of 57\n Reserving size (388) 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 257 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 258 for bucket 30\nGetting block 31 of 57\n Reserving size (388) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 31:\nGetting block 32 of 57\n bucket 31: 10%\n Reserving size (388) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 32:\n bucket 31: 20%\nGetting block 33 of 57\n Reserving size (388) for bucket 33\n Calculating Z arrays for bucket 33\nGetting block 34 of 57\n Reserving size (388) for bucket 34\n Calculating Z arrays for bucket 34\n bucket 31: 30%\n Entering block accumulator loop for bucket 33:\n bucket 32: 10%\n Entering block accumulator loop for bucket 34:\n bucket 31: 40%\n bucket 33: 10%\n bucket 32: 20%\n bucket 31: 50%\n bucket 34: 10%\n bucket 31: 60%\n bucket 34: 20%\n bucket 33: 20%\n bucket 32: 30%\n bucket 34: 30%\n bucket 31: 70%\n bucket 33: 30%\n bucket 32: 40%\n bucket 34: 40%\n bucket 31: 80%\n bucket 33: 40%\n bucket 32: 50%\n bucket 34: 50%\n bucket 34: 60%\n bucket 33: 50%\n bucket 32: 60%\n bucket 34: 70%\n bucket 31: 90%\n bucket 33: 60%\n bucket 34: 80%\n bucket 32: 70%\n bucket 34: 90%\n bucket 31: 100%\n bucket 33: 70%\n Sorting block of length 310 for bucket 31\n (Using difference cover)\n bucket 34: 100%\n Sorting block of length 275 for bucket 34\n (Using difference cover)\n bucket 32: 80%\n bucket 33: 80%\n bucket 32: 90%\n Sorting block time: 00:00:00\nReturning block of 276 for bucket 34\n bucket 33: 90%\n bucket 32: 100%\n Sorting block time: 00:00:00\n Sorting block of length 219 for bucket 32\n (Using difference cover)\nReturning block of 311 for bucket 31\n bucket 33: 100%\n Sorting block of length 387 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 220 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 33\nGetting block 35 of 57\n Reserving size (388) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 35:\nGetting block 36 of 57\n bucket 35: 10%\n Reserving size (388) for bucket 36\n Calculating Z arrays for bucket 36\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 bucket 36: 90%\n Sorting block of length 350 for bucket 35\n (Using difference cover)\n bucket 36: 100%\n Sorting block of length 150 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 351 for bucket 35\n Sorting block time: 00:00:00\nReturning block of 151 for bucket 36\nGetting block 37 of 57\n Reserving size (388) 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 267 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 268 for bucket 37\nGetting block 38 of 57\n Reserving size (388) for bucket 38\n Calculating Z arrays for bucket 38\nGetting block 39 of 57\n Reserving size (388) 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 38: 60%\n bucket 39: 50%\n bucket 38: 70%\n bucket 39: 60%\n bucket 38: 80%\n bucket 39: 70%\n bucket 38: 90%\n bucket 39: 80%\n bucket 38: 100%\n Sorting block of length 337 for bucket 38\n (Using difference cover)\n bucket 39: 90%\n bucket 39: 100%\n Sorting block of length 387 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 338 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 39\nGetting block 40 of 57\n Reserving size (388) for bucket 40\n Calculating Z arrays for bucket 40\nGetting block 41 of 57\n Entering block accumulator loop for bucket 40:\n Reserving size (388) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 41:\n bucket 40: 10%\n bucket 41: 10%\n bucket 40: 20%\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 41: 80%\n bucket 40: 100%\n bucket 41: 90%\n Sorting block of length 379 for bucket 40\n (Using difference cover)\n bucket 41: 100%\n Sorting block of length 330 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 380 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 331 for bucket 41\nGetting block 42 of 57\n Reserving size (388) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\nGetting block 43 of 57\n Reserving size (388) for bucket 43\n Calculating Z arrays for bucket 43\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 42: 90%\n bucket 43: 60%\n bucket 42: 100%\n Sorting block of length 188 for bucket 42\n (Using difference cover)\n bucket 43: 70%\n bucket 43: 80%\n bucket 43: 90%\n Sorting block time: 00:00:00\nReturning block of 189 for bucket 42\n bucket 43: 100%\n Sorting block of length 321 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 322 for bucket 43\nGetting block 44 of 57\n Reserving size (388) for bucket 44\n Calculating Z arrays for bucket 44\nGetting block 45 of 57\n Reserving size (388) for bucket 45\n Calculating Z arrays for bucket 45\n Entering block accumulator loop for bucket 44:\n Entering block accumulator loop for bucket 45:\n bucket 45: 10%\n bucket 44: 10%\n bucket 45: 20%\n bucket 44: 20%\n bucket 45: 30%\n bucket 44: 30%\n bucket 45: 40%\n bucket 44: 40%\n bucket 45: 50%\n bucket 44: 50%\n bucket 45: 60%\n bucket 44: 60%\n bucket 45: 70%\n bucket 44: 70%\n bucket 45: 80%\n bucket 44: 80%\n bucket 45: 90%\n bucket 44: 90%\n bucket 45: 100%\n bucket 44: 100%\n Sorting block of length 365 for bucket 45\n (Using difference cover)\n Sorting block of length 366 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 366 for bucket 45\n Sorting block time: 00:00:00\nReturning block of 367 for bucket 44\nGetting block 46 of 57\n Reserving size (388) for bucket 46\n Calculating Z arrays for bucket 46\nGetting block 47 of 57\n Entering block accumulator loop for bucket 46:\n Reserving size (388) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 47:\n bucket 46: 10%\n bucket 47: 10%\n bucket 46: 20%\n bucket 46: 30%\n bucket 47: 20%\n bucket 47: 30%\n bucket 46: 40%\n bucket 47: 40%\n bucket 46: 50%\n bucket 47: 50%\n bucket 46: 60%\n bucket 47: 60%\n bucket 46: 70%\n bucket 47: 70%\n bucket 46: 80%\n bucket 47: 80%\n bucket 47: 90%\n bucket 46: 90%\n bucket 47: 100%\n Sorting block of length 217 for bucket 47\n (Using difference cover)\n bucket 46: 100%\n Sorting block of length 253 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 218 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 254 for bucket 46\nGetting block 48 of 57\n Reserving size (388) 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 384 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 385 for bucket 48\nGetting block 49 of 57\n Reserving size (388) 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 57\n Reserving size (388) for bucket 50\n Calculating Z arrays for bucket 50\n bucket 49: 30%\n Entering block accumulator loop for bucket 50:\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 49: 90%\n bucket 50: 60%\n bucket 49: 100%\n Sorting block of length 112 for bucket 49\n (Using difference cover)\n bucket 50: 70%\n bucket 50: 80%\n Sorting block time: 00:00:00\n bucket 50: 90%\nReturning block of 113 for bucket 49\n bucket 50: 100%\n Sorting block of length 275 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 276 for bucket 50\nGetting block 51 of 57\n Reserving size (388) for bucket 51\nGetting block 52 of 57\n Calculating Z arrays for bucket 51\n Reserving size (388) for bucket 52\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 52: 30%\n bucket 51: 20%\n bucket 52: 40%\n bucket 51: 30%\n bucket 52: 50%\n bucket 52: 60%\n bucket 51: 40%\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 378 for bucket 52\n (Using difference cover)\n bucket 51: 80%\n bucket 51: 90%\n bucket 51: 100%\n Sorting block of length 350 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 379 for bucket 52\n Sorting block time: 00:00:00\nReturning block of 351 for bucket 51\nGetting block 53 of 57\n Reserving size (388) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 53:\nGetting block 54 of 57\n Reserving size (388) for bucket 54\n bucket 53: 10%\n Calculating Z arrays for bucket 54\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 53: 50%\n bucket 54: 40%\n bucket 54: 50%\n bucket 53: 60%\n bucket 54: 60%\n bucket 53: 70%\n bucket 54: 70%\n bucket 54: 80%\n bucket 53: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 237 for bucket 54\n (Using difference cover)\n bucket 53: 90%\n bucket 53: 100%\n Sorting block of length 370 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 238 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 371 for bucket 53\nGetting block 55 of 57\n Reserving size (388) 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 344 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 345 for bucket 55\nGetting block 56 of 57\n Reserving size (388) 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 57\n Reserving size (388) for bucket 57\n Calculating Z arrays for bucket 57\n bucket 56: 20%\n Entering block accumulator loop for bucket 57:\n bucket 56: 30%\n bucket 57: 10%\n bucket 56: 40%\n bucket 57: 20%\n bucket 56: 50%\n bucket 57: 30%\n bucket 57: 40%\n bucket 56: 60%\n bucket 57: 50%\n bucket 56: 70%\n bucket 57: 60%\n bucket 56: 80%\n bucket 57: 70%\n bucket 56: 90%\n bucket 57: 80%\n bucket 56: 100%\n Sorting block of length 270 for bucket 56\n (Using difference cover)\n bucket 57: 90%\n bucket 57: 100%\n Sorting block of length 132 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 271 for bucket 56\n Sorting block time: 00:00:00\nReturning block of 133 for bucket 57\nExited Ebwt loop\nfchr[A]: 0\nfchr[C]: 5124\nfchr[G]: 10305\nfchr[T]: 12474\nfchr[$]: 16568\nExiting Ebwt::buildToDisk()\nReturning from initFromVector\nWrote 4200050 bytes to primary EBWT file: genome.rev.1.bt2.tmp\nWrote 4148 bytes to secondary EBWT file: genome.rev.2.bt2.tmp\nRe-opening _in1 and _in2 as input streams\nReturning from Ebwt constructor\nHeaders:\n len: 16568\n bwtLen: 16569\n sz: 4142\n bwtSz: 4143\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 20\n eftabSz: 80\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 1036\n offsSz: 4144\n lineSz: 64\n sideSz: 64\n sideBwtSz: 48\n sideBwtLen: 192\n numSides: 87\n numLines: 87\n ebwtTotLen: 5568\n ebwtTotSz: 5568\n color: 0\n reverse: 1\nTotal time for backward call to driver() for mirror index: 00:00:00\n", "tool_stderr": "Building a SMALL index\nRenaming genome.3.bt2.tmp to genome.3.bt2\nRenaming genome.4.bt2.tmp to genome.4.bt2\nRenaming genome.1.bt2.tmp to genome.1.bt2\nRenaming genome.2.bt2.tmp to genome.2.bt2\nRenaming genome.rev.1.bt2.tmp to genome.rev.1.bt2\nRenaming genome.rev.2.bt2.tmp to genome.rev.2.bt2\n100 reads; of these:\n 100 (100.00%) were paired; of these:\n 97 (97.00%) aligned concordantly 0 times\n 3 (3.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 97 pairs aligned concordantly 0 times; of these:\n 8 (8.25%) aligned discordantly 1 time\n ----\n 89 pairs aligned 0 times concordantly or discordantly; of these:\n 178 mates make up the pairs; of these:\n 153 (85.96%) aligned 0 times\n 25 (14.04%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n23.50% overall alignment rate\n", "job_stdout": "", "job_stderr": "", "stdout": "Settings:\n Output files: \"genome.*.bt2\"\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 Max bucket size: default\n Max bucket size, sqrt multiplier: default\n Max bucket size, len divisor: 32\n Difference-cover sample period: 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 /galaxy/server/database/objects/a/c/9/dataset_ac9afe33-2307-41bc-a570-a82d482916b9.dat\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\nbmax according to bmaxDivN setting: 517\nUsing parameters --bmax 388 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 388 --dcv 1024\nConstructing suffix-array element generator\nBuilding DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 86 sample suffixes\nGenerating random suffixes\nQSorting 86 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 86 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 12, merged 41; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 6; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 284.672 (target: 387)\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering Ebwt loop\nGetting block 1 of 58\nGetting block 2 of 58\n Reserving size (388) for bucket 1\n Reserving size (388) for bucket 2\nGetting block 3 of 58\nGetting block 4 of 58\nGetting block 5 of 58\nGetting block 6 of 58\nGetting block 7 of 58\n Calculating Z arrays for bucket 1\n Calculating Z arrays for bucket 2\n Reserving size (388) for bucket 3\n Reserving size (388) for bucket 4\n Reserving size (388) for bucket 5\n Reserving size (388) for bucket 6\n Reserving size (388) for bucket 7\n Calculating Z arrays for bucket 3\n Entering block accumulator loop for bucket 1:\n Calculating Z arrays for bucket 4\n Calculating Z arrays for bucket 5\n Calculating Z arrays for bucket 6\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 2:\n Entering block accumulator loop for bucket 3:\n Entering block accumulator loop for bucket 4:\n Entering block accumulator loop for bucket 6:\n bucket 1: 10%\n Entering block accumulator loop for bucket 5:\n Entering block accumulator loop for bucket 7:\n bucket 3: 10%\n bucket 4: 10%\n bucket 2: 10%\n bucket 1: 20%\n bucket 6: 10%\n bucket 3: 20%\n bucket 5: 10%\n bucket 1: 30%\n bucket 4: 20%\n bucket 6: 20%\n bucket 2: 20%\n bucket 7: 10%\n bucket 3: 30%\n bucket 1: 40%\n bucket 4: 30%\n bucket 6: 30%\n bucket 5: 20%\n bucket 3: 40%\n bucket 1: 50%\n bucket 2: 30%\n bucket 4: 40%\n bucket 6: 40%\n bucket 7: 20%\n bucket 3: 50%\n bucket 1: 60%\n bucket 5: 30%\n bucket 4: 50%\n bucket 6: 50%\n bucket 2: 40%\n bucket 3: 60%\n bucket 1: 70%\n bucket 4: 60%\n bucket 7: 30%\n bucket 6: 60%\n bucket 5: 40%\n bucket 3: 70%\n bucket 1: 80%\n bucket 2: 50%\n bucket 4: 70%\n bucket 6: 70%\n bucket 3: 80%\n bucket 1: 90%\n bucket 7: 40%\n bucket 5: 50%\n bucket 4: 80%\n bucket 2: 60%\n bucket 1: 100%\n bucket 3: 90%\n bucket 6: 80%\n Sorting block of length 355 for bucket 1\n (Using difference cover)\n bucket 4: 90%\n bucket 7: 50%\n bucket 5: 60%\n bucket 3: 100%\n bucket 6: 90%\n Sorting block of length 370 for bucket 3\n (Using difference cover)\n bucket 2: 70%\n bucket 4: 100%\n Sorting block of length 328 for bucket 4\n (Using difference cover)\n bucket 6: 100%\n Sorting block of length 339 for bucket 6\n (Using difference cover)\n bucket 5: 70%\n bucket 7: 60%\n bucket 2: 80%\n bucket 5: 80%\n bucket 7: 70%\n bucket 2: 90%\n bucket 2: 100%\n bucket 5: 90%\n Sorting block of length 165 for bucket 2\n (Using difference cover)\n bucket 7: 80%\n bucket 5: 100%\n Sorting block of length 203 for bucket 5\n (Using difference cover)\n bucket 7: 90%\n bucket 7: 100%\n Sorting block of length 368 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 371 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 166 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 204 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 356 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 329 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 369 for bucket 7\nGetting block 8 of 58\n Reserving size (388) for bucket 8\n Calculating Z arrays for bucket 8\n Entering block accumulator loop for bucket 8:\nGetting block 9 of 58\n bucket 8: 10%\n Reserving size (388) for bucket 9\nGetting block 10 of 58\n Calculating Z arrays for bucket 9\n Reserving size (388) for bucket 10\n Calculating Z arrays for bucket 10\n bucket 8: 20%\n Entering block accumulator loop for bucket 9:\n Entering block accumulator loop for bucket 10:\n bucket 8: 30%\n bucket 9: 10%\n bucket 10: 10%\n bucket 9: 20%\n bucket 8: 40%\n bucket 10: 20%\n bucket 9: 30%\n bucket 8: 50%\n bucket 10: 30%\n bucket 9: 40%\n bucket 8: 60%\n bucket 10: 40%\n bucket 9: 50%\n bucket 8: 70%\n bucket 10: 50%\n bucket 9: 60%\n bucket 8: 80%\n bucket 10: 60%\n bucket 9: 70%\n bucket 8: 90%\n bucket 10: 70%\n bucket 9: 80%\n bucket 8: 100%\n Sorting block of length 171 for bucket 8\n (Using difference cover)\n bucket 10: 80%\n bucket 9: 90%\n bucket 10: 90%\n bucket 9: 100%\n Sorting block of length 339 for bucket 9\n (Using difference cover)\n bucket 10: 100%\n Sorting block of length 357 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 172 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 358 for bucket 10\nGetting block 11 of 58\n Reserving size (388) for bucket 11\nGetting block 12 of 58\n Calculating Z arrays for bucket 11\n Reserving size (388) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n Entering block accumulator loop for bucket 11:\n bucket 12: 10%\n bucket 11: 10%\n bucket 12: 20%\n bucket 12: 30%\n bucket 11: 20%\n bucket 12: 40%\n bucket 11: 30%\n bucket 12: 50%\n bucket 12: 60%\n bucket 11: 40%\n bucket 12: 70%\n bucket 11: 50%\n bucket 12: 80%\n bucket 12: 90%\n bucket 11: 60%\n bucket 12: 100%\n Sorting block of length 185 for bucket 12\n (Using difference cover)\n bucket 11: 70%\n bucket 11: 80%\n Sorting block time: 00:00:00\nReturning block of 186 for bucket 12\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 305 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 306 for bucket 11\nGetting block 13 of 58\n Reserving size (388) for bucket 13\n Calculating Z arrays for bucket 13\nGetting block 14 of 58\n Entering block accumulator loop for bucket 13:\n Reserving size (388) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 14:\n bucket 13: 10%\n bucket 13: 20%\n bucket 14: 10%\n bucket 14: 20%\n bucket 13: 30%\n bucket 14: 30%\n bucket 13: 40%\n bucket 14: 40%\n bucket 14: 50%\n bucket 13: 50%\n bucket 14: 60%\n bucket 13: 60%\n bucket 14: 70%\n bucket 13: 70%\n bucket 14: 80%\n bucket 14: 90%\n bucket 13: 80%\n bucket 14: 100%\n bucket 13: 90%\n Sorting block of length 339 for bucket 14\n (Using difference cover)\n bucket 13: 100%\n Sorting block of length 282 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 283 for bucket 13\nGetting block 15 of 58\n Reserving size (388) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\nGetting block 16 of 58\n Reserving size (388) for bucket 16\n bucket 15: 10%\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\n bucket 15: 20%\n bucket 15: 30%\n bucket 16: 10%\n bucket 15: 40%\n bucket 16: 20%\n bucket 15: 50%\n bucket 15: 60%\n bucket 16: 30%\n bucket 15: 70%\n bucket 16: 40%\n bucket 15: 80%\n bucket 16: 50%\n bucket 15: 90%\n bucket 16: 60%\n bucket 15: 100%\n bucket 16: 70%\n Sorting block of length 241 for bucket 15\n (Using difference cover)\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block time: 00:00:00\nReturning block of 242 for bucket 15\n Sorting block of length 379 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 380 for bucket 16\nGetting block 17 of 58\n Reserving size (388) for bucket 17\n Calculating Z arrays for bucket 17\nGetting block 18 of 58\n Entering block accumulator loop for bucket 17:\n Reserving size (388) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 17: 10%\n bucket 18: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 18: 20%\n bucket 17: 40%\n bucket 18: 30%\n bucket 18: 40%\n bucket 17: 50%\n bucket 18: 50%\n bucket 17: 60%\n bucket 18: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 18: 70%\n bucket 17: 90%\n bucket 18: 80%\n bucket 18: 90%\n bucket 17: 100%\n Sorting block of length 215 for bucket 17\n (Using difference cover)\n bucket 18: 100%\n Sorting block of length 378 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 216 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 379 for bucket 18\nGetting block 19 of 58\n Reserving size (388) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\nGetting block 20 of 58\n Reserving size (388) for bucket 20\n bucket 19: 10%\n Calculating Z arrays for bucket 20\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 20: 30%\n bucket 19: 40%\n bucket 20: 40%\n bucket 19: 50%\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 19: 100%\n bucket 20: 80%\n Sorting block of length 334 for bucket 19\n (Using difference cover)\n bucket 20: 90%\n Sorting block time: 00:00:00\n bucket 20: 100%\nReturning block of 335 for bucket 19\n Sorting block of length 313 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 314 for bucket 20\nGetting block 21 of 58\n Reserving size (388) for bucket 21\n Calculating Z arrays for bucket 21\nGetting block 22 of 58\n Reserving size (388) for bucket 22\n Entering block accumulator loop for bucket 21:\n Calculating Z arrays for bucket 22\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 21: 90%\n bucket 22: 80%\n bucket 21: 100%\n bucket 22: 90%\n Sorting block of length 210 for bucket 21\n (Using difference cover)\n bucket 22: 100%\n Sorting block of length 386 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 211 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 387 for bucket 22\nGetting block 23 of 58\n Reserving size (388) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n bucket 23: 20%\nGetting block 24 of 58\n bucket 23: 30%\n Reserving size (388) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\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 238 for bucket 23\n (Using difference cover)\n bucket 24: 70%\n bucket 24: 80%\n Sorting block time: 00:00:00\nReturning block of 239 for bucket 23\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 351 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 352 for bucket 24\nGetting block 25 of 58\n Reserving size (388) 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 105 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 106 for bucket 25\nGetting block 26 of 58\n Reserving size (388) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\nGetting block 27 of 58\n Reserving size (388) 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 27: 70%\n bucket 26: 80%\n bucket 27: 80%\n bucket 27: 90%\n bucket 26: 90%\n bucket 27: 100%\n bucket 26: 100%\n Sorting block of length 334 for bucket 27\n (Using difference cover)\n Sorting block of length 354 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 355 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 335 for bucket 27\nGetting block 28 of 58\n Reserving size (388) for bucket 28\nGetting block 29 of 58\n Calculating Z arrays for bucket 28\n Reserving size (388) for bucket 29\n Calculating Z arrays for bucket 29\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 28: 30%\n bucket 28: 40%\n bucket 29: 40%\n bucket 28: 50%\n bucket 29: 50%\n bucket 28: 60%\n bucket 29: 60%\n bucket 28: 70%\n bucket 29: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 29: 80%\n bucket 28: 100%\n Sorting block of length 253 for bucket 28\n (Using difference cover)\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 289 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 254 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 290 for bucket 29\nGetting block 30 of 58\n Reserving size (388) for bucket 30\n Calculating Z arrays for bucket 30\nGetting block 31 of 58\n Entering block accumulator loop for bucket 30:\n Reserving size (388) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 31:\n bucket 30: 10%\n bucket 31: 10%\n bucket 30: 20%\n bucket 31: 20%\n bucket 30: 30%\n bucket 31: 30%\n bucket 30: 40%\n bucket 31: 40%\n bucket 30: 50%\n bucket 31: 50%\n bucket 30: 60%\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 345 for bucket 30\n (Using difference cover)\n bucket 31: 90%\n bucket 31: 100%\n Sorting block of length 377 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 346 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 378 for bucket 31\nGetting block 32 of 58\n Reserving size (388) for bucket 32\nGetting block 33 of 58\n Calculating Z arrays for buc\n..\n0:00\nReturning block of 350 for bucket 23\nGetting block 24 of 57\n Reserving size (388) for bucket 24\n Calculating Z arrays for bucket 24\nGetting block 25 of 57\n Reserving size (388) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 24:\n Entering block accumulator loop for bucket 25:\n bucket 24: 10%\n bucket 25: 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 286 for bucket 25\n (Using difference cover)\n bucket 24: 100%\n Sorting block of length 245 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 287 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 246 for bucket 24\nGetting block 26 of 57\n Reserving size (388) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\nGetting block 27 of 57\n Reserving size (388) for bucket 27\n Calculating Z arrays for bucket 27\n bucket 26: 10%\n Entering block accumulator loop for bucket 27:\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 27: 60%\n bucket 26: 70%\n bucket 27: 70%\n bucket 26: 80%\n bucket 27: 80%\n bucket 26: 90%\n bucket 27: 90%\n bucket 26: 100%\n bucket 27: 100%\n Sorting block of length 384 for bucket 26\n (Using difference cover)\n Sorting block of length 359 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 385 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 360 for bucket 27\nGetting block 28 of 57\n Reserving size (388) for bucket 28\nGetting block 29 of 57\n Calculating Z arrays for bucket 28\n Reserving size (388) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 28:\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 28: 10%\n bucket 29: 20%\n bucket 28: 20%\n bucket 29: 30%\n bucket 28: 30%\n bucket 29: 40%\n bucket 28: 40%\n bucket 29: 50%\n bucket 28: 50%\n bucket 29: 60%\n bucket 28: 60%\n bucket 29: 70%\n bucket 28: 70%\n bucket 29: 80%\n bucket 28: 80%\n bucket 29: 90%\n bucket 28: 90%\n bucket 29: 100%\n Sorting block of length 195 for bucket 29\n (Using difference cover)\n bucket 28: 100%\n Sorting block of length 387 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 28\nGetting block 30 of 57\n Reserving size (388) 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 257 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 258 for bucket 30\nGetting block 31 of 57\n Reserving size (388) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 31:\nGetting block 32 of 57\n bucket 31: 10%\n Reserving size (388) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 32:\n bucket 31: 20%\nGetting block 33 of 57\n Reserving size (388) for bucket 33\n Calculating Z arrays for bucket 33\nGetting block 34 of 57\n Reserving size (388) for bucket 34\n Calculating Z arrays for bucket 34\n bucket 31: 30%\n Entering block accumulator loop for bucket 33:\n bucket 32: 10%\n Entering block accumulator loop for bucket 34:\n bucket 31: 40%\n bucket 33: 10%\n bucket 32: 20%\n bucket 31: 50%\n bucket 34: 10%\n bucket 31: 60%\n bucket 34: 20%\n bucket 33: 20%\n bucket 32: 30%\n bucket 34: 30%\n bucket 31: 70%\n bucket 33: 30%\n bucket 32: 40%\n bucket 34: 40%\n bucket 31: 80%\n bucket 33: 40%\n bucket 32: 50%\n bucket 34: 50%\n bucket 34: 60%\n bucket 33: 50%\n bucket 32: 60%\n bucket 34: 70%\n bucket 31: 90%\n bucket 33: 60%\n bucket 34: 80%\n bucket 32: 70%\n bucket 34: 90%\n bucket 31: 100%\n bucket 33: 70%\n Sorting block of length 310 for bucket 31\n (Using difference cover)\n bucket 34: 100%\n Sorting block of length 275 for bucket 34\n (Using difference cover)\n bucket 32: 80%\n bucket 33: 80%\n bucket 32: 90%\n Sorting block time: 00:00:00\nReturning block of 276 for bucket 34\n bucket 33: 90%\n bucket 32: 100%\n Sorting block time: 00:00:00\n Sorting block of length 219 for bucket 32\n (Using difference cover)\nReturning block of 311 for bucket 31\n bucket 33: 100%\n Sorting block of length 387 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 220 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 33\nGetting block 35 of 57\n Reserving size (388) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 35:\nGetting block 36 of 57\n bucket 35: 10%\n Reserving size (388) for bucket 36\n Calculating Z arrays for bucket 36\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 bucket 36: 90%\n Sorting block of length 350 for bucket 35\n (Using difference cover)\n bucket 36: 100%\n Sorting block of length 150 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 351 for bucket 35\n Sorting block time: 00:00:00\nReturning block of 151 for bucket 36\nGetting block 37 of 57\n Reserving size (388) 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 267 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 268 for bucket 37\nGetting block 38 of 57\n Reserving size (388) for bucket 38\n Calculating Z arrays for bucket 38\nGetting block 39 of 57\n Reserving size (388) 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 38: 60%\n bucket 39: 50%\n bucket 38: 70%\n bucket 39: 60%\n bucket 38: 80%\n bucket 39: 70%\n bucket 38: 90%\n bucket 39: 80%\n bucket 38: 100%\n Sorting block of length 337 for bucket 38\n (Using difference cover)\n bucket 39: 90%\n bucket 39: 100%\n Sorting block of length 387 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 338 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 39\nGetting block 40 of 57\n Reserving size (388) for bucket 40\n Calculating Z arrays for bucket 40\nGetting block 41 of 57\n Entering block accumulator loop for bucket 40:\n Reserving size (388) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 41:\n bucket 40: 10%\n bucket 41: 10%\n bucket 40: 20%\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 41: 80%\n bucket 40: 100%\n bucket 41: 90%\n Sorting block of length 379 for bucket 40\n (Using difference cover)\n bucket 41: 100%\n Sorting block of length 330 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 380 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 331 for bucket 41\nGetting block 42 of 57\n Reserving size (388) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\nGetting block 43 of 57\n Reserving size (388) for bucket 43\n Calculating Z arrays for bucket 43\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 42: 90%\n bucket 43: 60%\n bucket 42: 100%\n Sorting block of length 188 for bucket 42\n (Using difference cover)\n bucket 43: 70%\n bucket 43: 80%\n bucket 43: 90%\n Sorting block time: 00:00:00\nReturning block of 189 for bucket 42\n bucket 43: 100%\n Sorting block of length 321 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 322 for bucket 43\nGetting block 44 of 57\n Reserving size (388) for bucket 44\n Calculating Z arrays for bucket 44\nGetting block 45 of 57\n Reserving size (388) for bucket 45\n Calculating Z arrays for bucket 45\n Entering block accumulator loop for bucket 44:\n Entering block accumulator loop for bucket 45:\n bucket 45: 10%\n bucket 44: 10%\n bucket 45: 20%\n bucket 44: 20%\n bucket 45: 30%\n bucket 44: 30%\n bucket 45: 40%\n bucket 44: 40%\n bucket 45: 50%\n bucket 44: 50%\n bucket 45: 60%\n bucket 44: 60%\n bucket 45: 70%\n bucket 44: 70%\n bucket 45: 80%\n bucket 44: 80%\n bucket 45: 90%\n bucket 44: 90%\n bucket 45: 100%\n bucket 44: 100%\n Sorting block of length 365 for bucket 45\n (Using difference cover)\n Sorting block of length 366 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 366 for bucket 45\n Sorting block time: 00:00:00\nReturning block of 367 for bucket 44\nGetting block 46 of 57\n Reserving size (388) for bucket 46\n Calculating Z arrays for bucket 46\nGetting block 47 of 57\n Entering block accumulator loop for bucket 46:\n Reserving size (388) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 47:\n bucket 46: 10%\n bucket 47: 10%\n bucket 46: 20%\n bucket 46: 30%\n bucket 47: 20%\n bucket 47: 30%\n bucket 46: 40%\n bucket 47: 40%\n bucket 46: 50%\n bucket 47: 50%\n bucket 46: 60%\n bucket 47: 60%\n bucket 46: 70%\n bucket 47: 70%\n bucket 46: 80%\n bucket 47: 80%\n bucket 47: 90%\n bucket 46: 90%\n bucket 47: 100%\n Sorting block of length 217 for bucket 47\n (Using difference cover)\n bucket 46: 100%\n Sorting block of length 253 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 218 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 254 for bucket 46\nGetting block 48 of 57\n Reserving size (388) 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 384 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 385 for bucket 48\nGetting block 49 of 57\n Reserving size (388) 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 57\n Reserving size (388) for bucket 50\n Calculating Z arrays for bucket 50\n bucket 49: 30%\n Entering block accumulator loop for bucket 50:\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 49: 90%\n bucket 50: 60%\n bucket 49: 100%\n Sorting block of length 112 for bucket 49\n (Using difference cover)\n bucket 50: 70%\n bucket 50: 80%\n Sorting block time: 00:00:00\n bucket 50: 90%\nReturning block of 113 for bucket 49\n bucket 50: 100%\n Sorting block of length 275 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 276 for bucket 50\nGetting block 51 of 57\n Reserving size (388) for bucket 51\nGetting block 52 of 57\n Calculating Z arrays for bucket 51\n Reserving size (388) for bucket 52\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 52: 30%\n bucket 51: 20%\n bucket 52: 40%\n bucket 51: 30%\n bucket 52: 50%\n bucket 52: 60%\n bucket 51: 40%\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 378 for bucket 52\n (Using difference cover)\n bucket 51: 80%\n bucket 51: 90%\n bucket 51: 100%\n Sorting block of length 350 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 379 for bucket 52\n Sorting block time: 00:00:00\nReturning block of 351 for bucket 51\nGetting block 53 of 57\n Reserving size (388) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 53:\nGetting block 54 of 57\n Reserving size (388) for bucket 54\n bucket 53: 10%\n Calculating Z arrays for bucket 54\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 53: 50%\n bucket 54: 40%\n bucket 54: 50%\n bucket 53: 60%\n bucket 54: 60%\n bucket 53: 70%\n bucket 54: 70%\n bucket 54: 80%\n bucket 53: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 237 for bucket 54\n (Using difference cover)\n bucket 53: 90%\n bucket 53: 100%\n Sorting block of length 370 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 238 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 371 for bucket 53\nGetting block 55 of 57\n Reserving size (388) 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 344 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 345 for bucket 55\nGetting block 56 of 57\n Reserving size (388) 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 57\n Reserving size (388) for bucket 57\n Calculating Z arrays for bucket 57\n bucket 56: 20%\n Entering block accumulator loop for bucket 57:\n bucket 56: 30%\n bucket 57: 10%\n bucket 56: 40%\n bucket 57: 20%\n bucket 56: 50%\n bucket 57: 30%\n bucket 57: 40%\n bucket 56: 60%\n bucket 57: 50%\n bucket 56: 70%\n bucket 57: 60%\n bucket 56: 80%\n bucket 57: 70%\n bucket 56: 90%\n bucket 57: 80%\n bucket 56: 100%\n Sorting block of length 270 for bucket 56\n (Using difference cover)\n bucket 57: 90%\n bucket 57: 100%\n Sorting block of length 132 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 271 for bucket 56\n Sorting block time: 00:00:00\nReturning block of 133 for bucket 57\nExited Ebwt loop\nfchr[A]: 0\nfchr[C]: 5124\nfchr[G]: 10305\nfchr[T]: 12474\nfchr[$]: 16568\nExiting Ebwt::buildToDisk()\nReturning from initFromVector\nWrote 4200050 bytes to primary EBWT file: genome.rev.1.bt2.tmp\nWrote 4148 bytes to secondary EBWT file: genome.rev.2.bt2.tmp\nRe-opening _in1 and _in2 as input streams\nReturning from Ebwt constructor\nHeaders:\n len: 16568\n bwtLen: 16569\n sz: 4142\n bwtSz: 4143\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 20\n eftabSz: 80\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 1036\n offsSz: 4144\n lineSz: 64\n sideSz: 64\n sideBwtSz: 48\n sideBwtLen: 192\n numSides: 87\n numLines: 87\n ebwtTotLen: 5568\n ebwtTotSz: 5568\n color: 0\n reverse: 1\nTotal time for backward call to driver() for mirror index: 00:00:00\n", "stderr": "Building a SMALL index\nRenaming genome.3.bt2.tmp to genome.3.bt2\nRenaming genome.4.bt2.tmp to genome.4.bt2\nRenaming genome.1.bt2.tmp to genome.1.bt2\nRenaming genome.2.bt2.tmp to genome.2.bt2\nRenaming genome.rev.1.bt2.tmp to genome.rev.1.bt2\nRenaming genome.rev.2.bt2.tmp to genome.rev.2.bt2\n100 reads; of these:\n 100 (100.00%) were paired; of these:\n 97 (97.00%) aligned concordantly 0 times\n 3 (3.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 97 pairs aligned concordantly 0 times; of these:\n 8 (8.25%) aligned discordantly 1 time\n ----\n 89 pairs aligned 0 times concordantly or discordantly; of these:\n 178 mates make up the pairs; of these:\n 153 (85.96%) aligned 0 times\n 25 (14.04%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n23.50% overall alignment rate\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-08 18:54:16", "plugin": "core", "name": "end_epoch", "raw_value": "1731092056.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 18:54:15", "plugin": "core", "name": "start_epoch", "raw_value": "1731092055.0000000"}, {"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": "bowtie2/2.5.3+galaxy1-7", "has_data": true, "data": {"tool_id": "bowtie2", "tool_version": "2.5.3+galaxy1", "test_index": 7, "time_seconds": 43.765950441360474, "inputs": {"library|input_1": {"src": "hda", "id": "ba842aa808091507"}, "library|input_2": {"src": "hda", "id": "d715db4c907a8195"}, "library|unaligned_file": false, "library|paired_options|paired_options_selector": "no", "library|type": "paired", "reference_genome|own_file": {"src": "hda", "id": "0304bd7df663c49d"}, "reference_genome|source": "history", "analysis_type|analysis_type_selector": "simple"}, "job": {"model_class": "Job", "id": "d715db4c907a8195", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T18:54:58.139758", "update_time": "2024-11-08T18:55:13.224136", "galaxy_version": "24.1", "external_id": "gxy-55ngf", "handler": null, "job_runner_name": null, "command_line": "set -o | grep -q pipefail && set -o pipefail; bowtie2-build --threads ${GALAXY_SLOTS:-4} '/galaxy/server/database/objects/b/f/4/dataset_bf4208a1-3aee-4ac8-ab51-0ee4dbcf94a1.dat' genome && ln -s -f '/galaxy/server/database/objects/b/f/4/dataset_bf4208a1-3aee-4ac8-ab51-0ee4dbcf94a1.dat' genome.fa && ln -f -s '/galaxy/server/database/objects/c/2/5/dataset_c25ec8b2-ad83-42ec-a30a-d2bbd619e501.dat' input_f.fasta && ln -f -s '/galaxy/server/database/objects/5/9/c/dataset_59c35dbe-8b2f-4ab3-a306-ae0d9b92efdb.dat' input_r.fasta && THREADS=${GALAXY_SLOTS:-4} && if [ \"$THREADS\" -gt 1 ]; then (( THREADS-- )); fi && bowtie2 -p \"$THREADS\" -x 'genome' -f -1 'input_f.fasta' -2 'input_r.fasta' | samtools sort -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/7/0/b/dataset_70b2cdaf-930e-4d3d-9589-c2b5e39862c0.dat'", "user_email": "tests@fake.org", "command_version": "/usr/local/bin/bowtie2-align-s version 2.5.3\n64-bit\nBuilt on fv-az365-785\nWed Jan 17 04:43:48 UTC 2024\nCompiler: gcc version 12.3.0 (conda-forge gcc 12.3.0-3) \nOptions: -O3 -msse2 -funroll-loops -g3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /usr/local/include -fdebug-prefix-map=/opt/conda/conda-bld/bowtie2_1705465427853/work=/usr/local/src/conda/bowtie2-2.5.3 -fdebug-prefix-map=/usr/local=/usr/local/src/conda-prefix -std=c++11 -Wall -Wno-unused-but-set-variable -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -DWITH_ZSTD\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "save_mapping_stats": "false", "sam_options": "{\"__current_case__\": 1, \"sam_options_selector\": \"no\"}", "analysis_type": "{\"__current_case__\": 0, \"analysis_type_selector\": \"simple\", \"presets\": \"no_presets\"}", "rg": "{\"__current_case__\": 3, \"rg_selector\": \"do_not_set\"}", "reference_genome": "{\"__current_case__\": 1, \"own_file\": {\"values\": [{\"id\": 77, \"src\": \"hda\"}]}, \"source\": \"history\"}", "library": "{\"__current_case__\": 1, \"aligned_file\": false, \"input_1\": {\"values\": [{\"id\": 75, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 76, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 1, \"paired_options_selector\": \"no\"}, \"type\": \"paired\", \"unaligned_file\": false}"}, "inputs": {"library|input_1": {"id": "ba842aa808091507", "src": "hda", "uuid": "c25ec8b2-ad83-42ec-a30a-d2bbd619e501"}, "library|input_2": {"id": "d715db4c907a8195", "src": "hda", "uuid": "59c35dbe-8b2f-4ab3-a306-ae0d9b92efdb"}, "reference_genome|own_file": {"id": "0304bd7df663c49d", "src": "hda", "uuid": "bf4208a1-3aee-4ac8-ab51-0ee4dbcf94a1"}}, "outputs": {"output": {"id": "750f13f154bcda68", "src": "hda", "uuid": "70b2cdaf-930e-4d3d-9589-c2b5e39862c0"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Settings:\n Output files: \"genome.*.bt2\"\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 Max bucket size: default\n Max bucket size, sqrt multiplier: default\n Max bucket size, len divisor: 32\n Difference-cover sample period: 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 /galaxy/server/database/objects/b/f/4/dataset_bf4208a1-3aee-4ac8-ab51-0ee4dbcf94a1.dat\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\nbmax according to bmaxDivN setting: 517\nUsing parameters --bmax 388 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 388 --dcv 1024\nConstructing suffix-array element generator\nBuilding DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 86 sample suffixes\nGenerating random suffixes\nQSorting 86 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 86 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 12, merged 41; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 6; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 284.672 (target: 387)\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering Ebwt loop\nGetting block 1 of 58\n Reserving size (388) for bucket 1\nGetting block 2 of 58\nGetting block 3 of 58\nGetting block 4 of 58\nGetting block 5 of 58\n Calculating Z arrays for bucket 1\n Reserving size (388) for bucket 2\n Reserving size (388) for bucket 3\n Reserving size (388) for bucket 4\n Reserving size (388) for bucket 5\nGetting block 6 of 58\nGetting block 7 of 58\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 3\n Entering block accumulator loop for bucket 1:\n Calculating Z arrays for bucket 4\n Calculating Z arrays for bucket 5\n Reserving size (388) for bucket 6\n Reserving size (388) for bucket 7\n Calculating Z arrays for bucket 6\n Entering block accumulator loop for bucket 3:\n Entering block accumulator loop for bucket 2:\n Entering block accumulator loop for bucket 4:\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: 10%\n bucket 2: 10%\n bucket 3: 10%\n Entering block accumulator loop for bucket 7:\n bucket 5: 10%\n bucket 4: 10%\n bucket 1: 20%\n bucket 3: 20%\n bucket 2: 20%\n bucket 6: 10%\n bucket 5: 20%\n bucket 1: 30%\n bucket 4: 20%\n bucket 3: 30%\n bucket 7: 10%\n bucket 2: 30%\n bucket 1: 40%\n bucket 5: 30%\n bucket 4: 30%\n bucket 3: 40%\n bucket 6: 20%\n bucket 1: 50%\n bucket 5: 40%\n bucket 4: 40%\n bucket 2: 40%\n bucket 3: 50%\n bucket 7: 20%\n bucket 1: 60%\n bucket 4: 50%\n bucket 5: 50%\n bucket 3: 60%\n bucket 6: 30%\n bucket 1: 70%\n bucket 2: 50%\n bucket 4: 60%\n bucket 7: 30%\n bucket 5: 60%\n bucket 3: 70%\n bucket 1: 80%\n bucket 4: 70%\n bucket 6: 40%\n bucket 5: 70%\n bucket 2: 60%\n bucket 3: 80%\n bucket 1: 90%\n bucket 7: 40%\n bucket 4: 80%\n bucket 5: 80%\n bucket 3: 90%\n bucket 1: 100%\n Sorting block of length 355 for bucket 1\n (Using difference cover)\n bucket 2: 70%\n bucket 6: 50%\n bucket 4: 90%\n bucket 5: 90%\n bucket 3: 100%\n Sorting block of length 370 for bucket 3\n (Using difference cover)\n bucket 7: 50%\n bucket 4: 100%\n bucket 5: 100%\n bucket 2: 80%\n Sorting block of length 328 for bucket 4\n (Using difference cover)\n Sorting block of length 203 for bucket 5\n (Using difference cover)\n bucket 6: 60%\n bucket 7: 60%\n bucket 2: 90%\n bucket 6: 70%\n bucket 7: 70%\n bucket 2: 100%\n Sorting block of length 165 for bucket 2\n (Using difference cover)\n bucket 6: 80%\n bucket 7: 80%\n bucket 6: 90%\n bucket 7: 90%\n bucket 6: 100%\n Sorting block of length 339 for bucket 6\n (Using difference cover)\n bucket 7: 100%\n Sorting block of length 368 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 329 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 166 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 371 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 204 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 356 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 369 for bucket 7\nGetting block 8 of 58\n Reserving size (388) for bucket 8\nGetting block 9 of 58\n Calculating Z arrays for bucket 8\n Reserving size (388) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 8:\n Entering block accumulator loop for bucket 9:\n bucket 8: 10%\n bucket 9: 10%\n bucket 8: 20%\n bucket 9: 20%\n bucket 9: 30%\n bucket 8: 30%\n bucket 9: 40%\n bucket 8: 40%\n bucket 9: 50%\n bucket 8: 50%\n bucket 9: 60%\n bucket 8: 60%\n bucket 9: 70%\n bucket 9: 80%\n bucket 8: 70%\n bucket 9: 90%\n bucket 8: 80%\n bucket 9: 100%\n Sorting block of length 339 for bucket 9\n (Using difference cover)\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 171 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 172 for bucket 8\nGetting block 10 of 58\n Reserving size (388) 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 58\n bucket 10: 20%\n Reserving size (388) for bucket 11\n Calculating Z arrays for bucket 11\n bucket 10: 30%\n Entering block accumulator loop for bucket 11:\n bucket 10: 40%\n bucket 10: 50%\n bucket 11: 10%\n bucket 10: 60%\n bucket 10: 70%\n bucket 11: 20%\n bucket 10: 80%\n bucket 11: 30%\n bucket 10: 90%\n bucket 10: 100%\n bucket 11: 40%\n Sorting block of length 357 for bucket 10\n (Using difference cover)\n bucket 11: 50%\n bucket 11: 60%\n bucket 11: 70%\n bucket 11: 80%\n Sorting block time: 00:00:00\nReturning block of 358 for bucket 10\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 305 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 306 for bucket 11\nGetting block 12 of 58\n Reserving size (388) for bucket 12\nGetting block 13 of 58\n Calculating Z arrays for bucket 12\n Reserving size (388) 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 13: 10%\n bucket 12: 20%\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 12: 80%\n bucket 13: 50%\n bucket 12: 90%\n bucket 13: 60%\n bucket 12: 100%\n Sorting block of length 185 for bucket 12\n (Using difference cover)\n bucket 13: 70%\n bucket 13: 80%\n Sorting block time: 00:00:00\nReturning block of 186 for bucket 12\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 282 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 283 for bucket 13\nGetting block 14 of 58\n Reserving size (388) for bucket 14\n Calculating Z arrays for bucket 14\nGetting block 15 of 58\n Entering block accumulator loop for bucket 14:\n Reserving size (388) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\n bucket 14: 10%\n bucket 15: 10%\n bucket 14: 20%\n bucket 14: 30%\n bucket 15: 20%\n bucket 14: 40%\n bucket 15: 30%\n bucket 14: 50%\n bucket 14: 60%\n bucket 15: 40%\n bucket 14: 70%\n bucket 15: 50%\n bucket 14: 80%\n bucket 14: 90%\n bucket 15: 60%\n bucket 14: 100%\n Sorting block of length 339 for bucket 14\n (Using difference cover)\n bucket 15: 70%\n bucket 15: 80%\n bucket 15: 90%\n Sorting block time: 00:00:00\n bucket 15: 100%\nReturning block of 340 for bucket 14\n Sorting block of length 241 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 242 for bucket 15\nGetting block 16 of 58\n Reserving size (388) 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 379 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 380 for bucket 16\nGetting block 17 of 58\n Reserving size (388) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\nGetting block 18 of 58\n bucket 17: 10%\n Reserving size (388) for bucket 18\n Calculating Z arrays for bucket 18\nGetting block 19 of 58\n bucket 17: 20%\n Entering block accumulator loop for bucket 18:\n Reserving size (388) for bucket 19\n Calculating Z arrays for bucket 19\n bucket 17: 30%\n bucket 18: 10%\n Entering block accumulator loop for bucket 19:\n bucket 17: 40%\n bucket 18: 20%\n bucket 18: 30%\n bucket 17: 50%\n bucket 19: 10%\n bucket 17: 60%\n bucket 18: 40%\n bucket 17: 70%\n bucket 19: 20%\n bucket 18: 50%\n bucket 17: 80%\n bucket 19: 30%\n bucket 18: 60%\n bucket 17: 90%\n bucket 19: 40%\n bucket 18: 70%\n bucket 17: 100%\n bucket 19: 50%\n Sorting block of length 215 for bucket 17\n (Using difference cover)\n bucket 18: 80%\n bucket 19: 60%\n bucket 18: 90%\n bucket 19: 70%\n Sorting block time: 00:00:00\n bucket 18: 100%\nReturning block of 216 for bucket 17\n bucket 19: 80%\n Sorting block of length 378 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\n bucket 19: 90%\nReturning block of 379 for bucket 18\n bucket 19: 100%\n Sorting block of length 334 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 335 for bucket 19\nGetting block 20 of 58\n Reserving size (388) 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 313 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 314 for bucket 20\nGetting block 21 of 58\n Reserving size (388) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\nGetting block 22 of 58\n Reserving size (388) 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 22: 40%\n bucket 21: 60%\n bucket 22: 50%\n bucket 21: 70%\n bucket 21: 80%\n bucket 22: 60%\n bucket 22: 70%\n bucket 21: 90%\n bucket 22: 80%\n bucket 21: 100%\n Sorting block of length 210 for bucket 21\n (Using difference cover)\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 386 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 211 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 387 for bucket 22\nGetting block 23 of 58\n Reserving size (388) 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 238 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 239 for bucket 23\nGetting block 24 of 58\n Reserving size (388) for bucket 24\n Calculating Z arrays for bucket 24\nGetting block 25 of 58\n Reserving size (388) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 24:\n Entering block accumulator loop for bucket 25:\n bucket 24: 10%\n bucket 25: 10%\n bucket 24: 20%\n bucket 25: 20%\n bucket 24: 30%\n bucket 25: 30%\n bucket 24: 40%\n bucket 25: 40%\n bucket 24: 50%\n bucket 25: 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 25: 100%\n Sorting block of length 105 for bucket 25\n (Using difference cover)\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 351 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 106 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 352 for bucket 24\nGetting block 26 of 58\n Reserving size (388) 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%\nGetting block 27 of 58\n Reserving size (388) for bucket 27\n Calculating Z arrays for bucket 27\n bucket 26: 30%\n Entering block accumulator loop for bucket 27:\n bucket 26: 40%\n bucket 27: 10%\n bucket 26: 50%\n bucket 26: 60%\n bucket 27: 20%\n bucket 26: 70%\n bucket 27: 30%\n bucket 26: 80%\n bucket 26: 90%\n bucket 27: 40%\n bucket 26: 100%\n Sorting block of length 354 for bucket 26\n (Using difference cover)\n bucket 27: 50%\n bucket 27: 60%\n Sorting block time: 00:00:00\nReturning block of 355 for bucket 26\n bucket 27: 70%\n bucket 27: 80%\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 334 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 335 for bucket 27\nGetting block 28 of 58\n Reserving size (388) for bucket 28\n Calculating Z arrays for bucket 28\nGetting block 29 of 58\n Entering block accumulator loop for bucket 28:\n Reserving size (388) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 28: 10%\n bucket 29: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 29: 20%\n bucket 28: 40%\n bucket 29: 30%\n bucket 28: 50%\n bucket 29: 40%\n bucket 28: 60%\n bucket 29: 50%\n bucket 28: 70%\n bucket 29: 60%\n bucket 28: 80%\n bucket 29: 70%\n bucket 29: 80%\n bucket 28: 90%\n bucket 29: 90%\n bucket 28: 100%\n Sorting block of length 253 for bucket 28\n (Using difference cover)\n bucket 29: 100%\n Sorting block of length 289 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 254 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 290 for bucket 29\nGetting block 30 of 58\n Reserving size (388) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 30:\nGetting block 31 of 58\n Reserving size (388) for bucket 31\n Calculating Z arrays for bucket 31\n bucket 30: 10%\n Entering block accumulator loop for bucket 31:\n bucket 31: 10%\n bucket 30: 20%\n bucket 31: 20%\n bucket 30: 30%\n bucket 31: 30%\n bucket 30: 40%\n bucket 31: 40%\n bucket 30: 50%\n bucket 31: 50%\n bucket 31: 60%\n bucket 30: 60%\n bucket 31: 70%\n bucket 30: 70%\n bucket 31: 80%\n bucket 31: 90%\n bucket 30: 80%\n bucket 31: 100%\n Sorting block of length 377 for bucket 31\n (Using difference cover)\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 345 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 378 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 346 for bucket 30\nGetting block 32 of 58\n Reserving size (388) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block\n..\n0:00\nReturning block of 372 for bucket 22\nGetting block 24 of 57\n Reserving size (388) 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%\nGetting block 25 of 57\n Reserving size (388) for bucket 25\n Calculating Z arrays for bucket 25\n bucket 24: 30%\n Entering block accumulator loop for bucket 25:\n bucket 24: 40%\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 Sorting block of length 245 for bucket 24\n (Using difference cover)\n bucket 25: 50%\n bucket 25: 60%\n Sorting block time: 00:00:00\nReturning block of 246 for bucket 24\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 286 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 287 for bucket 25\nGetting block 26 of 57\n Reserving size (388) 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 384 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 385 for bucket 26\nGetting block 27 of 57\n Reserving size (388) 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 57\n Reserving size (388) for bucket 28\n Calculating Z arrays for bucket 28\n bucket 27: 20%\n Entering block accumulator loop for bucket 28:\n bucket 27: 30%\n bucket 27: 40%\n bucket 28: 10%\n bucket 27: 50%\n bucket 28: 20%\n bucket 27: 60%\n bucket 27: 70%\n bucket 28: 30%\n bucket 27: 80%\n bucket 27: 90%\n bucket 28: 40%\n bucket 27: 100%\n Sorting block of length 359 for bucket 27\n (Using difference cover)\n bucket 28: 50%\n bucket 28: 60%\n Sorting block time: 00:00:00\nReturning block of 360 for bucket 27\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 387 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 28\nGetting block 29 of 57\n Reserving size (388) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\nGetting block 30 of 57\n Reserving size (388) for bucket 30\n Calculating Z arrays for bucket 30\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 29: 60%\n bucket 30: 40%\n bucket 29: 70%\n bucket 29: 80%\n bucket 30: 50%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 195 for bucket 29\n (Using difference cover)\n bucket 30: 60%\n bucket 30: 70%\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 29\n bucket 30: 80%\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 257 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 258 for bucket 30\nGetting block 31 of 57\n Reserving size (388) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 31:\nGetting block 32 of 57\n bucket 31: 10%\n Reserving size (388) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 32:\n bucket 31: 20%\n bucket 32: 10%\n bucket 31: 30%\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 32: 70%\n bucket 31: 100%\n Sorting block of length 310 for bucket 31\n (Using difference cover)\n bucket 32: 80%\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 219 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 311 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 220 for bucket 32\nGetting block 33 of 57\n Reserving size (388) 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 387 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 33\nGetting block 34 of 57\n Reserving size (388) for bucket 34\n Calculating Z arrays for bucket 34\nGetting block 35 of 57\n Reserving size (388) 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 35: 10%\n bucket 34: 20%\n bucket 35: 20%\n bucket 34: 30%\n bucket 35: 30%\n bucket 34: 40%\n bucket 35: 40%\n bucket 34: 50%\n bucket 34: 60%\n bucket 35: 50%\n bucket 34: 70%\n bucket 35: 60%\n bucket 34: 80%\n bucket 35: 70%\n bucket 34: 90%\n bucket 35: 80%\n bucket 34: 100%\n Sorting block of length 275 for bucket 34\n (Using difference cover)\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 350 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 276 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 351 for bucket 35\nGetting block 36 of 57\n Reserving size (388) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\nGetting block 37 of 57\n Reserving size (388) for bucket 37\n Calculating Z arrays for bucket 37\n bucket 36: 10%\n Entering block accumulator loop for bucket 37:\nGetting block 38 of 57\n Reserving size (388) for bucket 38\n Calculating Z arrays for bucket 38\n bucket 37: 10%\n Entering block accumulator loop for bucket 38:\n bucket 36: 20%\n bucket 37: 20%\n bucket 38: 10%\n bucket 36: 30%\n bucket 38: 20%\n bucket 37: 30%\n bucket 36: 40%\n bucket 38: 30%\n bucket 37: 40%\n bucket 36: 50%\n bucket 37: 50%\n bucket 38: 40%\n bucket 38: 50%\n bucket 37: 60%\n bucket 36: 60%\n bucket 38: 60%\n bucket 37: 70%\n bucket 36: 70%\n bucket 38: 70%\n bucket 37: 80%\n bucket 36: 80%\n bucket 38: 80%\n bucket 37: 90%\n bucket 36: 90%\n bucket 38: 90%\n bucket 37: 100%\n Sorting block of length 267 for bucket 37\n (Using difference cover)\n bucket 38: 100%\n bucket 36: 100%\n Sorting block of length 337 for bucket 38\n (Using difference cover)\n Sorting block of length 150 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 268 for bucket 37\n Sorting block time: 00:00:00\nReturning block of 151 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 338 for bucket 38\nGetting block 39 of 57\n Reserving size (388) for bucket 39\n Calculating Z arrays for bucket 39\nGetting block 40 of 57\n Entering block accumulator loop for bucket 39:\n Reserving size (388) for bucket 40\n Calculating Z arrays for bucket 40\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 40: 60%\n bucket 39: 80%\n bucket 40: 70%\n bucket 39: 90%\n bucket 40: 80%\n bucket 39: 100%\n Sorting block of length 387 for bucket 39\n (Using difference cover)\n bucket 40: 90%\n bucket 40: 100%\n Sorting block of length 379 for bucket 40\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 39\n Sorting block time: 00:00:00\nReturning block of 380 for bucket 40\nGetting block 41 of 57\n Reserving size (388) for bucket 41\n Calculating Z arrays for bucket 41\nGetting block 42 of 57\n Reserving size (388) for bucket 42\n Entering block accumulator loop for bucket 41:\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\n bucket 41: 10%\n bucket 42: 10%\n bucket 41: 20%\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 41: 70%\n bucket 42: 50%\n bucket 41: 80%\n bucket 41: 90%\n bucket 42: 60%\n bucket 41: 100%\n Sorting block of length 330 for bucket 41\n (Using difference cover)\n bucket 42: 70%\n bucket 42: 80%\n Sorting block time: 00:00:00\nReturning block of 331 for bucket 41\n bucket 42: 90%\n bucket 42: 100%\n Sorting block of length 188 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 189 for bucket 42\nGetting block 43 of 57\n Reserving size (388) for bucket 43\nGetting block 44 of 57\n Calculating Z arrays for bucket 43\n Reserving size (388) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 43:\n Entering block accumulator loop for bucket 44:\n bucket 43: 10%\n bucket 44: 10%\n bucket 43: 20%\n bucket 44: 20%\n bucket 43: 30%\n bucket 43: 40%\n bucket 44: 30%\n bucket 43: 50%\n bucket 44: 40%\n bucket 43: 60%\n bucket 44: 50%\n bucket 43: 70%\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 321 for bucket 43\n (Using difference cover)\n bucket 44: 80%\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 366 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 322 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 367 for bucket 44\nGetting block 45 of 57\n Reserving size (388) 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 365 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 366 for bucket 45\nGetting block 46 of 57\n Reserving size (388) for bucket 46\n Calculating Z arrays for bucket 46\nGetting block 47 of 57\n Reserving size (388) 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 47: 10%\n bucket 46: 20%\n bucket 47: 20%\n bucket 46: 30%\n bucket 47: 30%\n bucket 47: 40%\n bucket 46: 40%\n bucket 47: 50%\n bucket 47: 60%\n bucket 46: 50%\n bucket 47: 70%\n bucket 46: 60%\n bucket 47: 80%\n bucket 47: 90%\n bucket 46: 70%\n bucket 47: 100%\n Sorting block of length 217 for bucket 47\n (Using difference cover)\n bucket 46: 80%\n Sorting block time: 00:00:00\nReturning block of 218 for bucket 47\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 253 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 254 for bucket 46\nGetting block 48 of 57\n Reserving size (388) for bucket 48\nGetting block 49 of 57\n Calculating Z arrays for bucket 48\n Reserving size (388) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 48:\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\n bucket 48: 10%\n bucket 49: 20%\n bucket 48: 20%\n bucket 49: 30%\n bucket 48: 30%\n bucket 48: 40%\n bucket 49: 40%\n bucket 48: 50%\n bucket 49: 50%\n bucket 48: 60%\n bucket 49: 60%\n bucket 49: 70%\n bucket 48: 70%\n bucket 49: 80%\n bucket 48: 80%\n bucket 48: 90%\n bucket 49: 90%\n bucket 48: 100%\n Sorting block of length 384 for bucket 48\n (Using difference cover)\n bucket 49: 100%\n Sorting block of length 112 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 385 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 49\nGetting block 50 of 57\n Reserving size (388) for bucket 50\n Calculating Z arrays for bucket 50\nGetting block 51 of 57\n Reserving size (388) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 50:\n Entering block accumulator loop for bucket 51:\n bucket 50: 10%\n bucket 51: 10%\n bucket 50: 20%\n bucket 51: 20%\n bucket 50: 30%\n bucket 50: 40%\n bucket 51: 30%\n bucket 50: 50%\n bucket 51: 40%\n bucket 50: 60%\n bucket 51: 50%\n bucket 50: 70%\n bucket 51: 60%\n bucket 50: 80%\n bucket 51: 70%\n bucket 50: 90%\n bucket 51: 80%\n bucket 50: 100%\n Sorting block of length 275 for bucket 50\n (Using difference cover)\n bucket 51: 90%\n bucket 51: 100%\n Sorting block of length 350 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 276 for bucket 50\n Sorting block time: 00:00:00\nReturning block of 351 for bucket 51\nGetting block 52 of 57\n Reserving size (388) 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 378 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 379 for bucket 52\nGetting block 53 of 57\n Reserving size (388) for bucket 53\n Calculating Z arrays for bucket 53\nGetting block 54 of 57\n Reserving size (388) 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 54: 10%\n bucket 53: 20%\n bucket 54: 20%\n bucket 53: 30%\n bucket 53: 40%\n bucket 54: 30%\n bucket 54: 40%\n bucket 53: 50%\n bucket 54: 50%\n bucket 53: 60%\n bucket 54: 60%\n bucket 53: 70%\n bucket 54: 70%\n bucket 53: 80%\n bucket 54: 80%\n bucket 53: 90%\n bucket 54: 90%\n bucket 54: 100%\n bucket 53: 100%\n Sorting block of length 237 for bucket 54\n (Using difference cover)\n Sorting block of length 370 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 238 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 371 for bucket 53\nGetting block 55 of 57\n Reserving size (388) for bucket 55\n Calculating Z arrays for bucket 55\nGetting block 56 of 57\n Reserving size (388) for bucket 56\n Calculating Z arrays for bucket 56\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 55: 40%\n bucket 56: 40%\n bucket 55: 50%\n bucket 56: 50%\n bucket 55: 60%\n bucket 56: 60%\n bucket 55: 70%\n bucket 56: 70%\n bucket 55: 80%\n bucket 56: 80%\n bucket 55: 90%\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 270 for bucket 56\n (Using difference cover)\n bucket 55: 100%\n Sorting block of length 344 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 271 for bucket 56\n Sorting block time: 00:00:00\nReturning block of 345 for bucket 55\nGetting block 57 of 57\n Reserving size (388) 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 132 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 133 for bucket 57\nExited Ebwt loop\nfchr[A]: 0\nfchr[C]: 5124\nfchr[G]: 10305\nfchr[T]: 12474\nfchr[$]: 16568\nExiting Ebwt::buildToDisk()\nReturning from initFromVector\nWrote 4200050 bytes to primary EBWT file: genome.rev.1.bt2.tmp\nWrote 4148 bytes to secondary EBWT file: genome.rev.2.bt2.tmp\nRe-opening _in1 and _in2 as input streams\nReturning from Ebwt constructor\nHeaders:\n len: 16568\n bwtLen: 16569\n sz: 4142\n bwtSz: 4143\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 20\n eftabSz: 80\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 1036\n offsSz: 4144\n lineSz: 64\n sideSz: 64\n sideBwtSz: 48\n sideBwtLen: 192\n numSides: 87\n numLines: 87\n ebwtTotLen: 5568\n ebwtTotSz: 5568\n color: 0\n reverse: 1\nTotal time for backward call to driver() for mirror index: 00:00:00\n", "tool_stderr": "Building a SMALL index\nRenaming genome.3.bt2.tmp to genome.3.bt2\nRenaming genome.4.bt2.tmp to genome.4.bt2\nRenaming genome.1.bt2.tmp to genome.1.bt2\nRenaming genome.2.bt2.tmp to genome.2.bt2\nRenaming genome.rev.1.bt2.tmp to genome.rev.1.bt2\nRenaming genome.rev.2.bt2.tmp to genome.rev.2.bt2\n100 reads; of these:\n 100 (100.00%) were paired; of these:\n 97 (97.00%) aligned concordantly 0 times\n 3 (3.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 97 pairs aligned concordantly 0 times; of these:\n 7 (7.22%) aligned discordantly 1 time\n ----\n 90 pairs aligned 0 times concordantly or discordantly; of these:\n 180 mates make up the pairs; of these:\n 156 (86.67%) aligned 0 times\n 24 (13.33%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n22.00% overall alignment rate\n", "job_stdout": "", "job_stderr": "", "stdout": "Settings:\n Output files: \"genome.*.bt2\"\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 Max bucket size: default\n Max bucket size, sqrt multiplier: default\n Max bucket size, len divisor: 32\n Difference-cover sample period: 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 /galaxy/server/database/objects/b/f/4/dataset_bf4208a1-3aee-4ac8-ab51-0ee4dbcf94a1.dat\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\nbmax according to bmaxDivN setting: 517\nUsing parameters --bmax 388 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 388 --dcv 1024\nConstructing suffix-array element generator\nBuilding DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 86 sample suffixes\nGenerating random suffixes\nQSorting 86 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 86 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 12, merged 41; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 6; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 284.672 (target: 387)\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering Ebwt loop\nGetting block 1 of 58\n Reserving size (388) for bucket 1\nGetting block 2 of 58\nGetting block 3 of 58\nGetting block 4 of 58\nGetting block 5 of 58\n Calculating Z arrays for bucket 1\n Reserving size (388) for bucket 2\n Reserving size (388) for bucket 3\n Reserving size (388) for bucket 4\n Reserving size (388) for bucket 5\nGetting block 6 of 58\nGetting block 7 of 58\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 3\n Entering block accumulator loop for bucket 1:\n Calculating Z arrays for bucket 4\n Calculating Z arrays for bucket 5\n Reserving size (388) for bucket 6\n Reserving size (388) for bucket 7\n Calculating Z arrays for bucket 6\n Entering block accumulator loop for bucket 3:\n Entering block accumulator loop for bucket 2:\n Entering block accumulator loop for bucket 4:\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: 10%\n bucket 2: 10%\n bucket 3: 10%\n Entering block accumulator loop for bucket 7:\n bucket 5: 10%\n bucket 4: 10%\n bucket 1: 20%\n bucket 3: 20%\n bucket 2: 20%\n bucket 6: 10%\n bucket 5: 20%\n bucket 1: 30%\n bucket 4: 20%\n bucket 3: 30%\n bucket 7: 10%\n bucket 2: 30%\n bucket 1: 40%\n bucket 5: 30%\n bucket 4: 30%\n bucket 3: 40%\n bucket 6: 20%\n bucket 1: 50%\n bucket 5: 40%\n bucket 4: 40%\n bucket 2: 40%\n bucket 3: 50%\n bucket 7: 20%\n bucket 1: 60%\n bucket 4: 50%\n bucket 5: 50%\n bucket 3: 60%\n bucket 6: 30%\n bucket 1: 70%\n bucket 2: 50%\n bucket 4: 60%\n bucket 7: 30%\n bucket 5: 60%\n bucket 3: 70%\n bucket 1: 80%\n bucket 4: 70%\n bucket 6: 40%\n bucket 5: 70%\n bucket 2: 60%\n bucket 3: 80%\n bucket 1: 90%\n bucket 7: 40%\n bucket 4: 80%\n bucket 5: 80%\n bucket 3: 90%\n bucket 1: 100%\n Sorting block of length 355 for bucket 1\n (Using difference cover)\n bucket 2: 70%\n bucket 6: 50%\n bucket 4: 90%\n bucket 5: 90%\n bucket 3: 100%\n Sorting block of length 370 for bucket 3\n (Using difference cover)\n bucket 7: 50%\n bucket 4: 100%\n bucket 5: 100%\n bucket 2: 80%\n Sorting block of length 328 for bucket 4\n (Using difference cover)\n Sorting block of length 203 for bucket 5\n (Using difference cover)\n bucket 6: 60%\n bucket 7: 60%\n bucket 2: 90%\n bucket 6: 70%\n bucket 7: 70%\n bucket 2: 100%\n Sorting block of length 165 for bucket 2\n (Using difference cover)\n bucket 6: 80%\n bucket 7: 80%\n bucket 6: 90%\n bucket 7: 90%\n bucket 6: 100%\n Sorting block of length 339 for bucket 6\n (Using difference cover)\n bucket 7: 100%\n Sorting block of length 368 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 329 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 166 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 371 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 204 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 356 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 369 for bucket 7\nGetting block 8 of 58\n Reserving size (388) for bucket 8\nGetting block 9 of 58\n Calculating Z arrays for bucket 8\n Reserving size (388) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 8:\n Entering block accumulator loop for bucket 9:\n bucket 8: 10%\n bucket 9: 10%\n bucket 8: 20%\n bucket 9: 20%\n bucket 9: 30%\n bucket 8: 30%\n bucket 9: 40%\n bucket 8: 40%\n bucket 9: 50%\n bucket 8: 50%\n bucket 9: 60%\n bucket 8: 60%\n bucket 9: 70%\n bucket 9: 80%\n bucket 8: 70%\n bucket 9: 90%\n bucket 8: 80%\n bucket 9: 100%\n Sorting block of length 339 for bucket 9\n (Using difference cover)\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 171 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 172 for bucket 8\nGetting block 10 of 58\n Reserving size (388) 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 58\n bucket 10: 20%\n Reserving size (388) for bucket 11\n Calculating Z arrays for bucket 11\n bucket 10: 30%\n Entering block accumulator loop for bucket 11:\n bucket 10: 40%\n bucket 10: 50%\n bucket 11: 10%\n bucket 10: 60%\n bucket 10: 70%\n bucket 11: 20%\n bucket 10: 80%\n bucket 11: 30%\n bucket 10: 90%\n bucket 10: 100%\n bucket 11: 40%\n Sorting block of length 357 for bucket 10\n (Using difference cover)\n bucket 11: 50%\n bucket 11: 60%\n bucket 11: 70%\n bucket 11: 80%\n Sorting block time: 00:00:00\nReturning block of 358 for bucket 10\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 305 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 306 for bucket 11\nGetting block 12 of 58\n Reserving size (388) for bucket 12\nGetting block 13 of 58\n Calculating Z arrays for bucket 12\n Reserving size (388) 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 13: 10%\n bucket 12: 20%\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 12: 80%\n bucket 13: 50%\n bucket 12: 90%\n bucket 13: 60%\n bucket 12: 100%\n Sorting block of length 185 for bucket 12\n (Using difference cover)\n bucket 13: 70%\n bucket 13: 80%\n Sorting block time: 00:00:00\nReturning block of 186 for bucket 12\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 282 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 283 for bucket 13\nGetting block 14 of 58\n Reserving size (388) for bucket 14\n Calculating Z arrays for bucket 14\nGetting block 15 of 58\n Entering block accumulator loop for bucket 14:\n Reserving size (388) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\n bucket 14: 10%\n bucket 15: 10%\n bucket 14: 20%\n bucket 14: 30%\n bucket 15: 20%\n bucket 14: 40%\n bucket 15: 30%\n bucket 14: 50%\n bucket 14: 60%\n bucket 15: 40%\n bucket 14: 70%\n bucket 15: 50%\n bucket 14: 80%\n bucket 14: 90%\n bucket 15: 60%\n bucket 14: 100%\n Sorting block of length 339 for bucket 14\n (Using difference cover)\n bucket 15: 70%\n bucket 15: 80%\n bucket 15: 90%\n Sorting block time: 00:00:00\n bucket 15: 100%\nReturning block of 340 for bucket 14\n Sorting block of length 241 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 242 for bucket 15\nGetting block 16 of 58\n Reserving size (388) 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 379 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 380 for bucket 16\nGetting block 17 of 58\n Reserving size (388) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\nGetting block 18 of 58\n bucket 17: 10%\n Reserving size (388) for bucket 18\n Calculating Z arrays for bucket 18\nGetting block 19 of 58\n bucket 17: 20%\n Entering block accumulator loop for bucket 18:\n Reserving size (388) for bucket 19\n Calculating Z arrays for bucket 19\n bucket 17: 30%\n bucket 18: 10%\n Entering block accumulator loop for bucket 19:\n bucket 17: 40%\n bucket 18: 20%\n bucket 18: 30%\n bucket 17: 50%\n bucket 19: 10%\n bucket 17: 60%\n bucket 18: 40%\n bucket 17: 70%\n bucket 19: 20%\n bucket 18: 50%\n bucket 17: 80%\n bucket 19: 30%\n bucket 18: 60%\n bucket 17: 90%\n bucket 19: 40%\n bucket 18: 70%\n bucket 17: 100%\n bucket 19: 50%\n Sorting block of length 215 for bucket 17\n (Using difference cover)\n bucket 18: 80%\n bucket 19: 60%\n bucket 18: 90%\n bucket 19: 70%\n Sorting block time: 00:00:00\n bucket 18: 100%\nReturning block of 216 for bucket 17\n bucket 19: 80%\n Sorting block of length 378 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\n bucket 19: 90%\nReturning block of 379 for bucket 18\n bucket 19: 100%\n Sorting block of length 334 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 335 for bucket 19\nGetting block 20 of 58\n Reserving size (388) 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 313 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 314 for bucket 20\nGetting block 21 of 58\n Reserving size (388) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\nGetting block 22 of 58\n Reserving size (388) 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 22: 40%\n bucket 21: 60%\n bucket 22: 50%\n bucket 21: 70%\n bucket 21: 80%\n bucket 22: 60%\n bucket 22: 70%\n bucket 21: 90%\n bucket 22: 80%\n bucket 21: 100%\n Sorting block of length 210 for bucket 21\n (Using difference cover)\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 386 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 211 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 387 for bucket 22\nGetting block 23 of 58\n Reserving size (388) 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 238 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 239 for bucket 23\nGetting block 24 of 58\n Reserving size (388) for bucket 24\n Calculating Z arrays for bucket 24\nGetting block 25 of 58\n Reserving size (388) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 24:\n Entering block accumulator loop for bucket 25:\n bucket 24: 10%\n bucket 25: 10%\n bucket 24: 20%\n bucket 25: 20%\n bucket 24: 30%\n bucket 25: 30%\n bucket 24: 40%\n bucket 25: 40%\n bucket 24: 50%\n bucket 25: 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 25: 100%\n Sorting block of length 105 for bucket 25\n (Using difference cover)\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 351 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 106 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 352 for bucket 24\nGetting block 26 of 58\n Reserving size (388) 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%\nGetting block 27 of 58\n Reserving size (388) for bucket 27\n Calculating Z arrays for bucket 27\n bucket 26: 30%\n Entering block accumulator loop for bucket 27:\n bucket 26: 40%\n bucket 27: 10%\n bucket 26: 50%\n bucket 26: 60%\n bucket 27: 20%\n bucket 26: 70%\n bucket 27: 30%\n bucket 26: 80%\n bucket 26: 90%\n bucket 27: 40%\n bucket 26: 100%\n Sorting block of length 354 for bucket 26\n (Using difference cover)\n bucket 27: 50%\n bucket 27: 60%\n Sorting block time: 00:00:00\nReturning block of 355 for bucket 26\n bucket 27: 70%\n bucket 27: 80%\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 334 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 335 for bucket 27\nGetting block 28 of 58\n Reserving size (388) for bucket 28\n Calculating Z arrays for bucket 28\nGetting block 29 of 58\n Entering block accumulator loop for bucket 28:\n Reserving size (388) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 28: 10%\n bucket 29: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 29: 20%\n bucket 28: 40%\n bucket 29: 30%\n bucket 28: 50%\n bucket 29: 40%\n bucket 28: 60%\n bucket 29: 50%\n bucket 28: 70%\n bucket 29: 60%\n bucket 28: 80%\n bucket 29: 70%\n bucket 29: 80%\n bucket 28: 90%\n bucket 29: 90%\n bucket 28: 100%\n Sorting block of length 253 for bucket 28\n (Using difference cover)\n bucket 29: 100%\n Sorting block of length 289 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 254 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 290 for bucket 29\nGetting block 30 of 58\n Reserving size (388) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 30:\nGetting block 31 of 58\n Reserving size (388) for bucket 31\n Calculating Z arrays for bucket 31\n bucket 30: 10%\n Entering block accumulator loop for bucket 31:\n bucket 31: 10%\n bucket 30: 20%\n bucket 31: 20%\n bucket 30: 30%\n bucket 31: 30%\n bucket 30: 40%\n bucket 31: 40%\n bucket 30: 50%\n bucket 31: 50%\n bucket 31: 60%\n bucket 30: 60%\n bucket 31: 70%\n bucket 30: 70%\n bucket 31: 80%\n bucket 31: 90%\n bucket 30: 80%\n bucket 31: 100%\n Sorting block of length 377 for bucket 31\n (Using difference cover)\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 345 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 378 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 346 for bucket 30\nGetting block 32 of 58\n Reserving size (388) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block\n..\n0:00\nReturning block of 372 for bucket 22\nGetting block 24 of 57\n Reserving size (388) 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%\nGetting block 25 of 57\n Reserving size (388) for bucket 25\n Calculating Z arrays for bucket 25\n bucket 24: 30%\n Entering block accumulator loop for bucket 25:\n bucket 24: 40%\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 Sorting block of length 245 for bucket 24\n (Using difference cover)\n bucket 25: 50%\n bucket 25: 60%\n Sorting block time: 00:00:00\nReturning block of 246 for bucket 24\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 286 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 287 for bucket 25\nGetting block 26 of 57\n Reserving size (388) 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 384 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 385 for bucket 26\nGetting block 27 of 57\n Reserving size (388) 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 57\n Reserving size (388) for bucket 28\n Calculating Z arrays for bucket 28\n bucket 27: 20%\n Entering block accumulator loop for bucket 28:\n bucket 27: 30%\n bucket 27: 40%\n bucket 28: 10%\n bucket 27: 50%\n bucket 28: 20%\n bucket 27: 60%\n bucket 27: 70%\n bucket 28: 30%\n bucket 27: 80%\n bucket 27: 90%\n bucket 28: 40%\n bucket 27: 100%\n Sorting block of length 359 for bucket 27\n (Using difference cover)\n bucket 28: 50%\n bucket 28: 60%\n Sorting block time: 00:00:00\nReturning block of 360 for bucket 27\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 387 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 28\nGetting block 29 of 57\n Reserving size (388) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\nGetting block 30 of 57\n Reserving size (388) for bucket 30\n Calculating Z arrays for bucket 30\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 29: 60%\n bucket 30: 40%\n bucket 29: 70%\n bucket 29: 80%\n bucket 30: 50%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 195 for bucket 29\n (Using difference cover)\n bucket 30: 60%\n bucket 30: 70%\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 29\n bucket 30: 80%\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 257 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 258 for bucket 30\nGetting block 31 of 57\n Reserving size (388) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 31:\nGetting block 32 of 57\n bucket 31: 10%\n Reserving size (388) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 32:\n bucket 31: 20%\n bucket 32: 10%\n bucket 31: 30%\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 32: 70%\n bucket 31: 100%\n Sorting block of length 310 for bucket 31\n (Using difference cover)\n bucket 32: 80%\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 219 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 311 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 220 for bucket 32\nGetting block 33 of 57\n Reserving size (388) 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 387 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 33\nGetting block 34 of 57\n Reserving size (388) for bucket 34\n Calculating Z arrays for bucket 34\nGetting block 35 of 57\n Reserving size (388) 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 35: 10%\n bucket 34: 20%\n bucket 35: 20%\n bucket 34: 30%\n bucket 35: 30%\n bucket 34: 40%\n bucket 35: 40%\n bucket 34: 50%\n bucket 34: 60%\n bucket 35: 50%\n bucket 34: 70%\n bucket 35: 60%\n bucket 34: 80%\n bucket 35: 70%\n bucket 34: 90%\n bucket 35: 80%\n bucket 34: 100%\n Sorting block of length 275 for bucket 34\n (Using difference cover)\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 350 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 276 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 351 for bucket 35\nGetting block 36 of 57\n Reserving size (388) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\nGetting block 37 of 57\n Reserving size (388) for bucket 37\n Calculating Z arrays for bucket 37\n bucket 36: 10%\n Entering block accumulator loop for bucket 37:\nGetting block 38 of 57\n Reserving size (388) for bucket 38\n Calculating Z arrays for bucket 38\n bucket 37: 10%\n Entering block accumulator loop for bucket 38:\n bucket 36: 20%\n bucket 37: 20%\n bucket 38: 10%\n bucket 36: 30%\n bucket 38: 20%\n bucket 37: 30%\n bucket 36: 40%\n bucket 38: 30%\n bucket 37: 40%\n bucket 36: 50%\n bucket 37: 50%\n bucket 38: 40%\n bucket 38: 50%\n bucket 37: 60%\n bucket 36: 60%\n bucket 38: 60%\n bucket 37: 70%\n bucket 36: 70%\n bucket 38: 70%\n bucket 37: 80%\n bucket 36: 80%\n bucket 38: 80%\n bucket 37: 90%\n bucket 36: 90%\n bucket 38: 90%\n bucket 37: 100%\n Sorting block of length 267 for bucket 37\n (Using difference cover)\n bucket 38: 100%\n bucket 36: 100%\n Sorting block of length 337 for bucket 38\n (Using difference cover)\n Sorting block of length 150 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 268 for bucket 37\n Sorting block time: 00:00:00\nReturning block of 151 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 338 for bucket 38\nGetting block 39 of 57\n Reserving size (388) for bucket 39\n Calculating Z arrays for bucket 39\nGetting block 40 of 57\n Entering block accumulator loop for bucket 39:\n Reserving size (388) for bucket 40\n Calculating Z arrays for bucket 40\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 40: 60%\n bucket 39: 80%\n bucket 40: 70%\n bucket 39: 90%\n bucket 40: 80%\n bucket 39: 100%\n Sorting block of length 387 for bucket 39\n (Using difference cover)\n bucket 40: 90%\n bucket 40: 100%\n Sorting block of length 379 for bucket 40\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 39\n Sorting block time: 00:00:00\nReturning block of 380 for bucket 40\nGetting block 41 of 57\n Reserving size (388) for bucket 41\n Calculating Z arrays for bucket 41\nGetting block 42 of 57\n Reserving size (388) for bucket 42\n Entering block accumulator loop for bucket 41:\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\n bucket 41: 10%\n bucket 42: 10%\n bucket 41: 20%\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 41: 70%\n bucket 42: 50%\n bucket 41: 80%\n bucket 41: 90%\n bucket 42: 60%\n bucket 41: 100%\n Sorting block of length 330 for bucket 41\n (Using difference cover)\n bucket 42: 70%\n bucket 42: 80%\n Sorting block time: 00:00:00\nReturning block of 331 for bucket 41\n bucket 42: 90%\n bucket 42: 100%\n Sorting block of length 188 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 189 for bucket 42\nGetting block 43 of 57\n Reserving size (388) for bucket 43\nGetting block 44 of 57\n Calculating Z arrays for bucket 43\n Reserving size (388) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 43:\n Entering block accumulator loop for bucket 44:\n bucket 43: 10%\n bucket 44: 10%\n bucket 43: 20%\n bucket 44: 20%\n bucket 43: 30%\n bucket 43: 40%\n bucket 44: 30%\n bucket 43: 50%\n bucket 44: 40%\n bucket 43: 60%\n bucket 44: 50%\n bucket 43: 70%\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 321 for bucket 43\n (Using difference cover)\n bucket 44: 80%\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 366 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 322 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 367 for bucket 44\nGetting block 45 of 57\n Reserving size (388) 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 365 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 366 for bucket 45\nGetting block 46 of 57\n Reserving size (388) for bucket 46\n Calculating Z arrays for bucket 46\nGetting block 47 of 57\n Reserving size (388) 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 47: 10%\n bucket 46: 20%\n bucket 47: 20%\n bucket 46: 30%\n bucket 47: 30%\n bucket 47: 40%\n bucket 46: 40%\n bucket 47: 50%\n bucket 47: 60%\n bucket 46: 50%\n bucket 47: 70%\n bucket 46: 60%\n bucket 47: 80%\n bucket 47: 90%\n bucket 46: 70%\n bucket 47: 100%\n Sorting block of length 217 for bucket 47\n (Using difference cover)\n bucket 46: 80%\n Sorting block time: 00:00:00\nReturning block of 218 for bucket 47\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 253 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 254 for bucket 46\nGetting block 48 of 57\n Reserving size (388) for bucket 48\nGetting block 49 of 57\n Calculating Z arrays for bucket 48\n Reserving size (388) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 48:\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\n bucket 48: 10%\n bucket 49: 20%\n bucket 48: 20%\n bucket 49: 30%\n bucket 48: 30%\n bucket 48: 40%\n bucket 49: 40%\n bucket 48: 50%\n bucket 49: 50%\n bucket 48: 60%\n bucket 49: 60%\n bucket 49: 70%\n bucket 48: 70%\n bucket 49: 80%\n bucket 48: 80%\n bucket 48: 90%\n bucket 49: 90%\n bucket 48: 100%\n Sorting block of length 384 for bucket 48\n (Using difference cover)\n bucket 49: 100%\n Sorting block of length 112 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 385 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 49\nGetting block 50 of 57\n Reserving size (388) for bucket 50\n Calculating Z arrays for bucket 50\nGetting block 51 of 57\n Reserving size (388) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 50:\n Entering block accumulator loop for bucket 51:\n bucket 50: 10%\n bucket 51: 10%\n bucket 50: 20%\n bucket 51: 20%\n bucket 50: 30%\n bucket 50: 40%\n bucket 51: 30%\n bucket 50: 50%\n bucket 51: 40%\n bucket 50: 60%\n bucket 51: 50%\n bucket 50: 70%\n bucket 51: 60%\n bucket 50: 80%\n bucket 51: 70%\n bucket 50: 90%\n bucket 51: 80%\n bucket 50: 100%\n Sorting block of length 275 for bucket 50\n (Using difference cover)\n bucket 51: 90%\n bucket 51: 100%\n Sorting block of length 350 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 276 for bucket 50\n Sorting block time: 00:00:00\nReturning block of 351 for bucket 51\nGetting block 52 of 57\n Reserving size (388) 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 378 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 379 for bucket 52\nGetting block 53 of 57\n Reserving size (388) for bucket 53\n Calculating Z arrays for bucket 53\nGetting block 54 of 57\n Reserving size (388) 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 54: 10%\n bucket 53: 20%\n bucket 54: 20%\n bucket 53: 30%\n bucket 53: 40%\n bucket 54: 30%\n bucket 54: 40%\n bucket 53: 50%\n bucket 54: 50%\n bucket 53: 60%\n bucket 54: 60%\n bucket 53: 70%\n bucket 54: 70%\n bucket 53: 80%\n bucket 54: 80%\n bucket 53: 90%\n bucket 54: 90%\n bucket 54: 100%\n bucket 53: 100%\n Sorting block of length 237 for bucket 54\n (Using difference cover)\n Sorting block of length 370 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 238 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 371 for bucket 53\nGetting block 55 of 57\n Reserving size (388) for bucket 55\n Calculating Z arrays for bucket 55\nGetting block 56 of 57\n Reserving size (388) for bucket 56\n Calculating Z arrays for bucket 56\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 55: 40%\n bucket 56: 40%\n bucket 55: 50%\n bucket 56: 50%\n bucket 55: 60%\n bucket 56: 60%\n bucket 55: 70%\n bucket 56: 70%\n bucket 55: 80%\n bucket 56: 80%\n bucket 55: 90%\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 270 for bucket 56\n (Using difference cover)\n bucket 55: 100%\n Sorting block of length 344 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 271 for bucket 56\n Sorting block time: 00:00:00\nReturning block of 345 for bucket 55\nGetting block 57 of 57\n Reserving size (388) 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 132 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 133 for bucket 57\nExited Ebwt loop\nfchr[A]: 0\nfchr[C]: 5124\nfchr[G]: 10305\nfchr[T]: 12474\nfchr[$]: 16568\nExiting Ebwt::buildToDisk()\nReturning from initFromVector\nWrote 4200050 bytes to primary EBWT file: genome.rev.1.bt2.tmp\nWrote 4148 bytes to secondary EBWT file: genome.rev.2.bt2.tmp\nRe-opening _in1 and _in2 as input streams\nReturning from Ebwt constructor\nHeaders:\n len: 16568\n bwtLen: 16569\n sz: 4142\n bwtSz: 4143\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 20\n eftabSz: 80\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 1036\n offsSz: 4144\n lineSz: 64\n sideSz: 64\n sideBwtSz: 48\n sideBwtLen: 192\n numSides: 87\n numLines: 87\n ebwtTotLen: 5568\n ebwtTotSz: 5568\n color: 0\n reverse: 1\nTotal time for backward call to driver() for mirror index: 00:00:00\n", "stderr": "Building a SMALL index\nRenaming genome.3.bt2.tmp to genome.3.bt2\nRenaming genome.4.bt2.tmp to genome.4.bt2\nRenaming genome.1.bt2.tmp to genome.1.bt2\nRenaming genome.2.bt2.tmp to genome.2.bt2\nRenaming genome.rev.1.bt2.tmp to genome.rev.1.bt2\nRenaming genome.rev.2.bt2.tmp to genome.rev.2.bt2\n100 reads; of these:\n 100 (100.00%) were paired; of these:\n 97 (97.00%) aligned concordantly 0 times\n 3 (3.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 97 pairs aligned concordantly 0 times; of these:\n 7 (7.22%) aligned discordantly 1 time\n ----\n 90 pairs aligned 0 times concordantly or discordantly; of these:\n 180 mates make up the pairs; of these:\n 156 (86.67%) aligned 0 times\n 24 (13.33%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n22.00% overall alignment rate\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-08 18:55:00", "plugin": "core", "name": "end_epoch", "raw_value": "1731092100.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 18:54:59", "plugin": "core", "name": "start_epoch", "raw_value": "1731092099.0000000"}, {"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": "bowtie2/2.5.3+galaxy1-8", "has_data": true, "data": {"tool_id": "bowtie2", "tool_version": "2.5.3+galaxy1", "test_index": 8, "time_seconds": 42.867969036102295, "inputs": {"library|input_1": {"src": "hda", "id": "c58c13568ec75757"}, "library|input_2": {"src": "hda", "id": "da3dc9239480763c"}, "library|unaligned_file": false, "library|paired_options|paired_options_selector": "no", "library|type": "paired", "reference_genome|own_file": {"src": "hda", "id": "e0eec9675b72ef01"}, "reference_genome|source": "history", "analysis_type|analysis_type_selector": "simple", "sam_options|reorder": true, "sam_options|sam_options_selector": "yes"}, "job": {"model_class": "Job", "id": "da3dc9239480763c", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T18:55:41.412535", "update_time": "2024-11-08T18:55:56.255773", "galaxy_version": "24.1", "external_id": "gxy-tx4kj", "handler": null, "job_runner_name": null, "command_line": "set -o | grep -q pipefail && set -o pipefail; bowtie2-build --threads ${GALAXY_SLOTS:-4} '/galaxy/server/database/objects/4/7/e/dataset_47e57be4-ec55-4919-8ca2-a97a2177da14.dat' genome && ln -s -f '/galaxy/server/database/objects/4/7/e/dataset_47e57be4-ec55-4919-8ca2-a97a2177da14.dat' genome.fa && ln -f -s '/galaxy/server/database/objects/f/e/3/dataset_fe347f83-4e98-43bb-9c2e-53df0e486f88.dat' input_f.fasta && ln -f -s '/galaxy/server/database/objects/d/c/b/dataset_dcbb39c2-f8c3-4657-90c9-364844bac9d4.dat' input_r.fasta && THREADS=${GALAXY_SLOTS:-4} && if [ \"$THREADS\" -gt 1 ]; then (( THREADS-- )); fi && bowtie2 -p \"$THREADS\" -x 'genome' -f -1 'input_f.fasta' -2 'input_r.fasta' --reorder | samtools view --no-PG -b -o '/galaxy/server/database/objects/4/b/b/dataset_4bbe6680-2be1-433e-a707-62ddc7330af0.dat'", "user_email": "tests@fake.org", "command_version": "/usr/local/bin/bowtie2-align-s version 2.5.3\n64-bit\nBuilt on fv-az365-785\nWed Jan 17 04:43:48 UTC 2024\nCompiler: gcc version 12.3.0 (conda-forge gcc 12.3.0-3) \nOptions: -O3 -msse2 -funroll-loops -g3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /usr/local/include -fdebug-prefix-map=/opt/conda/conda-bld/bowtie2_1705465427853/work=/usr/local/src/conda/bowtie2-2.5.3 -fdebug-prefix-map=/usr/local=/usr/local/src/conda-prefix -std=c++11 -Wall -Wno-unused-but-set-variable -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -DWITH_ZSTD\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "save_mapping_stats": "false", "sam_options": "{\"__current_case__\": 0, \"no_unal\": false, \"omit_sec_seq\": false, \"reorder\": true, \"sam_no_qname_trunc\": false, \"sam_opt\": false, \"sam_options_selector\": \"yes\", \"soft_clipped_unmapped_tlen\": false, \"xeq\": false}", "analysis_type": "{\"__current_case__\": 0, \"analysis_type_selector\": \"simple\", \"presets\": \"no_presets\"}", "rg": "{\"__current_case__\": 3, \"rg_selector\": \"do_not_set\"}", "reference_genome": "{\"__current_case__\": 1, \"own_file\": {\"values\": [{\"id\": 81, \"src\": \"hda\"}]}, \"source\": \"history\"}", "library": "{\"__current_case__\": 1, \"aligned_file\": false, \"input_1\": {\"values\": [{\"id\": 79, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 80, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 1, \"paired_options_selector\": \"no\"}, \"type\": \"paired\", \"unaligned_file\": false}"}, "inputs": {"library|input_1": {"id": "c58c13568ec75757", "src": "hda", "uuid": "fe347f83-4e98-43bb-9c2e-53df0e486f88"}, "library|input_2": {"id": "da3dc9239480763c", "src": "hda", "uuid": "dcbb39c2-f8c3-4657-90c9-364844bac9d4"}, "reference_genome|own_file": {"id": "e0eec9675b72ef01", "src": "hda", "uuid": "47e57be4-ec55-4919-8ca2-a97a2177da14"}}, "outputs": {"output": {"id": "45abc3d0f8b42070", "src": "hda", "uuid": "4bbe6680-2be1-433e-a707-62ddc7330af0"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Settings:\n Output files: \"genome.*.bt2\"\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 Max bucket size: default\n Max bucket size, sqrt multiplier: default\n Max bucket size, len divisor: 32\n Difference-cover sample period: 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 /galaxy/server/database/objects/4/7/e/dataset_47e57be4-ec55-4919-8ca2-a97a2177da14.dat\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\nbmax according to bmaxDivN setting: 517\nUsing parameters --bmax 388 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 388 --dcv 1024\nConstructing suffix-array element generator\nBuilding DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 86 sample suffixes\nGenerating random suffixes\nQSorting 86 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 86 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 12, merged 41; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 6; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 284.672 (target: 387)\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering Ebwt loop\nGetting block 1 of 58\n Reserving size (388) for bucket 1\nGetting block 2 of 58\nGetting block 3 of 58\nGetting block 4 of 58\nGetting block 5 of 58\n Calculating Z arrays for bucket 1\n Reserving size (388) for bucket 2\n Reserving size (388) for bucket 3\n Reserving size (388) for bucket 4\n Reserving size (388) for bucket 5\nGetting block 6 of 58\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 3\n Entering block accumulator loop for bucket 1:\n Calculating Z arrays for bucket 4\n Calculating Z arrays for bucket 5\n Reserving size (388) for bucket 6\n Calculating Z arrays for bucket 6\nGetting block 7 of 58\n Entering block accumulator loop for bucket 2:\n Entering block accumulator loop for bucket 3:\n Entering block accumulator loop for bucket 5:\n Entering block accumulator loop for bucket 4:\n Reserving size (388) for bucket 7\n Entering block accumulator loop for bucket 6:\n bucket 1: 10%\n Calculating Z arrays for bucket 7\n bucket 5: 10%\n bucket 3: 10%\n bucket 4: 10%\n bucket 1: 20%\n Entering block accumulator loop for bucket 7:\n bucket 6: 10%\n bucket 5: 20%\n bucket 3: 20%\n bucket 4: 20%\n bucket 2: 10%\n bucket 1: 30%\n bucket 6: 20%\n bucket 3: 30%\n bucket 5: 30%\n bucket 4: 30%\n bucket 2: 20%\n bucket 1: 40%\n bucket 3: 40%\n bucket 5: 40%\n bucket 4: 40%\n bucket 6: 30%\n bucket 7: 10%\n bucket 2: 30%\n bucket 3: 50%\n bucket 5: 50%\n bucket 4: 50%\n bucket 6: 40%\n bucket 2: 40%\n bucket 3: 60%\n bucket 5: 60%\n bucket 4: 60%\n bucket 7: 20%\n bucket 2: 50%\n bucket 3: 70%\n bucket 5: 70%\n bucket 4: 70%\n bucket 6: 50%\n bucket 1: 50%\n bucket 2: 60%\n bucket 3: 80%\n bucket 5: 80%\n bucket 4: 80%\n bucket 7: 30%\n bucket 6: 60%\n bucket 2: 70%\n bucket 3: 90%\n bucket 5: 90%\n bucket 4: 90%\n bucket 1: 60%\n bucket 2: 80%\n bucket 3: 100%\n bucket 5: 100%\n bucket 4: 100%\n bucket 6: 70%\n bucket 7: 40%\n Sorting block of length 370 for bucket 3\n (Using difference cover)\n Sorting block of length 203 for bucket 5\n (Using difference cover)\n Sorting block of length 328 for bucket 4\n (Using difference cover)\n bucket 2: 90%\n bucket 1: 70%\n bucket 6: 80%\n bucket 7: 50%\n bucket 2: 100%\n Sorting block of length 165 for bucket 2\n (Using difference cover)\n bucket 1: 80%\n bucket 7: 60%\n bucket 1: 90%\n bucket 6: 90%\n bucket 7: 70%\n bucket 7: 80%\n bucket 6: 100%\n bucket 1: 100%\n Sorting block of length 339 for bucket 6\n (Using difference cover)\n Sorting block of length 355 for bucket 1\n (Using difference cover)\n bucket 7: 90%\n bucket 7: 100%\n Sorting block of length 368 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 166 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 371 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 204 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 329 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 356 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 369 for bucket 7\nGetting block 8 of 58\n Reserving size (388) for bucket 8\n Calculating Z arrays for bucket 8\n Entering block accumulator loop for bucket 8:\nGetting block 9 of 58\n Reserving size (388) for bucket 9\n Calculating Z arrays for bucket 9\n bucket 8: 10%\n Entering block accumulator loop for bucket 9:\n bucket 8: 20%\n bucket 9: 10%\n bucket 8: 30%\n bucket 9: 20%\n bucket 8: 40%\n bucket 9: 30%\n bucket 8: 50%\n bucket 9: 40%\n bucket 8: 60%\n bucket 9: 50%\n bucket 8: 70%\n bucket 9: 60%\n bucket 8: 80%\n bucket 9: 70%\n bucket 8: 90%\n bucket 9: 80%\n bucket 8: 100%\n Sorting block of length 171 for bucket 8\n (Using difference cover)\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 339 for bucket 9\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 172 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 9\nGetting block 10 of 58\n Reserving size (388) for bucket 10\nGetting block 11 of 58\n Calculating Z arrays for bucket 10\n Reserving size (388) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 10:\n Entering block accumulator loop for bucket 11:\n bucket 11: 10%\n bucket 10: 10%\n bucket 11: 20%\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 11: 70%\n bucket 11: 80%\n bucket 10: 70%\n bucket 11: 90%\n bucket 10: 80%\n bucket 11: 100%\n Sorting block of length 305 for bucket 11\n (Using difference cover)\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 357 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 306 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 358 for bucket 10\nGetting block 12 of 58\n Reserving size (388) for bucket 12\nGetting block 13 of 58\n Calculating Z arrays for bucket 12\n Reserving size (388) for bucket 13\nGetting block 14 of 58\n Calculating Z arrays for bucket 13\n Reserving size (388) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 12:\n Entering block accumulator loop for bucket 14:\n Entering block accumulator loop for bucket 13:\n bucket 14: 10%\n bucket 12: 10%\n bucket 13: 10%\n bucket 14: 20%\n bucket 13: 20%\n bucket 12: 20%\n bucket 14: 30%\n bucket 13: 30%\n bucket 14: 40%\n bucket 12: 30%\n bucket 13: 40%\n bucket 14: 50%\n bucket 13: 50%\n bucket 12: 40%\n bucket 14: 60%\n bucket 13: 60%\n bucket 12: 50%\n bucket 13: 70%\n bucket 14: 70%\n bucket 12: 60%\n bucket 13: 80%\n bucket 14: 80%\n bucket 12: 70%\n bucket 13: 90%\n bucket 14: 90%\n bucket 13: 100%\n bucket 12: 80%\n Sorting block of length 282 for bucket 13\n (Using difference cover)\n bucket 14: 100%\n Sorting block of length 339 for bucket 14\n (Using difference cover)\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 185 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 283 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 186 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 14\nGetting block 15 of 58\n Reserving size (388) for bucket 15\nGetting block 16 of 58\n Calculating Z arrays for bucket 15\n Reserving size (388) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 15:\n Entering block accumulator loop for bucket 16:\n bucket 15: 10%\n bucket 16: 10%\n bucket 15: 20%\n bucket 16: 20%\n bucket 15: 30%\n bucket 16: 30%\n bucket 15: 40%\n bucket 16: 40%\n bucket 15: 50%\n bucket 15: 60%\n bucket 16: 50%\n bucket 15: 70%\n bucket 16: 60%\n bucket 15: 80%\n bucket 15: 90%\n bucket 16: 70%\n bucket 15: 100%\n Sorting block of length 241 for bucket 15\n (Using difference cover)\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 379 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 242 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 380 for bucket 16\nGetting block 17 of 58\n Reserving size (388) for bucket 17\n Calculating Z arrays for bucket 17\nGetting block 18 of 58\n Entering block accumulator loop for bucket 17:\n Reserving size (388) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 17: 10%\n bucket 18: 10%\n bucket 17: 20%\n bucket 18: 20%\n bucket 17: 30%\n bucket 18: 30%\n bucket 17: 40%\n bucket 18: 40%\n bucket 17: 50%\n bucket 18: 50%\n bucket 17: 60%\n bucket 18: 60%\n bucket 18: 70%\n bucket 17: 70%\n bucket 18: 80%\n bucket 17: 80%\n bucket 18: 90%\n bucket 17: 90%\n bucket 18: 100%\n Sorting block of length 378 for bucket 18\n (Using difference cover)\n bucket 17: 100%\n Sorting block of length 215 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 379 for bucket 18\n Sorting block time: 00:00:00\nReturning block of 216 for bucket 17\nGetting block 19 of 58\n Reserving size (388) for bucket 19\n Calculating Z arrays for bucket 19\nGetting block 20 of 58\n Entering block accumulator loop for bucket 19:\n Reserving size (388) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\n bucket 19: 10%\n bucket 20: 10%\n bucket 19: 20%\n bucket 20: 20%\n bucket 19: 30%\n bucket 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 19: 80%\n bucket 20: 60%\n bucket 19: 90%\n bucket 20: 70%\n bucket 19: 100%\n Sorting block of length 334 for bucket 19\n (Using difference cover)\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 313 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 335 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 314 for bucket 20\nGetting block 21 of 58\n Reserving size (388) 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 210 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 211 for bucket 21\nGetting block 22 of 58\n Reserving size (388) for bucket 22\nGetting block 23 of 58\n Calculating Z arrays for bucket 22\n Reserving size (388) 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 23: 90%\n bucket 22: 100%\n Sorting block of length 386 for bucket 22\n (Using difference cover)\n bucket 23: 100%\n Sorting block of length 238 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 387 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 239 for bucket 23\nGetting block 24 of 58\n Reserving size (388) for bucket 24\n Calculating Z arrays for bucket 24\nGetting block 25 of 58\n Reserving size (388) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 24:\n Entering block accumulator loop for bucket 25:\n bucket 24: 10%\n bucket 25: 10%\n bucket 24: 20%\n bucket 25: 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 25: 70%\n bucket 24: 60%\n bucket 25: 80%\n bucket 24: 70%\n bucket 25: 90%\n bucket 25: 100%\n bucket 24: 80%\n Sorting block of length 105 for bucket 25\n (Using difference cover)\n bucket 24: 90%\n Sorting block time: 00:00:00\nReturning block of 106 for bucket 25\n bucket 24: 100%\n Sorting block of length 351 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 352 for bucket 24\nGetting block 26 of 58\n Reserving size (388) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\nGetting block 27 of 58\n bucket 26: 10%\n Reserving size (388) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n bucket 26: 20%\n bucket 26: 30%\n bucket 27: 10%\n bucket 26: 40%\n bucket 27: 20%\n bucket 26: 50%\n bucket 26: 60%\n bucket 27: 30%\n bucket 26: 70%\n bucket 27: 40%\n bucket 26: 80%\n bucket 27: 50%\n bucket 26: 90%\n bucket 27: 60%\n bucket 26: 100%\n Sorting block of length 354 for bucket 26\n (Using difference cover)\n bucket 27: 70%\n bucket 27: 80%\n Sorting block time: 00:00:00\nReturning block of 355 for bucket 26\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 334 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 335 for bucket 27\nGetting block 28 of 58\n Reserving size (388) 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 253 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 254 for bucket 28\nGetting block 29 of 58\n Reserving size (388) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\nGetting block 30 of 58\n Reserving size (388) for bucket 30\n bucket 29: 10%\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 30:\n bucket 29: 20%\n bucket 29: 30%\n bucket 30: 10%\n bucket 29: 40%\n bucket 30: 20%\n bucket 29: 50%\n bucket 30: 30%\n bucket 29: 60%\n bucket 30: 40%\n bucket 29: 70%\n bucket 29: 80%\n bucket 30: 50%\n bucket 29: 90%\n bucket 30: 60%\n bucket 29: 100%\n Sorting block of length 289 for bucket 29\n (Using difference cover)\n bucket 30: 70%\n bucket 30: 80%\n Sorting block time: 00:00:00\nReturning block of 290 for bucket 29\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 345 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 346 for bucket 30\nGetting block 31 of 58\n Reserving size (388) for bucket 31\n Calculating Z arrays for bucket 31\nGetting block 32 of 58\n Entering block accumulator loop for bucket 31:\n Reserving size (388) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 32:\n bucket 31: 10%\n bucket 32: 10%\n bucket 31: 20%\n bucket 32: 20%\n bucket 31: 30%\n bucket 32: 30%\n bucket 31: 40%\n bucket 31: 50%\n bucket 32: 40%\n bucket 31: 60%\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 bu\n..\n0:00\nReturning block of 350 for bucket 23\nGetting block 24 of 57\n Reserving size (388) for bucket 24\nGetting block 25 of 57\n Calculating Z arrays for bucket 24\n Reserving size (388) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 24:\n Entering block accumulator loop for bucket 25:\n bucket 24: 10%\n bucket 25: 10%\n bucket 24: 20%\n bucket 25: 20%\n bucket 24: 30%\n bucket 25: 30%\n bucket 24: 40%\n bucket 25: 40%\n bucket 24: 50%\n bucket 25: 50%\n bucket 24: 60%\n bucket 25: 60%\n bucket 24: 70%\n bucket 25: 70%\n bucket 24: 80%\n bucket 25: 80%\n bucket 24: 90%\n bucket 25: 90%\n bucket 24: 100%\n Sorting block of length 245 for bucket 24\n (Using difference cover)\n bucket 25: 100%\n Sorting block of length 286 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 246 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 287 for bucket 25\nGetting block 26 of 57\n Reserving size (388) for bucket 26\nGetting block 27 of 57\n Calculating Z arrays for bucket 26\n Reserving size (388) 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 26: 60%\n bucket 27: 40%\n bucket 26: 70%\n bucket 26: 80%\n bucket 27: 50%\n bucket 26: 90%\n bucket 27: 60%\n bucket 26: 100%\n Sorting block of length 384 for bucket 26\n (Using difference cover)\n bucket 27: 70%\n bucket 27: 80%\n Sorting block time: 00:00:00\nReturning block of 385 for bucket 26\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 359 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 360 for bucket 27\nGetting block 28 of 57\n Reserving size (388) for bucket 28\n Calculating Z arrays for bucket 28\nGetting block 29 of 57\n Reserving size (388) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 28:\n Entering block accumulator loop for bucket 29:\n bucket 28: 10%\n bucket 29: 10%\n bucket 28: 20%\n bucket 29: 20%\n bucket 28: 30%\n bucket 29: 30%\n bucket 28: 40%\n bucket 29: 40%\n bucket 28: 50%\n bucket 29: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 29: 60%\n bucket 28: 80%\n bucket 29: 70%\n bucket 28: 90%\n bucket 28: 100%\n bucket 29: 80%\n Sorting block of length 387 for bucket 28\n (Using difference cover)\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 195 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 29\nGetting block 30 of 57\n Reserving size (388) 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 257 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 258 for bucket 30\nGetting block 31 of 57\n Reserving size (388) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 31:\nGetting block 32 of 57\n bucket 31: 10%\n Reserving size (388) for bucket 32\n Calculating Z arrays for bucket 32\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 32: 30%\n bucket 31: 60%\n bucket 31: 70%\n bucket 32: 40%\n bucket 31: 80%\n bucket 32: 50%\n bucket 31: 90%\n bucket 32: 60%\n bucket 31: 100%\n Sorting block of length 310 for bucket 31\n (Using difference cover)\n bucket 32: 70%\n bucket 32: 80%\n Sorting block time: 00:00:00\nReturning block of 311 for bucket 31\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 219 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 220 for bucket 32\nGetting block 33 of 57\n Reserving size (388) for bucket 33\n Calculating Z arrays for bucket 33\nGetting block 34 of 57\n Entering block accumulator loop for bucket 33:\n Reserving size (388) for bucket 34\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 34:\n bucket 33: 10%\n bucket 34: 10%\n bucket 33: 20%\n bucket 33: 30%\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 33: 70%\n bucket 34: 50%\n bucket 33: 80%\n bucket 34: 60%\n bucket 33: 90%\n bucket 34: 70%\n bucket 33: 100%\n Sorting block of length 387 for bucket 33\n (Using difference cover)\n bucket 34: 80%\n bucket 34: 90%\n bucket 34: 100%\n Sorting block time: 00:00:00\n Sorting block of length 275 for bucket 34\n (Using difference cover)\nReturning block of 388 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 276 for bucket 34\nGetting block 35 of 57\n Reserving size (388) for bucket 35\nGetting block 36 of 57\n Calculating Z arrays for bucket 35\n Reserving size (388) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 35:\n Entering block accumulator loop for bucket 36:\n bucket 36: 10%\n bucket 35: 10%\n bucket 36: 20%\n bucket 35: 20%\n bucket 36: 30%\n bucket 35: 30%\n bucket 36: 40%\n bucket 35: 40%\n bucket 36: 50%\n bucket 35: 50%\n bucket 36: 60%\n bucket 35: 60%\n bucket 36: 70%\n bucket 35: 70%\n bucket 36: 80%\n bucket 35: 80%\n bucket 36: 90%\n bucket 35: 90%\n bucket 36: 100%\n Sorting block of length 150 for bucket 36\n (Using difference cover)\n bucket 35: 100%\n Sorting block of length 350 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 151 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 351 for bucket 35\nGetting block 37 of 57\n Reserving size (388) for bucket 37\n Calculating Z arrays for bucket 37\nGetting block 38 of 57\n Reserving size (388) 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 37: 30%\n bucket 38: 30%\n bucket 37: 40%\n bucket 38: 40%\n bucket 37: 50%\n bucket 38: 50%\n bucket 38: 60%\n bucket 37: 60%\n bucket 38: 70%\n bucket 37: 70%\n bucket 38: 80%\n bucket 37: 80%\n bucket 37: 90%\n bucket 38: 90%\n bucket 37: 100%\n Sorting block of length 267 for bucket 37\n (Using difference cover)\n bucket 38: 100%\n Sorting block of length 337 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 268 for bucket 37\n Sorting block time: 00:00:00\nReturning block of 338 for bucket 38\nGetting block 39 of 57\n Reserving size (388) 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%\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 387 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 39\nGetting block 40 of 57\n Reserving size (388) for bucket 40\nGetting block 41 of 57\n Calculating Z arrays for bucket 40\n Reserving size (388) 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 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 41: 80%\n bucket 40: 70%\n bucket 41: 90%\n bucket 40: 80%\n bucket 41: 100%\n Sorting block of length 330 for bucket 41\n (Using difference cover)\n bucket 40: 90%\n bucket 40: 100%\n Sorting block of length 379 for bucket 40\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 331 for bucket 41\n Sorting block time: 00:00:00\nReturning block of 380 for bucket 40\nGetting block 42 of 57\n Reserving size (388) 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 188 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 189 for bucket 42\nGetting block 43 of 57\n Reserving size (388) 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 321 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 322 for bucket 43\nGetting block 44 of 57\n Reserving size (388) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 44:\n bucket 44: 10%\nGetting block 45 of 57\n Reserving size (388) for bucket 45\n Calculating Z arrays for bucket 45\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 45: 20%\n bucket 44: 50%\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 366 for bucket 44\n (Using difference cover)\n bucket 45: 60%\n Sorting block time: 00:00:00\nReturning block of 367 for bucket 44\n bucket 45: 70%\n bucket 45: 80%\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 365 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 366 for bucket 45\nGetting block 46 of 57\n Reserving size (388) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 46:\n bucket 46: 10%\nGetting block 47 of 57\n Reserving size (388) for bucket 47\n Calculating Z arrays for bucket 47\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 46: 50%\n bucket 47: 20%\n bucket 46: 60%\n bucket 46: 70%\n bucket 47: 30%\n bucket 46: 80%\n bucket 47: 40%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 253 for bucket 46\n bucket 47: 50%\n (Using difference cover)\n bucket 47: 60%\n bucket 47: 70%\n Sorting block time: 00:00:00\nReturning block of 254 for bucket 46\n bucket 47: 80%\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 217 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 218 for bucket 47\nGetting block 48 of 57\n Reserving size (388) 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 384 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 385 for bucket 48\nGetting block 49 of 57\n Reserving size (388) for bucket 49\n Calculating Z arrays for bucket 49\nGetting block 50 of 57\n Reserving size (388) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 49:\n Entering block accumulator loop for bucket 50:\n bucket 49: 10%\n bucket 50: 10%\n bucket 49: 20%\n bucket 50: 20%\n bucket 50: 30%\n bucket 49: 30%\n bucket 50: 40%\n bucket 49: 40%\n bucket 49: 50%\n bucket 50: 50%\n bucket 49: 60%\n bucket 49: 70%\n bucket 50: 60%\n bucket 49: 80%\n bucket 49: 90%\n bucket 50: 70%\n bucket 49: 100%\n bucket 50: 80%\n Sorting block of length 112 for bucket 49\n (Using difference cover)\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 275 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 276 for bucket 50\nGetting block 51 of 57\n Reserving size (388) for bucket 51\nGetting block 52 of 57\n Calculating Z arrays for bucket 51\n Reserving size (388) 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 52:\n bucket 51: 10%\n bucket 52: 10%\n bucket 51: 20%\n bucket 52: 20%\n bucket 51: 30%\n bucket 52: 30%\n bucket 51: 40%\n bucket 52: 40%\n bucket 51: 50%\n bucket 52: 50%\n bucket 51: 60%\n bucket 52: 60%\n bucket 51: 70%\n bucket 52: 70%\n bucket 51: 80%\n bucket 52: 80%\n bucket 51: 90%\n bucket 52: 90%\n bucket 51: 100%\n Sorting block of length 350 for bucket 51\n (Using difference cover)\n bucket 52: 100%\n Sorting block of length 378 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 379 for bucket 52\n Sorting block time: 00:00:00\nReturning block of 351 for bucket 51\nGetting block 53 of 57\n Reserving size (388) 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 370 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 371 for bucket 53\nGetting block 54 of 57\n Reserving size (388) 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 237 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 238 for bucket 54\nGetting block 55 of 57\n Reserving size (388) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\nGetting block 56 of 57\n Reserving size (388) for bucket 56\n Calculating Z arrays for bucket 56\nGetting block 57 of 57\n Entering block accumulator loop for bucket 56:\n Reserving size (388) for bucket 57\n bucket 55: 10%\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 57:\n bucket 56: 10%\n bucket 57: 10%\n bucket 55: 20%\n bucket 57: 20%\n bucket 57: 30%\n bucket 56: 20%\n bucket 57: 40%\n bucket 56: 30%\n bucket 57: 50%\n bucket 55: 30%\n bucket 57: 60%\n bucket 56: 40%\n bucket 57: 70%\n bucket 55: 40%\n bucket 57: 80%\n bucket 56: 50%\n bucket 57: 90%\n bucket 55: 50%\n bucket 57: 100%\n Sorting block of length 132 for bucket 57\n (Using difference cover)\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 Sorting block time: 00:00:00\nReturning block of 133 for bucket 57\n bucket 56: 90%\n bucket 55: 90%\n bucket 56: 100%\n Sorting block of length 270 for bucket 56\n (Using difference cover)\n bucket 55: 100%\n Sorting block of length 344 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 271 for bucket 56\n Sorting block time: 00:00:00\nReturning block of 345 for bucket 55\nExited Ebwt loop\nfchr[A]: 0\nfchr[C]: 5124\nfchr[G]: 10305\nfchr[T]: 12474\nfchr[$]: 16568\nExiting Ebwt::buildToDisk()\nReturning from initFromVector\nWrote 4200050 bytes to primary EBWT file: genome.rev.1.bt2.tmp\nWrote 4148 bytes to secondary EBWT file: genome.rev.2.bt2.tmp\nRe-opening _in1 and _in2 as input streams\nReturning from Ebwt constructor\nHeaders:\n len: 16568\n bwtLen: 16569\n sz: 4142\n bwtSz: 4143\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 20\n eftabSz: 80\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 1036\n offsSz: 4144\n lineSz: 64\n sideSz: 64\n sideBwtSz: 48\n sideBwtLen: 192\n numSides: 87\n numLines: 87\n ebwtTotLen: 5568\n ebwtTotSz: 5568\n color: 0\n reverse: 1\nTotal time for backward call to driver() for mirror index: 00:00:00\n", "tool_stderr": "Building a SMALL index\nRenaming genome.3.bt2.tmp to genome.3.bt2\nRenaming genome.4.bt2.tmp to genome.4.bt2\nRenaming genome.1.bt2.tmp to genome.1.bt2\nRenaming genome.2.bt2.tmp to genome.2.bt2\nRenaming genome.rev.1.bt2.tmp to genome.rev.1.bt2\nRenaming genome.rev.2.bt2.tmp to genome.rev.2.bt2\n100 reads; of these:\n 100 (100.00%) were paired; of these:\n 97 (97.00%) aligned concordantly 0 times\n 3 (3.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 97 pairs aligned concordantly 0 times; of these:\n 7 (7.22%) aligned discordantly 1 time\n ----\n 90 pairs aligned 0 times concordantly or discordantly; of these:\n 180 mates make up the pairs; of these:\n 156 (86.67%) aligned 0 times\n 24 (13.33%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n22.00% overall alignment rate\n", "job_stdout": "", "job_stderr": "", "stdout": "Settings:\n Output files: \"genome.*.bt2\"\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 Max bucket size: default\n Max bucket size, sqrt multiplier: default\n Max bucket size, len divisor: 32\n Difference-cover sample period: 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 /galaxy/server/database/objects/4/7/e/dataset_47e57be4-ec55-4919-8ca2-a97a2177da14.dat\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\nbmax according to bmaxDivN setting: 517\nUsing parameters --bmax 388 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 388 --dcv 1024\nConstructing suffix-array element generator\nBuilding DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 86 sample suffixes\nGenerating random suffixes\nQSorting 86 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 86 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 12, merged 41; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 6; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 5, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 3, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 284.672 (target: 387)\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering Ebwt loop\nGetting block 1 of 58\n Reserving size (388) for bucket 1\nGetting block 2 of 58\nGetting block 3 of 58\nGetting block 4 of 58\nGetting block 5 of 58\n Calculating Z arrays for bucket 1\n Reserving size (388) for bucket 2\n Reserving size (388) for bucket 3\n Reserving size (388) for bucket 4\n Reserving size (388) for bucket 5\nGetting block 6 of 58\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 3\n Entering block accumulator loop for bucket 1:\n Calculating Z arrays for bucket 4\n Calculating Z arrays for bucket 5\n Reserving size (388) for bucket 6\n Calculating Z arrays for bucket 6\nGetting block 7 of 58\n Entering block accumulator loop for bucket 2:\n Entering block accumulator loop for bucket 3:\n Entering block accumulator loop for bucket 5:\n Entering block accumulator loop for bucket 4:\n Reserving size (388) for bucket 7\n Entering block accumulator loop for bucket 6:\n bucket 1: 10%\n Calculating Z arrays for bucket 7\n bucket 5: 10%\n bucket 3: 10%\n bucket 4: 10%\n bucket 1: 20%\n Entering block accumulator loop for bucket 7:\n bucket 6: 10%\n bucket 5: 20%\n bucket 3: 20%\n bucket 4: 20%\n bucket 2: 10%\n bucket 1: 30%\n bucket 6: 20%\n bucket 3: 30%\n bucket 5: 30%\n bucket 4: 30%\n bucket 2: 20%\n bucket 1: 40%\n bucket 3: 40%\n bucket 5: 40%\n bucket 4: 40%\n bucket 6: 30%\n bucket 7: 10%\n bucket 2: 30%\n bucket 3: 50%\n bucket 5: 50%\n bucket 4: 50%\n bucket 6: 40%\n bucket 2: 40%\n bucket 3: 60%\n bucket 5: 60%\n bucket 4: 60%\n bucket 7: 20%\n bucket 2: 50%\n bucket 3: 70%\n bucket 5: 70%\n bucket 4: 70%\n bucket 6: 50%\n bucket 1: 50%\n bucket 2: 60%\n bucket 3: 80%\n bucket 5: 80%\n bucket 4: 80%\n bucket 7: 30%\n bucket 6: 60%\n bucket 2: 70%\n bucket 3: 90%\n bucket 5: 90%\n bucket 4: 90%\n bucket 1: 60%\n bucket 2: 80%\n bucket 3: 100%\n bucket 5: 100%\n bucket 4: 100%\n bucket 6: 70%\n bucket 7: 40%\n Sorting block of length 370 for bucket 3\n (Using difference cover)\n Sorting block of length 203 for bucket 5\n (Using difference cover)\n Sorting block of length 328 for bucket 4\n (Using difference cover)\n bucket 2: 90%\n bucket 1: 70%\n bucket 6: 80%\n bucket 7: 50%\n bucket 2: 100%\n Sorting block of length 165 for bucket 2\n (Using difference cover)\n bucket 1: 80%\n bucket 7: 60%\n bucket 1: 90%\n bucket 6: 90%\n bucket 7: 70%\n bucket 7: 80%\n bucket 6: 100%\n bucket 1: 100%\n Sorting block of length 339 for bucket 6\n (Using difference cover)\n Sorting block of length 355 for bucket 1\n (Using difference cover)\n bucket 7: 90%\n bucket 7: 100%\n Sorting block of length 368 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 166 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 371 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 204 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 329 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 356 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 369 for bucket 7\nGetting block 8 of 58\n Reserving size (388) for bucket 8\n Calculating Z arrays for bucket 8\n Entering block accumulator loop for bucket 8:\nGetting block 9 of 58\n Reserving size (388) for bucket 9\n Calculating Z arrays for bucket 9\n bucket 8: 10%\n Entering block accumulator loop for bucket 9:\n bucket 8: 20%\n bucket 9: 10%\n bucket 8: 30%\n bucket 9: 20%\n bucket 8: 40%\n bucket 9: 30%\n bucket 8: 50%\n bucket 9: 40%\n bucket 8: 60%\n bucket 9: 50%\n bucket 8: 70%\n bucket 9: 60%\n bucket 8: 80%\n bucket 9: 70%\n bucket 8: 90%\n bucket 9: 80%\n bucket 8: 100%\n Sorting block of length 171 for bucket 8\n (Using difference cover)\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 339 for bucket 9\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 172 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 9\nGetting block 10 of 58\n Reserving size (388) for bucket 10\nGetting block 11 of 58\n Calculating Z arrays for bucket 10\n Reserving size (388) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 10:\n Entering block accumulator loop for bucket 11:\n bucket 11: 10%\n bucket 10: 10%\n bucket 11: 20%\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 11: 70%\n bucket 11: 80%\n bucket 10: 70%\n bucket 11: 90%\n bucket 10: 80%\n bucket 11: 100%\n Sorting block of length 305 for bucket 11\n (Using difference cover)\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 357 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 306 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 358 for bucket 10\nGetting block 12 of 58\n Reserving size (388) for bucket 12\nGetting block 13 of 58\n Calculating Z arrays for bucket 12\n Reserving size (388) for bucket 13\nGetting block 14 of 58\n Calculating Z arrays for bucket 13\n Reserving size (388) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 12:\n Entering block accumulator loop for bucket 14:\n Entering block accumulator loop for bucket 13:\n bucket 14: 10%\n bucket 12: 10%\n bucket 13: 10%\n bucket 14: 20%\n bucket 13: 20%\n bucket 12: 20%\n bucket 14: 30%\n bucket 13: 30%\n bucket 14: 40%\n bucket 12: 30%\n bucket 13: 40%\n bucket 14: 50%\n bucket 13: 50%\n bucket 12: 40%\n bucket 14: 60%\n bucket 13: 60%\n bucket 12: 50%\n bucket 13: 70%\n bucket 14: 70%\n bucket 12: 60%\n bucket 13: 80%\n bucket 14: 80%\n bucket 12: 70%\n bucket 13: 90%\n bucket 14: 90%\n bucket 13: 100%\n bucket 12: 80%\n Sorting block of length 282 for bucket 13\n (Using difference cover)\n bucket 14: 100%\n Sorting block of length 339 for bucket 14\n (Using difference cover)\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 185 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 283 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 186 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 340 for bucket 14\nGetting block 15 of 58\n Reserving size (388) for bucket 15\nGetting block 16 of 58\n Calculating Z arrays for bucket 15\n Reserving size (388) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 15:\n Entering block accumulator loop for bucket 16:\n bucket 15: 10%\n bucket 16: 10%\n bucket 15: 20%\n bucket 16: 20%\n bucket 15: 30%\n bucket 16: 30%\n bucket 15: 40%\n bucket 16: 40%\n bucket 15: 50%\n bucket 15: 60%\n bucket 16: 50%\n bucket 15: 70%\n bucket 16: 60%\n bucket 15: 80%\n bucket 15: 90%\n bucket 16: 70%\n bucket 15: 100%\n Sorting block of length 241 for bucket 15\n (Using difference cover)\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 379 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 242 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 380 for bucket 16\nGetting block 17 of 58\n Reserving size (388) for bucket 17\n Calculating Z arrays for bucket 17\nGetting block 18 of 58\n Entering block accumulator loop for bucket 17:\n Reserving size (388) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 17: 10%\n bucket 18: 10%\n bucket 17: 20%\n bucket 18: 20%\n bucket 17: 30%\n bucket 18: 30%\n bucket 17: 40%\n bucket 18: 40%\n bucket 17: 50%\n bucket 18: 50%\n bucket 17: 60%\n bucket 18: 60%\n bucket 18: 70%\n bucket 17: 70%\n bucket 18: 80%\n bucket 17: 80%\n bucket 18: 90%\n bucket 17: 90%\n bucket 18: 100%\n Sorting block of length 378 for bucket 18\n (Using difference cover)\n bucket 17: 100%\n Sorting block of length 215 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 379 for bucket 18\n Sorting block time: 00:00:00\nReturning block of 216 for bucket 17\nGetting block 19 of 58\n Reserving size (388) for bucket 19\n Calculating Z arrays for bucket 19\nGetting block 20 of 58\n Entering block accumulator loop for bucket 19:\n Reserving size (388) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\n bucket 19: 10%\n bucket 20: 10%\n bucket 19: 20%\n bucket 20: 20%\n bucket 19: 30%\n bucket 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 19: 80%\n bucket 20: 60%\n bucket 19: 90%\n bucket 20: 70%\n bucket 19: 100%\n Sorting block of length 334 for bucket 19\n (Using difference cover)\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 313 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 335 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 314 for bucket 20\nGetting block 21 of 58\n Reserving size (388) 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 210 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 211 for bucket 21\nGetting block 22 of 58\n Reserving size (388) for bucket 22\nGetting block 23 of 58\n Calculating Z arrays for bucket 22\n Reserving size (388) 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 23: 90%\n bucket 22: 100%\n Sorting block of length 386 for bucket 22\n (Using difference cover)\n bucket 23: 100%\n Sorting block of length 238 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 387 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 239 for bucket 23\nGetting block 24 of 58\n Reserving size (388) for bucket 24\n Calculating Z arrays for bucket 24\nGetting block 25 of 58\n Reserving size (388) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 24:\n Entering block accumulator loop for bucket 25:\n bucket 24: 10%\n bucket 25: 10%\n bucket 24: 20%\n bucket 25: 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 25: 70%\n bucket 24: 60%\n bucket 25: 80%\n bucket 24: 70%\n bucket 25: 90%\n bucket 25: 100%\n bucket 24: 80%\n Sorting block of length 105 for bucket 25\n (Using difference cover)\n bucket 24: 90%\n Sorting block time: 00:00:00\nReturning block of 106 for bucket 25\n bucket 24: 100%\n Sorting block of length 351 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 352 for bucket 24\nGetting block 26 of 58\n Reserving size (388) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\nGetting block 27 of 58\n bucket 26: 10%\n Reserving size (388) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n bucket 26: 20%\n bucket 26: 30%\n bucket 27: 10%\n bucket 26: 40%\n bucket 27: 20%\n bucket 26: 50%\n bucket 26: 60%\n bucket 27: 30%\n bucket 26: 70%\n bucket 27: 40%\n bucket 26: 80%\n bucket 27: 50%\n bucket 26: 90%\n bucket 27: 60%\n bucket 26: 100%\n Sorting block of length 354 for bucket 26\n (Using difference cover)\n bucket 27: 70%\n bucket 27: 80%\n Sorting block time: 00:00:00\nReturning block of 355 for bucket 26\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 334 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 335 for bucket 27\nGetting block 28 of 58\n Reserving size (388) 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 253 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 254 for bucket 28\nGetting block 29 of 58\n Reserving size (388) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\nGetting block 30 of 58\n Reserving size (388) for bucket 30\n bucket 29: 10%\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 30:\n bucket 29: 20%\n bucket 29: 30%\n bucket 30: 10%\n bucket 29: 40%\n bucket 30: 20%\n bucket 29: 50%\n bucket 30: 30%\n bucket 29: 60%\n bucket 30: 40%\n bucket 29: 70%\n bucket 29: 80%\n bucket 30: 50%\n bucket 29: 90%\n bucket 30: 60%\n bucket 29: 100%\n Sorting block of length 289 for bucket 29\n (Using difference cover)\n bucket 30: 70%\n bucket 30: 80%\n Sorting block time: 00:00:00\nReturning block of 290 for bucket 29\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 345 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 346 for bucket 30\nGetting block 31 of 58\n Reserving size (388) for bucket 31\n Calculating Z arrays for bucket 31\nGetting block 32 of 58\n Entering block accumulator loop for bucket 31:\n Reserving size (388) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 32:\n bucket 31: 10%\n bucket 32: 10%\n bucket 31: 20%\n bucket 32: 20%\n bucket 31: 30%\n bucket 32: 30%\n bucket 31: 40%\n bucket 31: 50%\n bucket 32: 40%\n bucket 31: 60%\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 bu\n..\n0:00\nReturning block of 350 for bucket 23\nGetting block 24 of 57\n Reserving size (388) for bucket 24\nGetting block 25 of 57\n Calculating Z arrays for bucket 24\n Reserving size (388) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 24:\n Entering block accumulator loop for bucket 25:\n bucket 24: 10%\n bucket 25: 10%\n bucket 24: 20%\n bucket 25: 20%\n bucket 24: 30%\n bucket 25: 30%\n bucket 24: 40%\n bucket 25: 40%\n bucket 24: 50%\n bucket 25: 50%\n bucket 24: 60%\n bucket 25: 60%\n bucket 24: 70%\n bucket 25: 70%\n bucket 24: 80%\n bucket 25: 80%\n bucket 24: 90%\n bucket 25: 90%\n bucket 24: 100%\n Sorting block of length 245 for bucket 24\n (Using difference cover)\n bucket 25: 100%\n Sorting block of length 286 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 246 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 287 for bucket 25\nGetting block 26 of 57\n Reserving size (388) for bucket 26\nGetting block 27 of 57\n Calculating Z arrays for bucket 26\n Reserving size (388) 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 26: 60%\n bucket 27: 40%\n bucket 26: 70%\n bucket 26: 80%\n bucket 27: 50%\n bucket 26: 90%\n bucket 27: 60%\n bucket 26: 100%\n Sorting block of length 384 for bucket 26\n (Using difference cover)\n bucket 27: 70%\n bucket 27: 80%\n Sorting block time: 00:00:00\nReturning block of 385 for bucket 26\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 359 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 360 for bucket 27\nGetting block 28 of 57\n Reserving size (388) for bucket 28\n Calculating Z arrays for bucket 28\nGetting block 29 of 57\n Reserving size (388) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 28:\n Entering block accumulator loop for bucket 29:\n bucket 28: 10%\n bucket 29: 10%\n bucket 28: 20%\n bucket 29: 20%\n bucket 28: 30%\n bucket 29: 30%\n bucket 28: 40%\n bucket 29: 40%\n bucket 28: 50%\n bucket 29: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 29: 60%\n bucket 28: 80%\n bucket 29: 70%\n bucket 28: 90%\n bucket 28: 100%\n bucket 29: 80%\n Sorting block of length 387 for bucket 28\n (Using difference cover)\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 195 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 196 for bucket 29\nGetting block 30 of 57\n Reserving size (388) 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 257 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 258 for bucket 30\nGetting block 31 of 57\n Reserving size (388) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 31:\nGetting block 32 of 57\n bucket 31: 10%\n Reserving size (388) for bucket 32\n Calculating Z arrays for bucket 32\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 32: 30%\n bucket 31: 60%\n bucket 31: 70%\n bucket 32: 40%\n bucket 31: 80%\n bucket 32: 50%\n bucket 31: 90%\n bucket 32: 60%\n bucket 31: 100%\n Sorting block of length 310 for bucket 31\n (Using difference cover)\n bucket 32: 70%\n bucket 32: 80%\n Sorting block time: 00:00:00\nReturning block of 311 for bucket 31\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 219 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 220 for bucket 32\nGetting block 33 of 57\n Reserving size (388) for bucket 33\n Calculating Z arrays for bucket 33\nGetting block 34 of 57\n Entering block accumulator loop for bucket 33:\n Reserving size (388) for bucket 34\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 34:\n bucket 33: 10%\n bucket 34: 10%\n bucket 33: 20%\n bucket 33: 30%\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 33: 70%\n bucket 34: 50%\n bucket 33: 80%\n bucket 34: 60%\n bucket 33: 90%\n bucket 34: 70%\n bucket 33: 100%\n Sorting block of length 387 for bucket 33\n (Using difference cover)\n bucket 34: 80%\n bucket 34: 90%\n bucket 34: 100%\n Sorting block time: 00:00:00\n Sorting block of length 275 for bucket 34\n (Using difference cover)\nReturning block of 388 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 276 for bucket 34\nGetting block 35 of 57\n Reserving size (388) for bucket 35\nGetting block 36 of 57\n Calculating Z arrays for bucket 35\n Reserving size (388) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 35:\n Entering block accumulator loop for bucket 36:\n bucket 36: 10%\n bucket 35: 10%\n bucket 36: 20%\n bucket 35: 20%\n bucket 36: 30%\n bucket 35: 30%\n bucket 36: 40%\n bucket 35: 40%\n bucket 36: 50%\n bucket 35: 50%\n bucket 36: 60%\n bucket 35: 60%\n bucket 36: 70%\n bucket 35: 70%\n bucket 36: 80%\n bucket 35: 80%\n bucket 36: 90%\n bucket 35: 90%\n bucket 36: 100%\n Sorting block of length 150 for bucket 36\n (Using difference cover)\n bucket 35: 100%\n Sorting block of length 350 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 151 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 351 for bucket 35\nGetting block 37 of 57\n Reserving size (388) for bucket 37\n Calculating Z arrays for bucket 37\nGetting block 38 of 57\n Reserving size (388) 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 37: 30%\n bucket 38: 30%\n bucket 37: 40%\n bucket 38: 40%\n bucket 37: 50%\n bucket 38: 50%\n bucket 38: 60%\n bucket 37: 60%\n bucket 38: 70%\n bucket 37: 70%\n bucket 38: 80%\n bucket 37: 80%\n bucket 37: 90%\n bucket 38: 90%\n bucket 37: 100%\n Sorting block of length 267 for bucket 37\n (Using difference cover)\n bucket 38: 100%\n Sorting block of length 337 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 268 for bucket 37\n Sorting block time: 00:00:00\nReturning block of 338 for bucket 38\nGetting block 39 of 57\n Reserving size (388) 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%\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 387 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 388 for bucket 39\nGetting block 40 of 57\n Reserving size (388) for bucket 40\nGetting block 41 of 57\n Calculating Z arrays for bucket 40\n Reserving size (388) 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 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 41: 80%\n bucket 40: 70%\n bucket 41: 90%\n bucket 40: 80%\n bucket 41: 100%\n Sorting block of length 330 for bucket 41\n (Using difference cover)\n bucket 40: 90%\n bucket 40: 100%\n Sorting block of length 379 for bucket 40\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 331 for bucket 41\n Sorting block time: 00:00:00\nReturning block of 380 for bucket 40\nGetting block 42 of 57\n Reserving size (388) 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 188 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 189 for bucket 42\nGetting block 43 of 57\n Reserving size (388) 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 321 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 322 for bucket 43\nGetting block 44 of 57\n Reserving size (388) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 44:\n bucket 44: 10%\nGetting block 45 of 57\n Reserving size (388) for bucket 45\n Calculating Z arrays for bucket 45\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 45: 20%\n bucket 44: 50%\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 366 for bucket 44\n (Using difference cover)\n bucket 45: 60%\n Sorting block time: 00:00:00\nReturning block of 367 for bucket 44\n bucket 45: 70%\n bucket 45: 80%\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 365 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 366 for bucket 45\nGetting block 46 of 57\n Reserving size (388) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 46:\n bucket 46: 10%\nGetting block 47 of 57\n Reserving size (388) for bucket 47\n Calculating Z arrays for bucket 47\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 46: 50%\n bucket 47: 20%\n bucket 46: 60%\n bucket 46: 70%\n bucket 47: 30%\n bucket 46: 80%\n bucket 47: 40%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 253 for bucket 46\n bucket 47: 50%\n (Using difference cover)\n bucket 47: 60%\n bucket 47: 70%\n Sorting block time: 00:00:00\nReturning block of 254 for bucket 46\n bucket 47: 80%\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 217 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 218 for bucket 47\nGetting block 48 of 57\n Reserving size (388) 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 384 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 385 for bucket 48\nGetting block 49 of 57\n Reserving size (388) for bucket 49\n Calculating Z arrays for bucket 49\nGetting block 50 of 57\n Reserving size (388) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 49:\n Entering block accumulator loop for bucket 50:\n bucket 49: 10%\n bucket 50: 10%\n bucket 49: 20%\n bucket 50: 20%\n bucket 50: 30%\n bucket 49: 30%\n bucket 50: 40%\n bucket 49: 40%\n bucket 49: 50%\n bucket 50: 50%\n bucket 49: 60%\n bucket 49: 70%\n bucket 50: 60%\n bucket 49: 80%\n bucket 49: 90%\n bucket 50: 70%\n bucket 49: 100%\n bucket 50: 80%\n Sorting block of length 112 for bucket 49\n (Using difference cover)\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 275 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 276 for bucket 50\nGetting block 51 of 57\n Reserving size (388) for bucket 51\nGetting block 52 of 57\n Calculating Z arrays for bucket 51\n Reserving size (388) 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 52:\n bucket 51: 10%\n bucket 52: 10%\n bucket 51: 20%\n bucket 52: 20%\n bucket 51: 30%\n bucket 52: 30%\n bucket 51: 40%\n bucket 52: 40%\n bucket 51: 50%\n bucket 52: 50%\n bucket 51: 60%\n bucket 52: 60%\n bucket 51: 70%\n bucket 52: 70%\n bucket 51: 80%\n bucket 52: 80%\n bucket 51: 90%\n bucket 52: 90%\n bucket 51: 100%\n Sorting block of length 350 for bucket 51\n (Using difference cover)\n bucket 52: 100%\n Sorting block of length 378 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 379 for bucket 52\n Sorting block time: 00:00:00\nReturning block of 351 for bucket 51\nGetting block 53 of 57\n Reserving size (388) 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 370 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 371 for bucket 53\nGetting block 54 of 57\n Reserving size (388) 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 237 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 238 for bucket 54\nGetting block 55 of 57\n Reserving size (388) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\nGetting block 56 of 57\n Reserving size (388) for bucket 56\n Calculating Z arrays for bucket 56\nGetting block 57 of 57\n Entering block accumulator loop for bucket 56:\n Reserving size (388) for bucket 57\n bucket 55: 10%\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 57:\n bucket 56: 10%\n bucket 57: 10%\n bucket 55: 20%\n bucket 57: 20%\n bucket 57: 30%\n bucket 56: 20%\n bucket 57: 40%\n bucket 56: 30%\n bucket 57: 50%\n bucket 55: 30%\n bucket 57: 60%\n bucket 56: 40%\n bucket 57: 70%\n bucket 55: 40%\n bucket 57: 80%\n bucket 56: 50%\n bucket 57: 90%\n bucket 55: 50%\n bucket 57: 100%\n Sorting block of length 132 for bucket 57\n (Using difference cover)\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 Sorting block time: 00:00:00\nReturning block of 133 for bucket 57\n bucket 56: 90%\n bucket 55: 90%\n bucket 56: 100%\n Sorting block of length 270 for bucket 56\n (Using difference cover)\n bucket 55: 100%\n Sorting block of length 344 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 271 for bucket 56\n Sorting block time: 00:00:00\nReturning block of 345 for bucket 55\nExited Ebwt loop\nfchr[A]: 0\nfchr[C]: 5124\nfchr[G]: 10305\nfchr[T]: 12474\nfchr[$]: 16568\nExiting Ebwt::buildToDisk()\nReturning from initFromVector\nWrote 4200050 bytes to primary EBWT file: genome.rev.1.bt2.tmp\nWrote 4148 bytes to secondary EBWT file: genome.rev.2.bt2.tmp\nRe-opening _in1 and _in2 as input streams\nReturning from Ebwt constructor\nHeaders:\n len: 16568\n bwtLen: 16569\n sz: 4142\n bwtSz: 4143\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 20\n eftabSz: 80\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 1036\n offsSz: 4144\n lineSz: 64\n sideSz: 64\n sideBwtSz: 48\n sideBwtLen: 192\n numSides: 87\n numLines: 87\n ebwtTotLen: 5568\n ebwtTotSz: 5568\n color: 0\n reverse: 1\nTotal time for backward call to driver() for mirror index: 00:00:00\n", "stderr": "Building a SMALL index\nRenaming genome.3.bt2.tmp to genome.3.bt2\nRenaming genome.4.bt2.tmp to genome.4.bt2\nRenaming genome.1.bt2.tmp to genome.1.bt2\nRenaming genome.2.bt2.tmp to genome.2.bt2\nRenaming genome.rev.1.bt2.tmp to genome.rev.1.bt2\nRenaming genome.rev.2.bt2.tmp to genome.rev.2.bt2\n100 reads; of these:\n 100 (100.00%) were paired; of these:\n 97 (97.00%) aligned concordantly 0 times\n 3 (3.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 97 pairs aligned concordantly 0 times; of these:\n 7 (7.22%) aligned discordantly 1 time\n ----\n 90 pairs aligned 0 times concordantly or discordantly; of these:\n 180 mates make up the pairs; of these:\n 156 (86.67%) aligned 0 times\n 24 (13.33%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n22.00% overall alignment rate\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-08 18:55:43", "plugin": "core", "name": "end_epoch", "raw_value": "1731092143.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 18:55:42", "plugin": "core", "name": "start_epoch", "raw_value": "1731092142.0000000"}, {"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": "bowtie2/2.5.3+galaxy1-9", "has_data": true, "data": {"tool_id": "bowtie2", "tool_version": "2.5.3+galaxy1", "test_index": 9, "time_seconds": 22.04133939743042, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "datamash_reverse/1.8+galaxy0-0", "has_data": true, "data": {"tool_id": "datamash_reverse", "tool_version": "1.8+galaxy0", "test_index": 0, "time_seconds": 81.88291668891907, "inputs": {"in_file": {"src": "hda", "id": "da7414b0e37eac28"}}, "job": {"model_class": "Job", "id": "94c8c8b52917d0da", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.8+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T18:34:37.569763", "update_time": "2024-11-08T18:35:25.705137", "galaxy_version": "24.1", "external_id": "gxy-68xpc", "handler": null, "job_runner_name": null, "command_line": "datamash reverse < /galaxy/server/database/objects/5/2/2/dataset_5225d232-82bf-41ac-8f87-8a0b597f831d.dat > /galaxy/server/database/objects/3/c/3/dataset_3c3485fe-982a-4142-93d7-db9ae9bb67e5.dat", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\""}, "inputs": {"in_file": {"id": "da7414b0e37eac28", "src": "hda", "uuid": "5225d232-82bf-41ac-8f87-8a0b597f831d"}}, "outputs": {"out_file": {"id": "94c8c8b52917d0da", "src": "hda", "uuid": "3c3485fe-982a-4142-93d7-db9ae9bb67e5"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-11-08 18:35:13", "plugin": "core", "name": "end_epoch", "raw_value": "1731090913.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 18:35:13", "plugin": "core", "name": "start_epoch", "raw_value": "1731090913.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "deeptools_plot_enrichment/3.5.4+galaxy0-0", "has_data": true, "data": {"tool_id": "deeptools_plot_enrichment", "tool_version": "3.5.4+galaxy0", "test_index": 0, "time_seconds": 59.51053476333618, "inputs": {"multibam_conditional|bamfiles": [{"src": "hda", "id": "a9975e93915e7608"}, {"src": "hda", "id": "a9975e93915e7608"}], "BED": [{"src": "hda", "id": "e5042d7292e14fe6"}, {"src": "hda", "id": "e5042d7292e14fe6"}], "advancedOpt|regionLabels": "up down", "advancedOpt|minMappingQuality": "0", "advancedOpt|showAdvancedOpt": "yes", "outRawCounts": true}, "job": {"model_class": "Job", "id": "33e5e4773222c037", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/3.5.4+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T18:35:50.226073", "update_time": "2024-11-08T18:36:25.819161", "galaxy_version": "24.1", "external_id": "gxy-hv67m", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/4/8/6/dataset_486c17e6-8058-4b8a-a0ac-3d726396b06b.dat' './0.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/b/b/2/metadata_bb21a19d-288f-4048-beee-9b68c3c28f3e.dat' './0.bam.bai' && ln -s '/galaxy/server/database/objects/4/8/6/dataset_486c17e6-8058-4b8a-a0ac-3d726396b06b.dat' './1.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/b/b/2/metadata_bb21a19d-288f-4048-beee-9b68c3c28f3e.dat' './1.bam.bai' && plotEnrichment --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --plotFile '/galaxy/server/database/objects/7/c/8/dataset_7c80f44d-aefb-4c3c-b37b-0466f557e592.dat' --bamfiles '0.bam' '1.bam' --labels 'bowtie2 test1.bam' 'bowtie2 test1.bam' --BED '/galaxy/server/database/objects/7/7/4/dataset_774f50d7-f124-4851-bbe2-a98cc913a43f.dat' '/galaxy/server/database/objects/7/7/4/dataset_774f50d7-f124-4851-bbe2-a98cc913a43f.dat' --regionLabels 'multiBamSummary_regions.bed' 'multiBamSummary_regions.bed' --outRawCounts '/galaxy/server/database/objects/9/6/8/dataset_9687df7e-d2ab-409a-a6f7-1638a8e33e71.dat' --plotFileFormat 'png' --regionLabels up down --plotWidth '20' --plotHeight '20' --numPlotsPerRow '4' --alpha '0.9'", "user_email": "tests@fake.org", "command_version": "plotEnrichment 3.5.4", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "outRawCounts": "true", "advancedOpt": "{\"Offset\": \"\", \"__current_case__\": 1, \"alpha\": \"0.9\", \"attributeKey\": null, \"blackListFileName\": null, \"centerReads\": false, \"colors\": \"\", \"doExtendCustom\": {\"__current_case__\": 0, \"doExtend\": \"no\"}, \"ignoreDuplicates\": false, \"keepExons\": false, \"labels\": null, \"maxFragmentLength\": \"0\", \"minFragmentLength\": \"0\", \"minMappingQuality\": \"0\", \"numPlotsPerRow\": \"4\", \"perSample\": false, \"plotHeight\": \"20\", \"plotTitle\": \"\", \"plotWidth\": \"20\", \"regionLabels\": \"up down\", \"samFlagExclude\": \"\", \"samFlagInclude\": \"\", \"showAdvancedOpt\": \"yes\", \"variableScales\": false}", "outFileFormat": "\"png\"", "region": "\"\"", "custom_sample_labels_conditional": "{\"__current_case__\": 0, \"custom_labels_select\": \"No\"}", "multibam_conditional": "{\"__current_case__\": 0, \"bamfiles\": {\"values\": [{\"id\": 3, \"src\": \"hda\"}, {\"id\": 3, \"src\": \"hda\"}]}, \"orderMatters\": \"No\"}"}, "inputs": {"BED2": {"id": "e5042d7292e14fe6", "src": "hda", "uuid": "774f50d7-f124-4851-bbe2-a98cc913a43f"}, "BED1": {"id": "e5042d7292e14fe6", "src": "hda", "uuid": "774f50d7-f124-4851-bbe2-a98cc913a43f"}, "BED": {"id": "e5042d7292e14fe6", "src": "hda", "uuid": "774f50d7-f124-4851-bbe2-a98cc913a43f"}, "multibam_conditional|bamfiles2": {"id": "a9975e93915e7608", "src": "hda", "uuid": "486c17e6-8058-4b8a-a0ac-3d726396b06b"}, "multibam_conditional|bamfiles1": {"id": "a9975e93915e7608", "src": "hda", "uuid": "486c17e6-8058-4b8a-a0ac-3d726396b06b"}, "multibam_conditional|bamfiles": {"id": "a9975e93915e7608", "src": "hda", "uuid": "486c17e6-8058-4b8a-a0ac-3d726396b06b"}}, "outputs": {"outFileRawCounts": {"id": "3df03115672c8d19", "src": "hda", "uuid": "9687df7e-d2ab-409a-a6f7-1638a8e33e71"}, "outFileName": {"id": "33e5e4773222c037", "src": "hda", "uuid": "7c80f44d-aefb-4c3c-b37b-0466f557e592"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "3 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "3.0000000"}, {"title": "Job End Time", "value": "2024-11-08 18:36:09", "plugin": "core", "name": "end_epoch", "raw_value": "1731090969.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 18:36:06", "plugin": "core", "name": "start_epoch", "raw_value": "1731090966.0000000"}, {"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_filtervariants/1.4.3+galaxy0-0", "has_data": true, "data": {"tool_id": "ivar_filtervariants", "tool_version": "1.4.3+galaxy0", "test_index": 0, "time_seconds": 45.198490619659424, "inputs": {"inputs": [{"src": "hda", "id": "3026a95ac5c8a875"}, {"src": "hda", "id": "17abe4f2d7eb92c6"}]}, "job": {"model_class": "Job", "id": "13682044cce8454f", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.4.3+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:41:25.827122", "update_time": "2024-11-08T19:41:47.637949", "galaxy_version": "24.1", "external_id": "gxy-rvdsh", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/c/3/3/dataset_c3314b14-57c6-402c-8d69-0ae2e1dc7d53.dat' ./var_0.tsv && ln -s '/galaxy/server/database/objects/c/a/1/dataset_ca184929-d78a-435f-916d-489643e3f662.dat' ./var_1.tsv && ivar filtervariants -p filtered.tsv ./var_0.tsv ./var_1.tsv", "user_email": "tests@fake.org", "command_version": "iVar version 1.4.3", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\""}, "inputs": {"inputs": {"id": "3026a95ac5c8a875", "src": "hda", "uuid": "c3314b14-57c6-402c-8d69-0ae2e1dc7d53"}, "inputs1": {"id": "3026a95ac5c8a875", "src": "hda", "uuid": "c3314b14-57c6-402c-8d69-0ae2e1dc7d53"}, "inputs2": {"id": "17abe4f2d7eb92c6", "src": "hda", "uuid": "ca184929-d78a-435f-916d-489643e3f662"}}, "outputs": {"output_filtered": {"id": "5009e5615ffb11c0", "src": "hda", "uuid": "7903dfb7-adf9-4c71-aa4b-1ad68b6b80f3"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Header format of ./var_0.tsv did not match! Please use files generated using \"ivar variants\" command.\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "Header format of ./var_0.tsv did not match! Please use files generated using \"ivar variants\" command.\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-11-08 19:41:33", "plugin": "core", "name": "end_epoch", "raw_value": "1731094893.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:41:33", "plugin": "core", "name": "start_epoch", "raw_value": "1731094893.0000000"}, {"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": "lofreq_indelqual/2.1.5+galaxy1-0", "has_data": true, "data": {"tool_id": "lofreq_indelqual", "tool_version": "2.1.5+galaxy1", "test_index": 0, "time_seconds": 50.206469774246216, "inputs": {"reads": {"src": "hda", "id": "8e42b1fbf985c94c"}, "strategy|insertions": "20", "strategy|deletions": "30", "strategy|selector": "uniform"}, "job": {"model_class": "Job", "id": "07ef8540660ce7c0", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:32:09.043643", "update_time": "2024-11-08T19:32:35.002495", "galaxy_version": "24.1", "external_id": "gxy-gxflr", "handler": null, "job_runner_name": null, "command_line": "lofreq indelqual --uniform 20,30 -o output.bam /galaxy/server/database/objects/a/1/8/dataset_a18d6402-89bc-4a5c-a59f-a287ba5fb996.dat", "user_email": "tests@fake.org", "command_version": "2.1.5", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "strategy": "{\"__current_case__\": 0, \"deletions\": \"30\", \"insertions\": \"20\", \"selector\": \"uniform\"}"}, "inputs": {"reads": {"id": "8e42b1fbf985c94c", "src": "hda", "uuid": "a18d6402-89bc-4a5c-a59f-a287ba5fb996"}}, "outputs": {"output": {"id": "abfc816e136d4606", "src": "hda", "uuid": "214336bc-933c-4c31-a417-b951316b665c"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-11-08 19:32:19", "plugin": "core", "name": "end_epoch", "raw_value": "1731094339.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:32:19", "plugin": "core", "name": "start_epoch", "raw_value": "1731094339.0000000"}, {"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": "lofreq_indelqual/2.1.5+galaxy1-1", "has_data": true, "data": {"tool_id": "lofreq_indelqual", "tool_version": "2.1.5+galaxy1", "test_index": 1, "time_seconds": 38.39415454864502, "inputs": {"reads": {"src": "hda", "id": "f0d8602f1349bb9a"}, "strategy|reference_source|ref": {"src": "hda", "id": "778157054be0b652"}, "strategy|reference_source|ref_selector": "history", "strategy|selector": "dindel"}, "job": {"model_class": "Job", "id": "e527b0ee28d9e436", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:32:59.213542", "update_time": "2024-11-08T19:33:13.459817", "galaxy_version": "24.1", "external_id": "gxy-xvztd", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/b/6/9/dataset_b692258a-8fdd-4747-b742-ce22964afb16.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo \"Error running samtools faidx for indexing fasta reference for lofreq\" >&2 && lofreq indelqual --dindel --ref reference.fa -o output.bam /galaxy/server/database/objects/9/8/1/dataset_9818f2cb-3231-4955-be60-dcf4a8d782d3.dat", "user_email": "tests@fake.org", "command_version": "2.1.5", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "strategy": "{\"__current_case__\": 1, \"reference_source\": {\"__current_case__\": 1, \"ref\": {\"values\": [{\"id\": 224, \"src\": \"hda\"}]}, \"ref_selector\": \"history\"}, \"selector\": \"dindel\"}"}, "inputs": {"reads": {"id": "f0d8602f1349bb9a", "src": "hda", "uuid": "9818f2cb-3231-4955-be60-dcf4a8d782d3"}, "strategy|reference_source|ref": {"id": "778157054be0b652", "src": "hda", "uuid": "b692258a-8fdd-4747-b742-ce22964afb16"}}, "outputs": {"output": {"id": "c3e29e86a022cc7a", "src": "hda", "uuid": "40b3121a-2f0f-403c-aeca-0578e9c09806"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-08 19:33:01", "plugin": "core", "name": "end_epoch", "raw_value": "1731094381.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:33:00", "plugin": "core", "name": "start_epoch", "raw_value": "1731094380.0000000"}, {"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": "lofreq_indelqual/2.1.5+galaxy1-2", "has_data": true, "data": {"tool_id": "lofreq_indelqual", "tool_version": "2.1.5+galaxy1", "test_index": 2, "time_seconds": 37.62653183937073, "inputs": {"reads": {"src": "hda", "id": "073f4e1b7f3e599f"}, "strategy|insertions": "20", "strategy|selector": "uniform"}, "job": {"model_class": "Job", "id": "c88976d64d6b5b93", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:33:35.986166", "update_time": "2024-11-08T19:33:50.943437", "galaxy_version": "24.1", "external_id": "gxy-w9wvz", "handler": null, "job_runner_name": null, "command_line": "lofreq indelqual --uniform 20 -o output.bam /galaxy/server/database/objects/2/8/0/dataset_2809a6a4-ae29-4f0b-9ffc-3f55324a3c39.dat", "user_email": "tests@fake.org", "command_version": "2.1.5", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "strategy": "{\"__current_case__\": 0, \"deletions\": \"\", \"insertions\": \"20\", \"selector\": \"uniform\"}"}, "inputs": {"reads": {"id": "073f4e1b7f3e599f", "src": "hda", "uuid": "2809a6a4-ae29-4f0b-9ffc-3f55324a3c39"}}, "outputs": {"output": {"id": "7910a349b635709c", "src": "hda", "uuid": "0b4ccc1e-8cac-4dac-956f-d6b541806c36"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-08 19:33:38", "plugin": "core", "name": "end_epoch", "raw_value": "1731094418.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:33:37", "plugin": "core", "name": "start_epoch", "raw_value": "1731094417.0000000"}, {"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": "medaka_consensus_pipeline/1.7.2+galaxy1-0", "has_data": true, "data": {"tool_id": "medaka_consensus_pipeline", "tool_version": "1.7.2+galaxy1", "test_index": 0, "time_seconds": 107.0261173248291, "inputs": {"i": {"src": "hda", "id": "58bf2e5c3c465941"}, "d": {"src": "hda", "id": "d80711c863d86115"}}, "job": {"model_class": "Job", "id": "58bf2e5c3c465941", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T18:56:43.389276", "update_time": "2024-11-08T18:58:05.829701", "galaxy_version": "24.1", "external_id": "gxy-fqwkp", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/2/3/7/dataset_2377b491-1509-4322-b88d-9198c7618eba.dat' 'input_assembly.fa' && medaka_consensus -m r941_min_high_g360 -b 100 -o results -t ${GALAXY_SLOTS:-4} -i '/galaxy/server/database/objects/d/a/d/dataset_dad33dac-623c-47b1-a51f-66835be2651a.dat' -d 'input_assembly.fa' 2>&1 | tee 'XXXX'", "user_email": "tests@fake.org", "command_version": "medaka 1.7.2", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "out": "[\"consensus\", \"probs\", \"calls\"]", "g": "false", "b": "\"100\"", "m": "\"r941_min_high_g360\""}, "inputs": {"i": {"id": "58bf2e5c3c465941", "src": "hda", "uuid": "dad33dac-623c-47b1-a51f-66835be2651a"}, "d": {"id": "d80711c863d86115", "src": "hda", "uuid": "2377b491-1509-4322-b88d-9198c7618eba"}}, "outputs": {"out_consensus": {"id": "c4c7b330396a480d", "src": "hda", "uuid": "fd8067c9-d369-4f49-b68b-4271a548e6c0"}, "out_probs": {"id": "9e3f1c03a0a0d065", "src": "hda", "uuid": "3dc15a89-3cbd-4dd6-b7e2-874d59e892d5"}, "out_calls": {"id": "e86fce26d0e9f57d", "src": "hda", "uuid": "1d79d2b6-dc45-4456-ab97-a961522dcc74"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Checking program versions\nThis is medaka 1.7.2\nProgram Version Required Pass \nbcftools 1.15.1 1.11 True \nbgzip 1.16 1.11 True \nminimap2 2.24 2.11 True \nsamtools 1.15.1 1.11 True \ntabix 1.16 1.11 True \nAligning basecalls to draft\nCreating fai index file /galaxy/server/database/jobs_directory/000/86/working/input_assembly.fa.fai\nCreating mmi index file /galaxy/server/database/jobs_directory/000/86/working/input_assembly.fa.map-ont.mmi\n[M::mm_idx_gen::0.003*1.02] collected minimizers\n[M::mm_idx_gen::0.004*1.18] sorted minimizers\n[M::main::0.005*1.14] loaded/built the index for 1 target sequence(s)\n[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1\n[M::mm_idx_stat::0.005*1.13] distinct minimizers: 688 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.512; total length: 3792\n[M::main] Version: 2.24-r1122\n[M::main] CMD: minimap2 -I 16G -x map-ont -d /galaxy/server/database/jobs_directory/000/86/working/input_assembly.fa.map-ont.mmi /galaxy/server/database/jobs_directory/000/86/working/input_assembly.fa\n[M::main] Real time: 0.011 sec; CPU: 0.007 sec; Peak RSS: 0.003 GB\n[M::main::0.004*1.07] loaded/built the index for 1 target sequence(s)\n[M::mm_mapopt_update::0.005*1.07] mid_occ = 10\n[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1\n[M::mm_idx_stat::0.005*1.07] distinct minimizers: 688 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.512; total length: 3792\n[M::worker_pipeline::0.039*4.23] mapped 125 sequences\n[M::main] Version: 2.24-r1122\n[M::main] CMD: minimap2 -x map-ont --secondary=no -L --MD -A 2 -B 4 -O 4,24 -E 2,1 -t 8 -a /galaxy/server/database/jobs_directory/000/86/working/input_assembly.fa.map-ont.mmi /galaxy/server/database/objects/d/a/d/dataset_dad33dac-623c-47b1-a51f-66835be2651a.dat\n[M::main] Real time: 0.040 sec; CPU: 0.165 sec; Peak RSS: 0.015 GB\nRunning medaka consensus\n[18:57:26 - Predict] Reducing threads to 2, anymore is a waste.\n[18:57:26 - Predict] It looks like you are running medaka without a GPU and attempted to set a high number of threads. We have scaled this down to an optimal number. If you wish to improve performance please see https://nanoporetech.github.io/medaka/installation.html#improving-parallelism.\n[18:57:26 - Predict] Setting tensorflow inter/intra-op threads to 2/1.\n[18:57:26 - Predict] Processing region(s): 4:0-3792\n[18:57:26 - Predict] Using model: /usr/local/lib/python3.8/site-packages/medaka/data/r941_min_high_g360_model.hdf5.\n[18:57:26 - Predict] Processing 1 long region(s) with batching.\n[18:57:26 - MdlStore] filepath /usr/local/lib/python3.8/site-packages/medaka/data/r941_min_high_g360_model.hdf5\n[18:57:27 - BAMFile] Creating pool of 16 BAM file sets.\n[18:57:27 - Sampler] Initializing sampler for consensus of region 4:0-3792.\n[18:57:27 - PWorker] Running inference for 0.0M draft bases.\n[18:57:27 - Feature] Processed 4:0.0-3791.0 (median depth 78.0)\n[18:57:27 - Sampler] Took 0.58s to make features.\n[18:57:27 - Sampler] Region 4:0.0-3791.0 (7485 positions) is smaller than inference chunk length 10000, quarantining.\n[18:57:27 - PWorker] Processed 0 batches\n[18:57:27 - PWorker] All done, 1 remainder regions.\n[18:57:27 - Predict] Processing 1 short region(s).\n[18:57:27 - MdlStore] filepath /usr/local/lib/python3.8/site-packages/medaka/data/r941_min_high_g360_model.hdf5\n[18:57:28 - Sampler] Initializing sampler for consensus of region 4:0-3792.\n[18:57:28 - PWorker] Running inference for 0.0M draft bases.\n[18:57:29 - Feature] Processed 4:0.0-3791.0 (median depth 78.0)\n[18:57:29 - Sampler] Took 0.43s to make features.\n[18:57:50 - PWorker] Batches in cache: 1.\n[18:57:50 - PWorker] 88.7% Done (0.0/0.0 Mbases) in 21.5s\n[18:57:50 - PWorker] Processed 1 batches\n[18:57:50 - PWorker] All done, 0 remainder regions.\n[18:57:50 - Predict] Finished processing all regions.\n[18:57:52 - DataIndx] Loaded 1/1 (100.00%) sample files.\n[18:57:53 - DataIndx] Loaded 1/1 (100.00%) sample files.\nPolished assembly written to results/consensus.fasta, have a nice day.\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "Checking program versions\nThis is medaka 1.7.2\nProgram Version Required Pass \nbcftools 1.15.1 1.11 True \nbgzip 1.16 1.11 True \nminimap2 2.24 2.11 True \nsamtools 1.15.1 1.11 True \ntabix 1.16 1.11 True \nAligning basecalls to draft\nCreating fai index file /galaxy/server/database/jobs_directory/000/86/working/input_assembly.fa.fai\nCreating mmi index file /galaxy/server/database/jobs_directory/000/86/working/input_assembly.fa.map-ont.mmi\n[M::mm_idx_gen::0.003*1.02] collected minimizers\n[M::mm_idx_gen::0.004*1.18] sorted minimizers\n[M::main::0.005*1.14] loaded/built the index for 1 target sequence(s)\n[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1\n[M::mm_idx_stat::0.005*1.13] distinct minimizers: 688 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.512; total length: 3792\n[M::main] Version: 2.24-r1122\n[M::main] CMD: minimap2 -I 16G -x map-ont -d /galaxy/server/database/jobs_directory/000/86/working/input_assembly.fa.map-ont.mmi /galaxy/server/database/jobs_directory/000/86/working/input_assembly.fa\n[M::main] Real time: 0.011 sec; CPU: 0.007 sec; Peak RSS: 0.003 GB\n[M::main::0.004*1.07] loaded/built the index for 1 target sequence(s)\n[M::mm_mapopt_update::0.005*1.07] mid_occ = 10\n[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1\n[M::mm_idx_stat::0.005*1.07] distinct minimizers: 688 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.512; total length: 3792\n[M::worker_pipeline::0.039*4.23] mapped 125 sequences\n[M::main] Version: 2.24-r1122\n[M::main] CMD: minimap2 -x map-ont --secondary=no -L --MD -A 2 -B 4 -O 4,24 -E 2,1 -t 8 -a /galaxy/server/database/jobs_directory/000/86/working/input_assembly.fa.map-ont.mmi /galaxy/server/database/objects/d/a/d/dataset_dad33dac-623c-47b1-a51f-66835be2651a.dat\n[M::main] Real time: 0.040 sec; CPU: 0.165 sec; Peak RSS: 0.015 GB\nRunning medaka consensus\n[18:57:26 - Predict] Reducing threads to 2, anymore is a waste.\n[18:57:26 - Predict] It looks like you are running medaka without a GPU and attempted to set a high number of threads. We have scaled this down to an optimal number. If you wish to improve performance please see https://nanoporetech.github.io/medaka/installation.html#improving-parallelism.\n[18:57:26 - Predict] Setting tensorflow inter/intra-op threads to 2/1.\n[18:57:26 - Predict] Processing region(s): 4:0-3792\n[18:57:26 - Predict] Using model: /usr/local/lib/python3.8/site-packages/medaka/data/r941_min_high_g360_model.hdf5.\n[18:57:26 - Predict] Processing 1 long region(s) with batching.\n[18:57:26 - MdlStore] filepath /usr/local/lib/python3.8/site-packages/medaka/data/r941_min_high_g360_model.hdf5\n[18:57:27 - BAMFile] Creating pool of 16 BAM file sets.\n[18:57:27 - Sampler] Initializing sampler for consensus of region 4:0-3792.\n[18:57:27 - PWorker] Running inference for 0.0M draft bases.\n[18:57:27 - Feature] Processed 4:0.0-3791.0 (median depth 78.0)\n[18:57:27 - Sampler] Took 0.58s to make features.\n[18:57:27 - Sampler] Region 4:0.0-3791.0 (7485 positions) is smaller than inference chunk length 10000, quarantining.\n[18:57:27 - PWorker] Processed 0 batches\n[18:57:27 - PWorker] All done, 1 remainder regions.\n[18:57:27 - Predict] Processing 1 short region(s).\n[18:57:27 - MdlStore] filepath /usr/local/lib/python3.8/site-packages/medaka/data/r941_min_high_g360_model.hdf5\n[18:57:28 - Sampler] Initializing sampler for consensus of region 4:0-3792.\n[18:57:28 - PWorker] Running inference for 0.0M draft bases.\n[18:57:29 - Feature] Processed 4:0.0-3791.0 (median depth 78.0)\n[18:57:29 - Sampler] Took 0.43s to make features.\n[18:57:50 - PWorker] Batches in cache: 1.\n[18:57:50 - PWorker] 88.7% Done (0.0/0.0 Mbases) in 21.5s\n[18:57:50 - PWorker] Processed 1 batches\n[18:57:50 - PWorker] All done, 0 remainder regions.\n[18:57:50 - Predict] Finished processing all regions.\n[18:57:52 - DataIndx] Loaded 1/1 (100.00%) sample files.\n[18:57:53 - DataIndx] Loaded 1/1 (100.00%) sample files.\nPolished assembly written to results/consensus.fasta, have a nice day.\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "44 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "44.0000000"}, {"title": "Job End Time", "value": "2024-11-08 18:57:53", "plugin": "core", "name": "end_epoch", "raw_value": "1731092273.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 18:57:09", "plugin": "core", "name": "start_epoch", "raw_value": "1731092229.0000000"}, {"title": "Memory Allocated (MB)", "value": "12884", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12884.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "medaka_consensus_pipeline/1.7.2+galaxy1-1", "has_data": true, "data": {"tool_id": "medaka_consensus_pipeline", "tool_version": "1.7.2+galaxy1", "test_index": 1, "time_seconds": 86.20013284683228, "inputs": {"i": {"src": "hda", "id": "28658ca89303d4c0"}, "d": {"src": "hda", "id": "ba2f9b7b32bd1439"}, "m": "r941_min_fast_g303", "b": "99", "out": ["consensus", "probs", "calls", "log", "gaps"]}, "job": {"model_class": "Job", "id": "9e3f1c03a0a0d065", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T18:58:30.971838", "update_time": "2024-11-08T18:59:31.338764", "galaxy_version": "24.1", "external_id": "gxy-2j5nb", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/0/3/e/dataset_03e883e6-94d4-49c0-9040-0945d579975b.dat' 'input_assembly.fa' && medaka_consensus -m r941_min_fast_g303 -b 99 -o results -t ${GALAXY_SLOTS:-4} -i '/galaxy/server/database/objects/c/8/a/dataset_c8a79b6c-f9ad-42f3-9f86-6404739394c8.dat' -d 'input_assembly.fa' 2>&1 | tee '/galaxy/server/database/objects/b/7/a/dataset_b7a6d96e-3626-46e4-a802-1bab74e093e7.dat'", "user_email": "tests@fake.org", "command_version": "medaka 1.7.2", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "out": "[\"consensus\", \"probs\", \"calls\", \"log\", \"gaps\"]", "g": "false", "b": "\"99\"", "m": "\"r941_min_fast_g303\""}, "inputs": {"i": {"id": "28658ca89303d4c0", "src": "hda", "uuid": "c8a79b6c-f9ad-42f3-9f86-6404739394c8"}, "d": {"id": "ba2f9b7b32bd1439", "src": "hda", "uuid": "03e883e6-94d4-49c0-9040-0945d579975b"}}, "outputs": {"out_consensus": {"id": "ab5fd516df9874c8", "src": "hda", "uuid": "efb03f03-fbb0-49b4-a9dc-b369e7f2a892"}, "out_probs": {"id": "d735f44e26e51317", "src": "hda", "uuid": "fc5e53ff-1189-40f3-aee5-083ba3273752"}, "out_calls": {"id": "af996437f79bb890", "src": "hda", "uuid": "58761afb-8edf-4f77-ae88-82c3b24dff1e"}, "out_gaps": {"id": "2cd95566f4d04a2a", "src": "hda", "uuid": "5b8e2cb2-0d11-4f04-bffc-2f52c48a4ba9"}, "out_log": {"id": "05703a60fce6b467", "src": "hda", "uuid": "b7a6d96e-3626-46e4-a802-1bab74e093e7"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Checking program versions\nThis is medaka 1.7.2\nProgram Version Required Pass \nbcftools 1.15.1 1.11 True \nbgzip 1.16 1.11 True \nminimap2 2.24 2.11 True \nsamtools 1.15.1 1.11 True \ntabix 1.16 1.11 True \nAligning basecalls to draft\nCreating fai index file /galaxy/server/database/jobs_directory/000/89/working/input_assembly.fa.fai\nCreating mmi index file /galaxy/server/database/jobs_directory/000/89/working/input_assembly.fa.map-ont.mmi\n[M::mm_idx_gen::0.004*1.12] collected minimizers\n[M::mm_idx_gen::0.005*1.38] sorted minimizers\n[M::main::0.006*1.30] loaded/built the index for 1 target sequence(s)\n[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1\n[M::mm_idx_stat::0.006*1.29] distinct minimizers: 688 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.512; total length: 3792\n[M::main] Version: 2.24-r1122\n[M::main] CMD: minimap2 -I 16G -x map-ont -d /galaxy/server/database/jobs_directory/000/89/working/input_assembly.fa.map-ont.mmi /galaxy/server/database/jobs_directory/000/89/working/input_assembly.fa\n[M::main] Real time: 0.011 sec; CPU: 0.008 sec; Peak RSS: 0.003 GB\n[M::main::0.004*1.15] loaded/built the index for 1 target sequence(s)\n[M::mm_mapopt_update::0.004*1.15] mid_occ = 10\n[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1\n[M::mm_idx_stat::0.004*1.14] distinct minimizers: 688 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.512; total length: 3792\n[M::worker_pipeline::0.039*4.20] mapped 125 sequences\n[M::main] Version: 2.24-r1122\n[M::main] CMD: minimap2 -x map-ont --secondary=no -L --MD -A 2 -B 4 -O 4,24 -E 2,1 -t 8 -a /galaxy/server/database/jobs_directory/000/89/working/input_assembly.fa.map-ont.mmi /galaxy/server/database/objects/c/8/a/dataset_c8a79b6c-f9ad-42f3-9f86-6404739394c8.dat\n[M::main] Real time: 0.040 sec; CPU: 0.163 sec; Peak RSS: 0.015 GB\nRunning medaka consensus\n[18:58:49 - Predict] Reducing threads to 2, anymore is a waste.\n[18:58:49 - Predict] It looks like you are running medaka without a GPU and attempted to set a high number of threads. We have scaled this down to an optimal number. If you wish to improve performance please see https://nanoporetech.github.io/medaka/installation.html#improving-parallelism.\n[18:58:49 - Predict] Setting tensorflow inter/intra-op threads to 2/1.\n[18:58:49 - Predict] Processing region(s): 4:0-3792\n[18:58:49 - Predict] Using model: /usr/local/lib/python3.8/site-packages/medaka/data/r941_min_fast_g303_model.hdf5.\n[18:58:49 - Predict] Processing 1 long region(s) with batching.\n[18:58:49 - MdlStore] filepath /usr/local/lib/python3.8/site-packages/medaka/data/r941_min_fast_g303_model.hdf5\n[18:58:50 - BAMFile] Creating pool of 16 BAM file sets.\n[18:58:50 - Sampler] Initializing sampler for consensus of region 4:0-3792.\n[18:58:50 - PWorker] Running inference for 0.0M draft bases.\n[18:58:51 - Feature] Processed 4:0.0-3791.0 (median depth 78.0)\n[18:58:51 - Sampler] Took 0.47s to make features.\n[18:58:51 - Sampler] Region 4:0.0-3791.0 (7485 positions) is smaller than inference chunk length 10000, quarantining.\n[18:58:51 - PWorker] Processed 0 batches\n[18:58:51 - PWorker] All done, 1 remainder regions.\n[18:58:51 - Predict] Processing 1 short region(s).\n[18:58:51 - MdlStore] filepath /usr/local/lib/python3.8/site-packages/medaka/data/r941_min_fast_g303_model.hdf5\n[18:58:51 - Sampler] Initializing sampler for consensus of region 4:0-3792.\n[18:58:51 - PWorker] Running inference for 0.0M draft bases.\n[18:58:52 - Feature] Processed 4:0.0-3791.0 (median depth 78.0)\n[18:58:52 - Sampler] Took 0.32s to make features.\n[18:59:14 - PWorker] Batches in cache: 1.\n[18:59:14 - PWorker] 88.7% Done (0.0/0.0 Mbases) in 22.7s\n[18:59:14 - PWorker] Processed 1 batches\n[18:59:14 - PWorker] All done, 0 remainder regions.\n[18:59:14 - Predict] Finished processing all regions.\n[18:59:17 - DataIndx] Loaded 1/1 (100.00%) sample files.\n[18:59:17 - DataIndx] Loaded 1/1 (100.00%) sample files.\nPolished assembly written to results/consensus.fasta, have a nice day.\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "Checking program versions\nThis is medaka 1.7.2\nProgram Version Required Pass \nbcftools 1.15.1 1.11 True \nbgzip 1.16 1.11 True \nminimap2 2.24 2.11 True \nsamtools 1.15.1 1.11 True \ntabix 1.16 1.11 True \nAligning basecalls to draft\nCreating fai index file /galaxy/server/database/jobs_directory/000/89/working/input_assembly.fa.fai\nCreating mmi index file /galaxy/server/database/jobs_directory/000/89/working/input_assembly.fa.map-ont.mmi\n[M::mm_idx_gen::0.004*1.12] collected minimizers\n[M::mm_idx_gen::0.005*1.38] sorted minimizers\n[M::main::0.006*1.30] loaded/built the index for 1 target sequence(s)\n[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1\n[M::mm_idx_stat::0.006*1.29] distinct minimizers: 688 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.512; total length: 3792\n[M::main] Version: 2.24-r1122\n[M::main] CMD: minimap2 -I 16G -x map-ont -d /galaxy/server/database/jobs_directory/000/89/working/input_assembly.fa.map-ont.mmi /galaxy/server/database/jobs_directory/000/89/working/input_assembly.fa\n[M::main] Real time: 0.011 sec; CPU: 0.008 sec; Peak RSS: 0.003 GB\n[M::main::0.004*1.15] loaded/built the index for 1 target sequence(s)\n[M::mm_mapopt_update::0.004*1.15] mid_occ = 10\n[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1\n[M::mm_idx_stat::0.004*1.14] distinct minimizers: 688 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.512; total length: 3792\n[M::worker_pipeline::0.039*4.20] mapped 125 sequences\n[M::main] Version: 2.24-r1122\n[M::main] CMD: minimap2 -x map-ont --secondary=no -L --MD -A 2 -B 4 -O 4,24 -E 2,1 -t 8 -a /galaxy/server/database/jobs_directory/000/89/working/input_assembly.fa.map-ont.mmi /galaxy/server/database/objects/c/8/a/dataset_c8a79b6c-f9ad-42f3-9f86-6404739394c8.dat\n[M::main] Real time: 0.040 sec; CPU: 0.163 sec; Peak RSS: 0.015 GB\nRunning medaka consensus\n[18:58:49 - Predict] Reducing threads to 2, anymore is a waste.\n[18:58:49 - Predict] It looks like you are running medaka without a GPU and attempted to set a high number of threads. We have scaled this down to an optimal number. If you wish to improve performance please see https://nanoporetech.github.io/medaka/installation.html#improving-parallelism.\n[18:58:49 - Predict] Setting tensorflow inter/intra-op threads to 2/1.\n[18:58:49 - Predict] Processing region(s): 4:0-3792\n[18:58:49 - Predict] Using model: /usr/local/lib/python3.8/site-packages/medaka/data/r941_min_fast_g303_model.hdf5.\n[18:58:49 - Predict] Processing 1 long region(s) with batching.\n[18:58:49 - MdlStore] filepath /usr/local/lib/python3.8/site-packages/medaka/data/r941_min_fast_g303_model.hdf5\n[18:58:50 - BAMFile] Creating pool of 16 BAM file sets.\n[18:58:50 - Sampler] Initializing sampler for consensus of region 4:0-3792.\n[18:58:50 - PWorker] Running inference for 0.0M draft bases.\n[18:58:51 - Feature] Processed 4:0.0-3791.0 (median depth 78.0)\n[18:58:51 - Sampler] Took 0.47s to make features.\n[18:58:51 - Sampler] Region 4:0.0-3791.0 (7485 positions) is smaller than inference chunk length 10000, quarantining.\n[18:58:51 - PWorker] Processed 0 batches\n[18:58:51 - PWorker] All done, 1 remainder regions.\n[18:58:51 - Predict] Processing 1 short region(s).\n[18:58:51 - MdlStore] filepath /usr/local/lib/python3.8/site-packages/medaka/data/r941_min_fast_g303_model.hdf5\n[18:58:51 - Sampler] Initializing sampler for consensus of region 4:0-3792.\n[18:58:51 - PWorker] Running inference for 0.0M draft bases.\n[18:58:52 - Feature] Processed 4:0.0-3791.0 (median depth 78.0)\n[18:58:52 - Sampler] Took 0.32s to make features.\n[18:59:14 - PWorker] Batches in cache: 1.\n[18:59:14 - PWorker] 88.7% Done (0.0/0.0 Mbases) in 22.7s\n[18:59:14 - PWorker] Processed 1 batches\n[18:59:14 - PWorker] All done, 0 remainder regions.\n[18:59:14 - Predict] Finished processing all regions.\n[18:59:17 - DataIndx] Loaded 1/1 (100.00%) sample files.\n[18:59:17 - DataIndx] Loaded 1/1 (100.00%) sample files.\nPolished assembly written to results/consensus.fasta, have a nice day.\n", "stderr": "", "job_messages": [], "dependencies": [], 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/galaxy/server/database/objects/b/e/3/dataset_be3a9eb5-f90a-4a34-9103-93cc7874539f.dat 0.quantmerge/quant.sf && rank_of_series=1 mkdir 1.quantmerge && ln -s /galaxy/server/database/objects/b/a/b/dataset_babe25da-8ea8-4dcc-9f37-1d32fa018376.dat 1.quantmerge/quant.sf && salmon quantmerge --quants *.quantmerge --names 'asdf' 'qwerty' --column 'len' -o qmergeout.tab", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "missing": "\"\"", "genes": "false", "column": "\"len\"", "quantfiles": "[{\"__index__\": 0, \"names\": \"asdf\", \"quants\": {\"values\": [{\"id\": 212, \"src\": \"hda\"}]}}, {\"__index__\": 1, \"names\": \"qwerty\", \"quants\": {\"values\": [{\"id\": 213, \"src\": \"hda\"}]}}]"}, "inputs": {"quantfiles_0|quants": {"id": "d2999df588b66189", "src": "hda", "uuid": "be3a9eb5-f90a-4a34-9103-93cc7874539f"}, "quantfiles_1|quants": {"id": "e84d5d005471e063", "src": "hda", "uuid": "babe25da-8ea8-4dcc-9f37-1d32fa018376"}}, "outputs": {"mergedfile": {"id": "d79761699b67b292", "src": "hda", "uuid": "018aeafa-b438-43c1-a03a-da428e3f7159"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[2024-11-08 19:29:20.889] [mergeLog] [info] samples: [ 0.quantmerge, 1.quantmerge ]\n[2024-11-08 19:29:20.889] [mergeLog] [info] sample names : [ asdf, qwerty ]\n[2024-11-08 19:29:20.889] [mergeLog] [info] output column : LEN\n[2024-11-08 19:29:20.889] [mergeLog] [info] output file : qmergeout.tab\n[2024-11-08 19:29:20.889] [mergeLog] [info] Parsing 0.quantmerge/quant.sf\n[2024-11-08 19:29:20.891] [mergeLog] [info] Parsing 1.quantmerge/quant.sf\n[2024-11-08 19:29:20.896] [mergeLog] [warning] There were 3 missing entries (recorded as \"NA\") in the output\n", "tool_stderr": "Version Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###", "job_stdout": "", "job_stderr": "", "stdout": "[2024-11-08 19:29:20.889] [mergeLog] [info] samples: [ 0.quantmerge, 1.quantmerge ]\n[2024-11-08 19:29:20.889] [mergeLog] [info] sample names : [ asdf, qwerty ]\n[2024-11-08 19:29:20.889] [mergeLog] [info] output column : LEN\n[2024-11-08 19:29:20.889] [mergeLog] [info] output file : qmergeout.tab\n[2024-11-08 19:29:20.889] [mergeLog] [info] Parsing 0.quantmerge/quant.sf\n[2024-11-08 19:29:20.891] [mergeLog] [info] Parsing 1.quantmerge/quant.sf\n[2024-11-08 19:29:20.896] [mergeLog] [warning] There were 3 missing entries (recorded as \"NA\") in the output\n", "stderr": "Version Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-11-08 19:29:20", "plugin": "core", "name": "end_epoch", "raw_value": "1731094160.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:29:20", "plugin": "core", "name": "start_epoch", "raw_value": "1731094160.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "samtools_markdup/1.9+galaxy2-0", "has_data": true, "data": {"tool_id": "samtools_markdup", "tool_version": "1.9+galaxy2", "test_index": 0, "time_seconds": 52.750569105148315, "inputs": {"bamfile": {"src": "hda", "id": "58dccf0d0bd14a40"}}, "job": {"model_class": "Job", "id": "313122af5a7398a2", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:10:08.500901", "update_time": "2024-11-08T19:10:39.645826", "galaxy_version": "24.1", "external_id": "gxy-zcjzt", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && samtools sort -@ $addthreads -m ${GALAXY_MEMORY_MB:-768}M -T \"${TMPDIR:-.}\" -O sam -o coordsort.sam '/galaxy/server/database/objects/8/1/0/dataset_8103817b-d5cb-4cc0-9429-64e32c6b08cb.dat' && samtools markdup -@ $addthreads coordsort.sam '/galaxy/server/database/objects/5/a/5/dataset_5a52145f-cbfb-421c-8a96-519a1d68b4ec.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"sam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "supp": "false", "stats": "false", "maxlen": "\"\"", "remove": "false"}, "inputs": {"bamfile": {"id": "58dccf0d0bd14a40", "src": "hda", "uuid": "8103817b-d5cb-4cc0-9429-64e32c6b08cb"}}, "outputs": {"output": {"id": "84e25ac3b5653ceb", "src": "hda", "uuid": "5a52145f-cbfb-421c-8a96-519a1d68b4ec"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-11-08 19:10:26", "plugin": "core", "name": "end_epoch", "raw_value": "1731093026.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:10:26", "plugin": "core", "name": "start_epoch", "raw_value": "1731093026.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output output: Test output file (5_markdup.expected.bam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_markdup/1.9+galaxy2-0", "has_data": true, "data": {"tool_id": "samtools_markdup", "tool_version": "1.9+galaxy2", "test_index": 0, "time_seconds": 36.95435094833374, "inputs": {"bamfile": {"src": "hda", "id": "edcc5d810d7f2cbe"}}, "job": {"model_class": "Job", "id": "5a20d38e9bb241c0", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:12:53.037166", "update_time": "2024-11-08T19:13:07.795407", "galaxy_version": "24.1", "external_id": "gxy-hjtb6", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && samtools sort -@ $addthreads -m ${GALAXY_MEMORY_MB:-768}M -T \"${TMPDIR:-.}\" -O sam -o coordsort.sam '/galaxy/server/database/objects/7/e/a/dataset_7ea4a1ca-c098-48d8-af25-223ddb18b060.dat' && samtools markdup -@ $addthreads coordsort.sam '/galaxy/server/database/objects/e/4/d/dataset_e4dae36d-3883-449f-ad21-dad36e431aef.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"sam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "supp": "false", "stats": "false", "maxlen": "\"\"", "remove": "false"}, "inputs": {"bamfile": {"id": "edcc5d810d7f2cbe", "src": "hda", "uuid": "7ea4a1ca-c098-48d8-af25-223ddb18b060"}}, "outputs": {"output": {"id": "a26c5048a128464f", "src": "hda", "uuid": "e4dae36d-3883-449f-ad21-dad36e431aef"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-11-08 19:12:55", "plugin": "core", "name": "end_epoch", "raw_value": "1731093175.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:12:55", "plugin": "core", "name": "start_epoch", "raw_value": "1731093175.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output output: Test output file (5_markdup.expected.bam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_markdup/1.9+galaxy2-1", "has_data": true, "data": {"tool_id": "samtools_markdup", "tool_version": "1.9+galaxy2", "test_index": 1, "time_seconds": 37.238877058029175, "inputs": {"bamfile": {"src": "hda", "id": "6da69afd6692ab80"}, "remove": true}, "job": {"model_class": "Job", "id": "87a90ca5ab392bca", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:11:01.845405", "update_time": "2024-11-08T19:11:16.765811", "galaxy_version": "24.1", "external_id": "gxy-hppp6", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && samtools sort -@ $addthreads -m ${GALAXY_MEMORY_MB:-768}M -T \"${TMPDIR:-.}\" -O sam -o coordsort.sam '/galaxy/server/database/objects/f/5/6/dataset_f560e931-b896-47d7-ba04-5d310e4baf10.dat' && samtools markdup -@ $addthreads -r coordsort.sam '/galaxy/server/database/objects/3/2/9/dataset_329591ab-e197-4aee-a1f3-26c53da2afe6.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"sam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "supp": "false", "stats": "false", "maxlen": "\"\"", "remove": "true"}, "inputs": {"bamfile": {"id": "6da69afd6692ab80", "src": "hda", "uuid": "f560e931-b896-47d7-ba04-5d310e4baf10"}}, "outputs": {"output": {"id": "fa3b2a0beafdfdbd", "src": "hda", "uuid": "329591ab-e197-4aee-a1f3-26c53da2afe6"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-11-08 19:11:04", "plugin": "core", "name": "end_epoch", "raw_value": "1731093064.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:11:04", "plugin": "core", "name": "start_epoch", "raw_value": "1731093064.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output output: Test output file (6_remove_dups.expected.bam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_markdup/1.9+galaxy2-1", "has_data": true, "data": {"tool_id": "samtools_markdup", "tool_version": "1.9+galaxy2", "test_index": 1, "time_seconds": 35.93983030319214, "inputs": {"bamfile": {"src": "hda", "id": "3b1d785838fcf855"}, "remove": true}, "job": {"model_class": "Job", "id": "c0004b57c32be191", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:13:29.973700", "update_time": "2024-11-08T19:13:43.836994", "galaxy_version": "24.1", "external_id": "gxy-zqkg8", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && samtools sort -@ $addthreads -m ${GALAXY_MEMORY_MB:-768}M -T \"${TMPDIR:-.}\" -O sam -o coordsort.sam '/galaxy/server/database/objects/7/0/1/dataset_7017ce3e-dcf6-4bed-ac6e-f0f9d6b53950.dat' && samtools markdup -@ $addthreads -r coordsort.sam '/galaxy/server/database/objects/7/9/6/dataset_7964d901-4f95-4549-a315-fadd8e828faf.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"sam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "supp": "false", "stats": "false", "maxlen": "\"\"", "remove": "true"}, "inputs": {"bamfile": {"id": "3b1d785838fcf855", "src": "hda", "uuid": "7017ce3e-dcf6-4bed-ac6e-f0f9d6b53950"}}, "outputs": {"output": {"id": "0f8a361424c463d6", "src": "hda", "uuid": "7964d901-4f95-4549-a315-fadd8e828faf"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-11-08 19:13:31", "plugin": "core", "name": "end_epoch", "raw_value": "1731093211.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:13:31", "plugin": "core", "name": "start_epoch", "raw_value": "1731093211.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output output: Test output file (6_remove_dups.expected.bam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_markdup/1.9+galaxy2-2", "has_data": true, "data": {"tool_id": "samtools_markdup", "tool_version": "1.9+galaxy2", "test_index": 2, "time_seconds": 37.236971855163574, "inputs": {"bamfile": {"src": "hda", "id": "dba0a91ab7c50a76"}, "supp": true}, "job": {"model_class": "Job", "id": "0875c422d93fe122", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:11:39.479669", "update_time": "2024-11-08T19:11:54.128286", "galaxy_version": "24.1", "external_id": "gxy-k2lhl", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/b/f/d/dataset_bfd57f96-cfc4-49e2-81f0-e7d812490c54.dat' coordsort.sam && samtools markdup -@ $addthreads -S coordsort.sam '/galaxy/server/database/objects/8/7/c/dataset_87c9898e-7138-4c1e-a182-c4855e321b85.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "supp": "true", "stats": "false", "maxlen": "\"\"", "remove": "false"}, "inputs": {"bamfile": {"id": "dba0a91ab7c50a76", "src": "hda", "uuid": "bfd57f96-cfc4-49e2-81f0-e7d812490c54"}}, "outputs": {"output": {"id": "a2f86245bd71b4cb", "src": "hda", "uuid": "87c9898e-7138-4c1e-a182-c4855e321b85"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-11-08 19:11:41", "plugin": "core", "name": "end_epoch", "raw_value": "1731093101.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:11:41", "plugin": "core", "name": "start_epoch", "raw_value": "1731093101.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output output: Test output file (7_mark_supp_dup.expected.bam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_markdup/1.9+galaxy2-2", "has_data": true, "data": {"tool_id": "samtools_markdup", "tool_version": "1.9+galaxy2", "test_index": 2, "time_seconds": 37.56330871582031, "inputs": {"bamfile": {"src": "hda", "id": "63c2ba7411f9dc82"}, "supp": true}, "job": {"model_class": "Job", "id": "e9cb4075989abeb8", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:14:06.607473", "update_time": "2024-11-08T19:14:21.410268", "galaxy_version": "24.1", "external_id": "gxy-dqw66", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/f/8/b/dataset_f8bf62c9-c988-417f-8292-f65c47ebf122.dat' coordsort.sam && samtools markdup -@ $addthreads -S coordsort.sam '/galaxy/server/database/objects/7/e/9/dataset_7e947de6-f24b-474e-aa4c-b4556ff875f8.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "supp": "true", "stats": "false", "maxlen": "\"\"", "remove": "false"}, "inputs": {"bamfile": {"id": "63c2ba7411f9dc82", "src": "hda", "uuid": "f8bf62c9-c988-417f-8292-f65c47ebf122"}}, "outputs": {"output": {"id": "449cf9cc7d01dc92", "src": "hda", "uuid": "7e947de6-f24b-474e-aa4c-b4556ff875f8"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-11-08 19:14:08", "plugin": "core", "name": "end_epoch", "raw_value": "1731093248.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:14:08", "plugin": "core", "name": "start_epoch", "raw_value": "1731093248.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output output: Test output file (7_mark_supp_dup.expected.bam) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "samtools_markdup/1.9+galaxy2-3", "has_data": true, "data": {"tool_id": "samtools_markdup", "tool_version": "1.9+galaxy2", "test_index": 3, "time_seconds": 35.5696964263916, "inputs": {"bamfile": {"src": "hda", "id": "237e69e4ea734e4b"}, "stats": true}, "job": {"model_class": "Job", "id": "7807a571f0107626", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:12:15.531657", "update_time": "2024-11-08T19:12:29.569329", "galaxy_version": "24.1", "external_id": "gxy-8vtzv", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && samtools sort -@ $addthreads -m ${GALAXY_MEMORY_MB:-768}M -T \"${TMPDIR:-.}\" -O sam -o coordsort.sam '/galaxy/server/database/objects/7/9/8/dataset_7987bd7d-c3de-4191-a73a-09c9b8d2e0c1.dat' && samtools markdup -@ $addthreads -s coordsort.sam '/galaxy/server/database/objects/a/3/8/dataset_a381acff-c390-4722-8db9-4896465abef7.dat' 2> '/galaxy/server/database/objects/3/8/b/dataset_38b96997-56c4-412a-8b9b-d042882631f3.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"sam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "supp": "false", "stats": "true", "maxlen": "\"\"", "remove": "false"}, "inputs": {"bamfile": {"id": "237e69e4ea734e4b", "src": "hda", "uuid": "7987bd7d-c3de-4191-a73a-09c9b8d2e0c1"}}, "outputs": {"output": {"id": "538f8a97f78e293e", "src": "hda", "uuid": "a381acff-c390-4722-8db9-4896465abef7"}, "stats_output": {"id": "7b35e56724bdc701", "src": "hda", "uuid": "38b96997-56c4-412a-8b9b-d042882631f3"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-11-08 19:12:17", "plugin": "core", "name": "end_epoch", "raw_value": "1731093137.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:12:17", "plugin": "core", "name": "start_epoch", "raw_value": "1731093137.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output output: Test output file (5_markdup.expected.bam) is missing. If you are using planemo, try adding --update_test_data to generate it.", "Output stats_output: different than expected, difference (using diff):\n( /tmp/tmpw8ixzrthstats.txt v. /tmp/tmpv4zahm19stats.txt )\n--- local_file\n+++ history_data\n@@ -1,17 +1,5 @@\n-COMMAND: samtools markdup -@ 0 -m t -s -f /tmp/tmpo1hsz7dc/job_working_directory/000/8/outputs/dataset_9e69bd59-3165-4ede-92bf-2f438627a6a1.dat -O BAM coordsort.sam /tmp/tmpo1hsz7dc/job_working_directory/000/8/outputs/dataset_ccf59cfe-ffbd-41d5-9412-d7a7ac6e65d9.dat\n-READ: 16\n-WRITTEN: 16\n-EXCLUDED: 3\n-EXAMINED: 13\n-PAIRED: 10\n-SINGLE: 3\n-DUPLICATE PAIR: 4\n-DUPLICATE SINGLE: 2\n-DUPLICATE PAIR OPTICAL: 0\n-DUPLICATE SINGLE OPTICAL: 0\n-DUPLICATE NON PRIMARY: 0\n-DUPLICATE NON PRIMARY OPTICAL: 0\n-DUPLICATE PRIMARY TOTAL: 6\n-DUPLICATE TOTAL: 6\n-ESTIMATED_LIBRARY_SIZE: 4\n-\n+READ 16 WRITTEN 16 \n+EXCLUDED 3 EXAMINED 13\n+PAIRED 10 SINGLE 3\n+DULPICATE PAIR 4 DUPLICATE SINGLE 2\n+DUPLICATE TOTAL 6\n"], "status": "failure"}}, {"id": "samtools_markdup/1.9+galaxy2-3", "has_data": true, "data": {"tool_id": "samtools_markdup", "tool_version": "1.9+galaxy2", "test_index": 3, "time_seconds": 36.45379042625427, "inputs": {"bamfile": {"src": "hda", "id": "64bb9a27eebe46a5"}, "stats": true}, "job": {"model_class": "Job", "id": "93d2fe7f03087140", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:14:42.964979", "update_time": "2024-11-08T19:14:57.757725", "galaxy_version": "24.1", "external_id": "gxy-ttplf", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && samtools sort -@ $addthreads -m ${GALAXY_MEMORY_MB:-768}M -T \"${TMPDIR:-.}\" -O sam -o coordsort.sam '/galaxy/server/database/objects/b/6/5/dataset_b65d9f13-faa3-4e6c-bdfc-69cbb6cdcf07.dat' && samtools markdup -@ $addthreads -s coordsort.sam '/galaxy/server/database/objects/e/9/0/dataset_e90b742d-0c63-40eb-9490-2ec8e6f415cb.dat' 2> '/galaxy/server/database/objects/7/b/3/dataset_7b38485f-eeb6-4b3b-a342-b5124eb826a7.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"sam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "supp": "false", "stats": "true", "maxlen": "\"\"", "remove": "false"}, "inputs": {"bamfile": {"id": "64bb9a27eebe46a5", "src": "hda", "uuid": "b65d9f13-faa3-4e6c-bdfc-69cbb6cdcf07"}}, "outputs": {"output": {"id": "74798f5cd5fbe7e1", "src": "hda", "uuid": "e90b742d-0c63-40eb-9490-2ec8e6f415cb"}, "stats_output": {"id": "6941a67834a7dc0d", "src": "hda", "uuid": "7b38485f-eeb6-4b3b-a342-b5124eb826a7"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-08 19:14:45", "plugin": "core", "name": "end_epoch", "raw_value": "1731093285.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:14:44", "plugin": "core", "name": "start_epoch", "raw_value": "1731093284.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output output: Test output file (5_markdup.expected.bam) is missing. If you are using planemo, try adding --update_test_data to generate it.", "Output stats_output: different than expected, difference (using diff):\n( /tmp/tmpur892afcstats.txt v. /tmp/tmp9tkvhsssstats.txt )\n--- local_file\n+++ history_data\n@@ -1,17 +1,5 @@\n-COMMAND: samtools markdup -@ 0 -m t -s -f /tmp/tmpo1hsz7dc/job_working_directory/000/8/outputs/dataset_9e69bd59-3165-4ede-92bf-2f438627a6a1.dat -O BAM coordsort.sam /tmp/tmpo1hsz7dc/job_working_directory/000/8/outputs/dataset_ccf59cfe-ffbd-41d5-9412-d7a7ac6e65d9.dat\n-READ: 16\n-WRITTEN: 16\n-EXCLUDED: 3\n-EXAMINED: 13\n-PAIRED: 10\n-SINGLE: 3\n-DUPLICATE PAIR: 4\n-DUPLICATE SINGLE: 2\n-DUPLICATE PAIR OPTICAL: 0\n-DUPLICATE SINGLE OPTICAL: 0\n-DUPLICATE NON PRIMARY: 0\n-DUPLICATE NON PRIMARY OPTICAL: 0\n-DUPLICATE PRIMARY TOTAL: 6\n-DUPLICATE TOTAL: 6\n-ESTIMATED_LIBRARY_SIZE: 4\n-\n+READ 16 WRITTEN 16 \n+EXCLUDED 3 EXAMINED 13\n+PAIRED 10 SINGLE 3\n+DULPICATE PAIR 4 DUPLICATE SINGLE 2\n+DUPLICATE TOTAL 6\n"], "status": "failure"}}, {"id": "scanpy_compute_graph/1.9.3+galaxy0-0", "has_data": true, "data": {"tool_id": "scanpy_compute_graph", "tool_version": "1.9.3+galaxy0", "test_index": 0, "time_seconds": 0.09598922729492188, "execution_problem": "Input staging problem: Test input file (run_pca.h5) cannot be found.", "status": "error"}}, {"id": "scanpy_compute_graph/1.9.3+galaxy0-0", "has_data": true, "data": {"tool_id": "scanpy_compute_graph", "tool_version": "1.9.3+galaxy0", "test_index": 0, "time_seconds": 0.09647870063781738, "execution_problem": "Input staging problem: Test input file (run_pca.h5) cannot be found.", "status": "error"}}, {"id": "scanpy_compute_graph/1.9.3+galaxy0-1", "has_data": true, "data": {"tool_id": "scanpy_compute_graph", "tool_version": "1.9.3+galaxy0", "test_index": 1, "time_seconds": 0.052007198333740234, "execution_problem": "Input staging problem: Test input file (run_pca.h5) cannot be found.", "status": "error"}}, {"id": "scanpy_compute_graph/1.9.3+galaxy0-1", "has_data": true, "data": {"tool_id": "scanpy_compute_graph", "tool_version": "1.9.3+galaxy0", "test_index": 1, "time_seconds": 0.05334782600402832, "execution_problem": "Input staging problem: Test input file (run_pca.h5) cannot be found.", "status": "error"}}, {"id": "scanpy_remove_confounders/1.9.6+galaxy4-0", "has_data": true, "data": {"tool_id": "scanpy_remove_confounders", "tool_version": "1.9.6+galaxy4", "test_index": 0, "time_seconds": 83.71624851226807, "inputs": {"adata": {"src": "hda", "id": "7e9b3f6181d9f21f"}, "method|keys": "cell_type", "method|method": "pp.regress_out", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "66940b1e901b3834", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.9.6+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:29:59.451693", "update_time": "2024-11-08T19:31:01.204101", "galaxy_version": "24.1", "external_id": "gxy-q55vd", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/e/b/3/dataset_eb3817fd-954b-4d67-8502-a69493f8970b.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/195/configs/tmpdgkre4tr' > '/galaxy/server/database/objects/e/1/7/dataset_e17b784b-5eea-4a1e-8d93-a8c25a26a867.dat' && python '/galaxy/server/database/jobs_directory/000/195/configs/tmpdgkre4tr' >> '/galaxy/server/database/objects/e/1/7/dataset_e17b784b-5eea-4a1e-8d93-a8c25a26a867.dat' && ls . >> '/galaxy/server/database/objects/e/1/7/dataset_e17b784b-5eea-4a1e-8d93-a8c25a26a867.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 0, \"keys\": \"cell_type\", \"method\": \"pp.regress_out\"}"}, "inputs": {"adata": {"id": "7e9b3f6181d9f21f", "src": "hda", "uuid": "eb3817fd-954b-4d67-8502-a69493f8970b"}}, "outputs": {"anndata_out": {"id": "4516f1481323ade4", "src": "hda", "uuid": "420285c6-8434-4c1b-a028-e2a193938d2e"}, "hidden_output": {"id": "454e5a69a5cfe987", "src": "hda", "uuid": "e17b784b-5eea-4a1e-8d93-a8c25a26a867"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- cell_type\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- cell_type\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "3 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "3.0000000"}, {"title": "Job End Time", "value": "2024-11-08 19:30:38", "plugin": "core", "name": "end_epoch", "raw_value": "1731094238.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:30:35", "plugin": "core", "name": "start_epoch", "raw_value": "1731094235.0000000"}, {"title": "Memory Allocated (MB)", "value": "32641", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "32641.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "scanpy_remove_confounders/1.9.6+galaxy4-1", "has_data": true, "data": {"tool_id": "scanpy_remove_confounders", "tool_version": "1.9.6+galaxy4", "test_index": 1, "time_seconds": 39.197073221206665, "inputs": {"adata": {"src": "hda", "id": "38e2156fd7401822"}, "method|key": "blobs", "method|method": "pp.combat", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "a62fb4db4837b8ab", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.9.6+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:31:23.566922", "update_time": "2024-11-08T19:31:40.564237", "galaxy_version": "24.1", "external_id": "gxy-jvsxf", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/3/f/0/dataset_3f0e5f62-79a0-4088-adcf-11f31d12aa69.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/197/configs/tmp0cvl6uyc' > '/galaxy/server/database/objects/1/2/7/dataset_127b2d88-f382-4501-8937-c2c5261d40c9.dat' && python '/galaxy/server/database/jobs_directory/000/197/configs/tmp0cvl6uyc' >> '/galaxy/server/database/objects/1/2/7/dataset_127b2d88-f382-4501-8937-c2c5261d40c9.dat' && ls . >> '/galaxy/server/database/objects/1/2/7/dataset_127b2d88-f382-4501-8937-c2c5261d40c9.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 2, \"key\": \"blobs\", \"method\": \"pp.combat\"}"}, "inputs": {"adata": {"id": "38e2156fd7401822", "src": "hda", "uuid": "3f0e5f62-79a0-4088-adcf-11f31d12aa69"}}, "outputs": {"anndata_out": {"id": "0a6da04fcad59fe6", "src": "hda", "uuid": "c5ababc8-e477-40c2-9b10-99b664057de7"}, "hidden_output": {"id": "4c694d23b823468b", "src": "hda", "uuid": "127b2d88-f382-4501-8937-c2c5261d40c9"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- blobs\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- blobs\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "3 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "3.0000000"}, {"title": "Job End Time", "value": "2024-11-08 19:31:28", "plugin": "core", "name": "end_epoch", "raw_value": "1731094288.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:31:25", "plugin": "core", "name": "start_epoch", "raw_value": "1731094285.0000000"}, {"title": "Memory Allocated (MB)", "value": "32641", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "32641.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "stringtie/2.2.3+galaxy0-0", "has_data": true, "data": {"tool_id": "stringtie", "tool_version": "2.2.3+galaxy0", "test_index": 0, "time_seconds": 50.73204708099365, "inputs": {"input_options|input_bam": {"src": "hda", "id": "2274d9bc56091239"}, "input_options|input_mode": "short_reads"}, "job": {"model_class": "Job", "id": "9f31ce1d612eb955", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:03:18.414163", "update_time": "2024-11-08T19:03:46.397979", "galaxy_version": "24.1", "external_id": "gxy-vp77n", "handler": null, "job_runner_name": null, "command_line": "mkdir -p ./special_de_output/sample1/ && stringtie '/galaxy/server/database/objects/9/c/6/dataset_9c6a2ced-b768-45b4-8c20-dcbaaf079761.dat' -o '/galaxy/server/database/objects/a/c/d/dataset_acdfa6a2-a109-4ff4-9a5c-f3fe1ecc4b61.dat' -p \"${GALAXY_SLOTS:-1}\" -f '0.01' -m '200' -a '10' -j '1' -c '1' -g '50' -M '1.0'", "user_email": "tests@fake.org", "command_version": "2.2.3", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": 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"\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"abundance_estimation\": false, \"bdist\": \"50\", \"bundle_fraction\": \"1.0\", \"disable_trimming\": false, \"fraction\": \"0.17\", \"min_anchor_cov\": \"1\", \"min_anchor_len\": \"10\", \"min_bundle_cov\": \"1\", \"min_tlen\": \"200\", \"multi_mapping\": false, \"name_prefix\": null, \"omit_sequences\": \"\", \"point_features\": null}", "guide": "{\"__current_case__\": 0, \"use_guide\": \"no\"}", "rna_strandness": "\"\"", "input_options": "{\"__current_case__\": 0, \"input_bam\": {\"values\": [{\"id\": 109, \"src\": \"hda\"}]}, \"input_mode\": \"short_reads\"}"}, "inputs": {"input_options|input_bam": {"id": "c5b19d90d64a0b32", "src": "hda", "uuid": "d2b59e62-c6ee-45a3-b3c8-f13acf0df5b3"}}, "outputs": {"output_gtf": {"id": "34911ce9f087078e", "src": "hda", "uuid": "98c0ccc0-bfe2-4b1e-a55c-9ae96f018313"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-11-08 19:04:10", "plugin": "core", "name": "end_epoch", "raw_value": "1731092650.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:04:10", "plugin": "core", "name": "start_epoch", "raw_value": "1731092650.0000000"}, {"title": "Memory Allocated (MB)", "value": "26843", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "26843.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "stringtie/2.2.3+galaxy0-10", "has_data": true, "data": {"tool_id": "stringtie", "tool_version": "2.2.3+galaxy0", "test_index": 10, "time_seconds": 13.361477613449097, "execution_problem": "Input staging problem: Job in error 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"input_options": "{\"__current_case__\": 2, \"error_splice\": \"25\", \"input_bam_long\": {\"values\": [{\"id\": 143, \"src\": \"hda\"}]}, \"input_bam_short\": {\"values\": [{\"id\": 142, \"src\": \"hda\"}]}, \"input_mode\": \"mixed_reads\"}"}, "inputs": {"input_options|input_bam_short": {"id": "cc9d8bb46765f933", "src": "hda", "uuid": "d8771fc1-c251-4061-8b41-eb887ab6b50d"}, "input_options|input_bam_long": {"id": "93d2fe7f03087140", "src": "hda", "uuid": "d5de7dbd-1178-48de-bdfc-f8df69f9c14f"}}, "outputs": {"output_gtf": {"id": "7764c94f267f71be", "src": "hda", "uuid": "3718ca85-c02c-4622-9dcb-62b695a35a2c"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0, exit_code: None, stderr: .", "Job in 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"input_options": "{\"__current_case__\": 2, \"error_splice\": \"25\", \"input_bam_long\": {\"values\": [{\"id\": 145, \"src\": \"hda\"}]}, \"input_bam_short\": {\"values\": [{\"id\": 145, \"src\": \"hda\"}]}, \"input_mode\": \"mixed_reads\"}"}, "inputs": {"input_options|input_bam_short": {"id": "290b901b9cbb0bd1", "src": "hda", "uuid": "1070f1db-e019-4924-a4aa-19798055077e"}, "input_options|input_bam_long": {"id": "290b901b9cbb0bd1", "src": "hda", "uuid": "1070f1db-e019-4924-a4aa-19798055077e"}}, "outputs": {"output_gtf": {"id": "479f81759fe14964", "src": "hda", "uuid": "d5aad371-a438-432f-9100-8b77b0d259e0"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": 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"\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"abundance_estimation\": false, \"bdist\": \"50\", \"bundle_fraction\": \"1.0\", \"disable_trimming\": false, \"fraction\": \"0.01\", \"min_anchor_cov\": \"1\", \"min_anchor_len\": \"10\", \"min_bundle_cov\": \"1\", \"min_tlen\": \"200\", \"multi_mapping\": false, \"name_prefix\": null, \"omit_sequences\": \"\", \"point_features\": null}", "guide": "{\"__current_case__\": 1, \"coverage_file\": false, \"guide_source\": {\"__current_case__\": 1, \"guide_gff_select\": \"history\", \"ref_hist\": {\"values\": [{\"id\": 112, \"src\": \"hda\"}]}}, \"input_estimation\": false, \"special_outputs\": {\"__current_case__\": 2, \"special_outputs_select\": \"no\"}, \"use_guide\": \"yes\"}", "rna_strandness": "\"\"", "input_options": "{\"__current_case__\": 0, \"input_bam\": {\"values\": [{\"id\": 111, \"src\": \"hda\"}]}, \"input_mode\": \"short_reads\"}"}, "inputs": {"input_options|input_bam": {"id": "83aa9bcb838125e8", "src": "hda", "uuid": "2cab388f-b96a-4fc4-bb3d-d69932a03b80"}, "guide|guide_source|ref_hist": {"id": "b19cc830d5a63129", "src": "hda", "uuid": "84c10f8d-b3ef-4c1f-bef9-3297c3ef4800"}}, "outputs": {"output_gtf": {"id": "d9e73d5a86ad4a25", "src": "hda", "uuid": "2c9cf8c3-44d2-48f2-80cd-7b1ffe528eb1"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-11-08 19:04:48", "plugin": "core", "name": "end_epoch", "raw_value": "1731092688.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:04:48", "plugin": "core", "name": "start_epoch", "raw_value": "1731092688.0000000"}, {"title": "Memory Allocated (MB)", "value": "26843", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "26843.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "stringtie/2.2.3+galaxy0-3", "has_data": true, "data": {"tool_id": "stringtie", "tool_version": "2.2.3+galaxy0", "test_index": 3, "time_seconds": 38.05444002151489, "inputs": {"input_options|input_bam": {"src": "hda", "id": "b5df49ef3bf6281c"}, "input_options|input_mode": "short_reads", "guide|guide_source|ref_hist": {"src": "hda", "id": "60e8d7b20ea99c2a"}, "guide|guide_source|guide_gff_select": "history", "guide|use_guide": "yes", "adv|fraction": "0.17"}, "job": {"model_class": "Job", "id": "2c1230cb190434eb", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:05:24.994752", "update_time": "2024-11-08T19:05:39.697538", "galaxy_version": "24.1", "external_id": "gxy-mnh8z", "handler": null, "job_runner_name": null, "command_line": "mkdir -p ./special_de_output/sample1/ && ln -s '/galaxy/server/database/objects/0/f/b/dataset_0fb37cdd-d80a-4dbe-9f8d-06a611b3b869.dat' guide.gff && stringtie '/galaxy/server/database/objects/e/f/c/dataset_efc1de1b-66f4-4fbc-9873-62c45bbb4515.dat' -o '/galaxy/server/database/objects/1/3/5/dataset_1350d7a0-00ae-459b-8447-9dd40e3f9197.dat' -p \"${GALAXY_SLOTS:-1}\" -G guide.gff -b ./special_de_output/sample1/ -f '0.17' -m '200' -a '10' -j '1' -c '1' -g '50' -M '1.0'", "user_email": "tests@fake.org", "command_version": "2.2.3", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"abundance_estimation\": false, \"bdist\": \"50\", \"bundle_fraction\": \"1.0\", \"disable_trimming\": false, \"fraction\": \"0.17\", \"min_anchor_cov\": \"1\", \"min_anchor_len\": \"10\", \"min_bundle_cov\": \"1\", \"min_tlen\": \"200\", \"multi_mapping\": false, \"name_prefix\": null, \"omit_sequences\": \"\", \"point_features\": null}", "guide": "{\"__current_case__\": 1, \"coverage_file\": false, \"guide_source\": {\"__current_case__\": 1, \"guide_gff_select\": \"history\", \"ref_hist\": {\"values\": [{\"id\": 115, \"src\": \"hda\"}]}}, \"input_estimation\": false, \"special_outputs\": {\"__current_case__\": 2, \"special_outputs_select\": \"no\"}, \"use_guide\": \"yes\"}", "rna_strandness": "\"\"", "input_options": "{\"__current_case__\": 0, \"input_bam\": {\"values\": [{\"id\": 114, \"src\": \"hda\"}]}, \"input_mode\": \"short_reads\"}"}, "inputs": {"input_options|input_bam": {"id": "b5df49ef3bf6281c", "src": "hda", "uuid": "efc1de1b-66f4-4fbc-9873-62c45bbb4515"}, "guide|guide_source|ref_hist": {"id": "60e8d7b20ea99c2a", "src": "hda", "uuid": "0fb37cdd-d80a-4dbe-9f8d-06a611b3b869"}}, "outputs": {"output_gtf": {"id": "6ec9315ee735f78a", "src": "hda", "uuid": "1350d7a0-00ae-459b-8447-9dd40e3f9197"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-11-08 19:05:26", "plugin": "core", "name": "end_epoch", "raw_value": "1731092726.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:05:26", "plugin": "core", "name": "start_epoch", "raw_value": "1731092726.0000000"}, {"title": "Memory Allocated (MB)", "value": "26843", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "26843.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "stringtie/2.2.3+galaxy0-4", "has_data": true, "data": {"tool_id": "stringtie", "tool_version": "2.2.3+galaxy0", "test_index": 4, "time_seconds": 40.99363303184509, "inputs": {"input_options|input_bam": {"src": "hda", "id": "87afed66c00a7675"}, "input_options|input_mode": "short_reads", "guide|guide_source|ref_hist": {"src": "hda", "id": "b760d2295e3f99a5"}, "guide|guide_source|guide_gff_select": "history", "guide|special_outputs|special_outputs_select": "ballgown", "guide|coverage_file": true, "guide|use_guide": "yes"}, "job": {"model_class": "Job", "id": "83aa9bcb838125e8", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:06:02.776760", "update_time": "2024-11-08T19:06:18.459266", "galaxy_version": "24.1", "external_id": "gxy-lhjj2", "handler": null, "job_runner_name": null, "command_line": "mkdir -p ./special_de_output/sample1/ && ln -s '/galaxy/server/database/objects/b/9/3/dataset_b93643c6-86c0-4db6-8605-4ae9441ff170.dat' guide.gff && stringtie '/galaxy/server/database/objects/6/0/f/dataset_60f2d9e2-a974-4859-bbd7-cf64ed1913fe.dat' -o '/galaxy/server/database/objects/9/4/a/dataset_94ac8ce3-9a47-463b-8486-b2544e2b092d.dat' -p \"${GALAXY_SLOTS:-1}\" -G guide.gff -C '/galaxy/server/database/objects/8/4/2/dataset_842b1133-b6c0-49fe-ac16-13f3d18af7e0.dat' -b ./special_de_output/sample1/ -f '0.01' -m '200' -a '10' -j '1' -c '1' -g '50' -M '1.0'", "user_email": "tests@fake.org", "command_version": "2.2.3", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"abundance_estimation\": false, \"bdist\": \"50\", \"bundle_fraction\": \"1.0\", \"disable_trimming\": false, \"fraction\": \"0.01\", \"min_anchor_cov\": \"1\", \"min_anchor_len\": \"10\", \"min_bundle_cov\": \"1\", \"min_tlen\": \"200\", \"multi_mapping\": false, \"name_prefix\": null, \"omit_sequences\": \"\", \"point_features\": null}", "guide": "{\"__current_case__\": 1, \"coverage_file\": true, \"guide_source\": {\"__current_case__\": 1, \"guide_gff_select\": \"history\", \"ref_hist\": {\"values\": [{\"id\": 118, \"src\": \"hda\"}]}}, \"input_estimation\": false, \"special_outputs\": {\"__current_case__\": 0, \"special_outputs_select\": \"ballgown\"}, \"use_guide\": \"yes\"}", "rna_strandness": "\"\"", "input_options": "{\"__current_case__\": 0, \"input_bam\": {\"values\": [{\"id\": 117, \"src\": \"hda\"}]}, \"input_mode\": \"short_reads\"}"}, "inputs": {"input_options|input_bam": {"id": "87afed66c00a7675", "src": "hda", "uuid": "60f2d9e2-a974-4859-bbd7-cf64ed1913fe"}, "guide|guide_source|ref_hist": {"id": "b760d2295e3f99a5", "src": "hda", "uuid": "b93643c6-86c0-4db6-8605-4ae9441ff170"}}, "outputs": {"output_gtf": {"id": "b48563d4d6a24bed", "src": "hda", "uuid": "94ac8ce3-9a47-463b-8486-b2544e2b092d"}, "coverage": {"id": "1c0b833cfd710b29", "src": "hda", "uuid": "842b1133-b6c0-49fe-ac16-13f3d18af7e0"}, "exon_expression": {"id": "ce14c2d285f898d3", "src": "hda", "uuid": "5068689c-a589-41af-accc-6f334c99aae1"}, "intron_expression": {"id": "28ca52757f505a15", "src": "hda", "uuid": "dc0c8e9e-a7bd-4bee-a13f-bd795ee1e005"}, "transcript_expression": {"id": "9bb1cfbf7563a675", "src": "hda", "uuid": "ee4d8aef-5716-4ded-a025-74ebb9a0d612"}, "exon_transcript_mapping": {"id": "54b93943e9609524", "src": "hda", "uuid": "82a0dce5-945e-4346-9a10-3602d980bd2c"}, "intron_transcript_mapping": {"id": "f31638072f02b299", "src": "hda", "uuid": "961b1e74-f4b7-4f88-9e40-e389a59c1046"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-11-08 19:06:04", "plugin": "core", "name": "end_epoch", "raw_value": "1731092764.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:06:04", "plugin": "core", "name": "start_epoch", "raw_value": "1731092764.0000000"}, {"title": "Memory Allocated (MB)", "value": "26843", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "26843.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "stringtie/2.2.3+galaxy0-5", "has_data": true, "data": {"tool_id": "stringtie", "tool_version": "2.2.3+galaxy0", "test_index": 5, "time_seconds": 39.51148009300232, "inputs": {"input_options|input_bam": {"src": "hda", "id": "6f41adfb187630ce"}, "input_options|input_mode": "short_reads", "guide|guide_source|ref_hist": {"src": "hda", "id": "e9997d48d76616b2"}, "guide|guide_source|guide_gff_select": "history", "guide|input_estimation": true, "guide|special_outputs|clustering": true, "guide|special_outputs|special_outputs_select": "deseq2", "guide|coverage_file": true, "guide|use_guide": "yes"}, "job": {"model_class": "Job", "id": "b5df49ef3bf6281c", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:06:44.099990", "update_time": "2024-11-08T19:06:58.930304", "galaxy_version": "24.1", "external_id": "gxy-74rgw", "handler": null, "job_runner_name": null, "command_line": "mkdir -p ./special_de_output/sample1/ && ln -s '/galaxy/server/database/objects/0/7/4/dataset_0748de08-5a80-4b0e-bcc0-4b69d3f4b083.dat' guide.gff && stringtie '/galaxy/server/database/objects/1/e/f/dataset_1efc5208-2eff-4831-acae-77c21c0ad3d4.dat' -o '/galaxy/server/database/objects/e/f/2/dataset_ef26d61a-a09c-4cd4-8885-295289f512d2.dat' -p \"${GALAXY_SLOTS:-1}\" -G guide.gff -C '/galaxy/server/database/objects/9/6/7/dataset_9674492a-24c3-46d3-8c74-e33386d7f965.dat' -e -b ./special_de_output/sample1/ -f '0.01' -m '200' -a '10' -j '1' -c '1' -g '50' -M '1.0' && ln -s '/galaxy/server/database/objects/e/f/2/dataset_ef26d61a-a09c-4cd4-8885-295289f512d2.dat' ./special_de_output/sample1/output.gtf && TAB=$(printf '\\t') && CR=$(printf '\\r') && prepDE.py -i ./special_de_output/ -g gene_counts.csv -t transcript_counts.csv -l 75 -c --legend '/galaxy/server/database/objects/1/e/9/dataset_1e9343f9-929e-4c3f-8c38-4abf103bd145.dat' > /dev/null && sed -i.bak -e \"s/,/${TAB}/g\" -e \"s/${CR}//g\" '/galaxy/server/database/objects/1/e/9/dataset_1e9343f9-929e-4c3f-8c38-4abf103bd145.dat' && sed -i.bak -e \"s/,/${TAB}/g\" -e \"s/${CR}//g\" gene_counts.csv transcript_counts.csv && head -n 1 gene_counts.csv | sed -e 's/sample1/stringtie_in1_bam/' > '/galaxy/server/database/objects/e/b/3/dataset_eb34ab7e-6496-4d2a-a9e6-d0fb9ed732b1.dat' && head -n 1 transcript_counts.csv | sed -e 's/sample1/stringtie_in1_bam/' > '/galaxy/server/database/objects/8/7/d/dataset_87d0f954-43ef-485f-98d1-b118db5d3794.dat' && tail -n +2 gene_counts.csv | sort -t\"${TAB}\" -k1,1 >> '/galaxy/server/database/objects/e/b/3/dataset_eb34ab7e-6496-4d2a-a9e6-d0fb9ed732b1.dat' && tail -n +2 transcript_counts.csv | sort -t\"${TAB}\" -k1,1 >> '/galaxy/server/database/objects/8/7/d/dataset_87d0f954-43ef-485f-98d1-b118db5d3794.dat'", "user_email": "tests@fake.org", "command_version": "2.2.3", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"abundance_estimation\": false, \"bdist\": \"50\", \"bundle_fraction\": \"1.0\", \"disable_trimming\": false, \"fraction\": \"0.01\", \"min_anchor_cov\": \"1\", \"min_anchor_len\": \"10\", \"min_bundle_cov\": \"1\", \"min_tlen\": \"200\", \"multi_mapping\": false, \"name_prefix\": null, \"omit_sequences\": \"\", \"point_features\": null}", "guide": "{\"__current_case__\": 1, \"coverage_file\": true, \"guide_source\": {\"__current_case__\": 1, \"guide_gff_select\": \"history\", \"ref_hist\": {\"values\": [{\"id\": 127, \"src\": \"hda\"}]}}, \"input_estimation\": true, \"special_outputs\": {\"__current_case__\": 1, \"clustering\": true, \"key\": null, \"read_length\": \"75\", \"special_outputs_select\": \"deseq2\", \"string\": null}, \"use_guide\": \"yes\"}", "rna_strandness": "\"\"", "input_options": "{\"__current_case__\": 0, \"input_bam\": {\"values\": [{\"id\": 126, \"src\": \"hda\"}]}, \"input_mode\": \"short_reads\"}"}, "inputs": {"input_options|input_bam": {"id": "6f41adfb187630ce", "src": "hda", "uuid": "1efc5208-2eff-4831-acae-77c21c0ad3d4"}, "guide|guide_source|ref_hist": {"id": "e9997d48d76616b2", "src": "hda", "uuid": "0748de08-5a80-4b0e-bcc0-4b69d3f4b083"}}, "outputs": {"output_gtf": {"id": "467b61757452b047", "src": "hda", "uuid": "ef26d61a-a09c-4cd4-8885-295289f512d2"}, "coverage": {"id": "313122af5a7398a2", "src": "hda", "uuid": "9674492a-24c3-46d3-8c74-e33386d7f965"}, "gene_counts": {"id": "5507ca7bde5d08ca", "src": "hda", "uuid": "eb34ab7e-6496-4d2a-a9e6-d0fb9ed732b1"}, "transcript_counts": {"id": "87a90ca5ab392bca", "src": "hda", "uuid": "87d0f954-43ef-485f-98d1-b118db5d3794"}, "legend": {"id": "800f121972d7125d", "src": "hda", "uuid": "1e9343f9-929e-4c3f-8c38-4abf103bd145"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-11-08 19:06:45", "plugin": "core", "name": "end_epoch", "raw_value": "1731092805.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:06:45", "plugin": "core", "name": "start_epoch", "raw_value": "1731092805.0000000"}, {"title": "Memory Allocated (MB)", "value": "26843", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "26843.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "stringtie/2.2.3+galaxy0-6", "has_data": true, "data": {"tool_id": "stringtie", "tool_version": "2.2.3+galaxy0", "test_index": 6, "time_seconds": 28.900150775909424, "inputs": {"input_options|input_bam": {"src": "hda", "id": "0875c422d93fe122"}, "input_options|input_mode": "short_reads", "guide|guide_source|ref_hist": {"src": "hda", "id": "d4aba126f7fdc3f6"}, "guide|guide_source|guide_gff_select": "history", "guide|use_guide": "yes", "adv|abundance_estimation": true, "adv|fraction": "0.17"}, "job": {"model_class": "Job", "id": "87afed66c00a7675", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0", "state": "error", "exit_code": null, "create_time": "2024-11-08T19:07:23.730144", "update_time": "2024-11-08T19:07:29.338183", "galaxy_version": "24.1", "external_id": "gxy-jvrng", "handler": null, "job_runner_name": null, "command_line": "mkdir -p ./special_de_output/sample1/ && ln -s '/galaxy/server/database/objects/b/5/9/dataset_b5948e20-50b6-4e9f-bf48-07845a8d3710.dat' guide.gff && stringtie '/galaxy/server/database/objects/e/f/1/dataset_ef1e9415-0b70-45ee-844d-a778ac4ee621.dat' -o '/galaxy/server/database/objects/d/d/9/dataset_dd909ae8-ad9e-450d-89e3-30605e6a5aff.dat' -p \"${GALAXY_SLOTS:-1}\" -G guide.gff -b ./special_de_output/sample1/ -f '0.17' -m '200' -a '10' -j '1' -c '1' -g '50' -M '1.0' -A '/galaxy/server/database/objects/b/4/6/dataset_b46627df-7520-449d-85d7-60f9a4e3540c.dat'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"abundance_estimation\": true, \"bdist\": \"50\", \"bundle_fraction\": \"1.0\", \"disable_trimming\": false, \"fraction\": \"0.17\", \"min_anchor_cov\": \"1\", \"min_anchor_len\": \"10\", \"min_bundle_cov\": \"1\", \"min_tlen\": \"200\", \"multi_mapping\": false, \"name_prefix\": null, \"omit_sequences\": \"\", \"point_features\": null}", "guide": "{\"__current_case__\": 1, \"coverage_file\": false, \"guide_source\": {\"__current_case__\": 1, \"guide_gff_select\": \"history\", \"ref_hist\": {\"values\": [{\"id\": 134, \"src\": \"hda\"}]}}, \"input_estimation\": false, \"special_outputs\": {\"__current_case__\": 2, \"special_outputs_select\": \"no\"}, \"use_guide\": \"yes\"}", "rna_strandness": "\"\"", "input_options": "{\"__current_case__\": 0, \"input_bam\": {\"values\": [{\"id\": 133, \"src\": \"hda\"}]}, \"input_mode\": \"short_reads\"}"}, "inputs": {"guide|guide_source|ref_hist": {"id": "d4aba126f7fdc3f6", "src": "hda", "uuid": "b5948e20-50b6-4e9f-bf48-07845a8d3710"}, "input_options|input_bam": {"id": "0875c422d93fe122", "src": "hda", "uuid": "ef1e9415-0b70-45ee-844d-a778ac4ee621"}}, "outputs": {"output_gtf": {"id": "7807a571f0107626", "src": "hda", "uuid": "dd909ae8-ad9e-450d-89e3-30605e6a5aff"}, "gene_abundance_estimation": {"id": "d29a7e08587fb6be", "src": "hda", "uuid": "b46627df-7520-449d-85d7-60f9a4e3540c"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0, exit_code: None, stderr: ."], "status": "failure"}}, {"id": "stringtie/2.2.3+galaxy0-7", "has_data": true, "data": {"tool_id": "stringtie", "tool_version": "2.2.3+galaxy0", "test_index": 7, "time_seconds": 12.522840976715088, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "stringtie/2.2.3+galaxy0-8", "has_data": true, "data": {"tool_id": "stringtie", "tool_version": "2.2.3+galaxy0", "test_index": 8, "time_seconds": 21.129746198654175, "inputs": {"input_options|input_bam": {"src": "hda", "id": "c0004b57c32be191"}, "input_options|input_mode": "short_reads", "guide|guide_source|guide_gff_select": "cached", "guide|use_guide": "yes", "adv|fraction": "0.15"}, "execution_problem": "parameter 'ref_builtin': an invalid option (None) was selected, please verify", "dynamic_param_error": true, "status": "error"}}, {"id": "stringtie/2.2.3+galaxy0-9", "has_data": true, "data": {"tool_id": "stringtie", "tool_version": "2.2.3+galaxy0", "test_index": 9, "time_seconds": 22.729411840438843, "inputs": {"input_options|input_bam": {"src": "hda", "id": "3ddf019855fbe017"}, "input_options|input_mode": "long_reads", "guide|guide_source|guide_gff_select": "cached", "guide|use_guide": "yes", "adv|fraction": "0.15"}, "execution_problem": "parameter 'ref_builtin': an invalid option (None) was selected, please verify", "dynamic_param_error": true, "status": "error"}}, {"id": "umi_tools_count/1.1.2+galaxy2-0", "has_data": true, "data": {"tool_id": "umi_tools_count", "tool_version": "1.1.2+galaxy2", "test_index": 0, "time_seconds": 53.335585594177246, "inputs": {"input": {"src": "hda", "id": "e9b0e4d46bcc827e"}, "wide_format_cell_counts": false, "bc|extract_umi_method": "umis", "umi|method": "directional", "sc|gene_tag": "XF", "sc|skip_tags_regex": "^[__|Unassigned]", "sc|per_cell": false, "advanced|random_seed": "123456789"}, "job": {"model_class": "Job", "id": "e9b0e4d46bcc827e", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T18:36:49.107591", "update_time": "2024-11-08T18:37:20.446190", "galaxy_version": "24.1", "external_id": "gxy-ljfq8", "handler": null, "job_runner_name": null, "command_line": "ln -sf '/galaxy/server/database/objects/b/b/f/dataset_bbf9ea06-c833-43f6-a2cb-1b86d3ba3e03.dat' 'input.bam' && ln -sf '/galaxy/server/database/objects/_metadata_files/3/0/8/metadata_308aca2a-c6c9-4f40-ba2e-d5d63c17cc75.dat' 'input.bam.bai' && umi_tools count '' --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag 'XF' --skip-tags-regex '^[__Unassigned]' --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed='123456789' -I 'input.bam' -S '/galaxy/server/database/objects/b/9/e/dataset_b9e32134-5bc7-4ccb-a6e2-0ac4cd7661c7.dat' --log2stderr", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "log": "false", "cond_extra": "{\"__current_case__\": 0, \"prepender\": \"none\"}", "advanced": "{\"random_seed\": \"123456789\"}", "sc": "{\"assigned_status_tag\": null, \"gene_tag\": \"XF\", \"gene_transcript_map\": null, \"per_cell\": false, \"per_contig\": false, \"skip_tags_regex\": \"^[__|Unassigned]\"}", "sambam": "{\"chimeric_pairs\": null, \"chrom\": \"\", \"ignore_tlen\": false, \"ignore_umi\": false, \"mapping_quality\": \"0\", \"paired\": false, \"subset\": \"1.0\", \"unmapped_reads\": \"discard\", \"unpaired_reads\": null}", "umi": "{\"edit_distance_threshold\": \"1\", \"method\": \"directional\", \"read_length\": false, \"soft_clip_threshold\": \"4\", \"spliced_is_unique\": false}", "bc": "{\"__current_case__\": 2, \"extract_umi_method\": \"umis\"}", "wide_format_cell_counts": "false"}, "inputs": {"input": {"id": "e9b0e4d46bcc827e", "src": "hda", "uuid": "bbf9ea06-c833-43f6-a2cb-1b86d3ba3e03"}}, "outputs": {"out_counts": {"id": "05730410412536ea", "src": "hda", "uuid": "b9e32134-5bc7-4ccb-a6e2-0ac4cd7661c7"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "# UMI-tools version: 1.1.2\n# output generated by count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/b/9/e/dataset_b9e32134-5bc7-4ccb-a6e2-0ac4cd7661c7.dat --log2stderr\n# job started at Fri Nov 8 18:37:04 2024 on gxy-ljfq8-2vh49 -- 6d88f1e9-b106-4dd4-921f-4cb2f48c723d\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XF\n# gene_transcript_map : None\n# get_umi_method : umis\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : directional\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : False\n# per_contig : False\n# per_gene : False\n# random_seed : 123456789\n# read_length : False\n# short_help : None\n# skip_regex : ^[__Unassigned]\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/b/9/e/dataset_b9e32134-5bc7-4ccb-a6e2-0ac4cd7661c7.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : False\n2024-11-08 18:37:04,792 INFO command: count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/b/9/e/dataset_b9e32134-5bc7-4ccb-a6e2-0ac4cd7661c7.dat --log2stderr\n2024-11-08 18:37:04,821 INFO Input Reads: 1203\n2024-11-08 18:37:04,821 INFO Read skipped - assigned tag matches skip_regex: 120\n2024-11-08 18:37:04,821 INFO Number of (post deduplication) reads counted: 141\n# job finished in 0 seconds at Fri Nov 8 18:37:04 2024 -- 0.92 0.27 0.00 0.00 -- 6d88f1e9-b106-4dd4-921f-4cb2f48c723d\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "# UMI-tools version: 1.1.2\n# output generated by count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/b/9/e/dataset_b9e32134-5bc7-4ccb-a6e2-0ac4cd7661c7.dat --log2stderr\n# job started at Fri Nov 8 18:37:04 2024 on gxy-ljfq8-2vh49 -- 6d88f1e9-b106-4dd4-921f-4cb2f48c723d\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XF\n# gene_transcript_map : None\n# get_umi_method : umis\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : directional\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : False\n# per_contig : False\n# per_gene : False\n# random_seed : 123456789\n# read_length : False\n# short_help : None\n# skip_regex : ^[__Unassigned]\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/b/9/e/dataset_b9e32134-5bc7-4ccb-a6e2-0ac4cd7661c7.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : False\n2024-11-08 18:37:04,792 INFO command: count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/b/9/e/dataset_b9e32134-5bc7-4ccb-a6e2-0ac4cd7661c7.dat --log2stderr\n2024-11-08 18:37:04,821 INFO Input Reads: 1203\n2024-11-08 18:37:04,821 INFO Read skipped - assigned tag matches skip_regex: 120\n2024-11-08 18:37:04,821 INFO Number of (post deduplication) reads counted: 141\n# job finished in 0 seconds at Fri Nov 8 18:37:04 2024 -- 0.92 0.27 0.00 0.00 -- 6d88f1e9-b106-4dd4-921f-4cb2f48c723d\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-08 18:37:04", "plugin": "core", "name": "end_epoch", "raw_value": "1731091024.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 18:37:03", "plugin": "core", "name": "start_epoch", "raw_value": "1731091023.0000000"}, {"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": "umi_tools_count/1.1.2+galaxy2-0", "has_data": true, "data": {"tool_id": "umi_tools_count", "tool_version": "1.1.2+galaxy2", "test_index": 0, "time_seconds": 13.631751537322998, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "umi_tools_count/1.1.2+galaxy2-0", "has_data": true, "data": {"tool_id": "umi_tools_count", "tool_version": "1.1.2+galaxy2", "test_index": 0, "time_seconds": 28.434705018997192, "inputs": {"input": {"src": "hda", "id": "eae541d28ead1c6d"}, "wide_format_cell_counts": false, "bc|extract_umi_method": "umis", "umi|method": "directional", "sc|gene_tag": "XF", "sc|skip_tags_regex": "^[__|Unassigned]", "sc|per_cell": false, "advanced|random_seed": "123456789"}, "job": {"model_class": "Job", "id": "eae541d28ead1c6d", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2", "state": "error", "exit_code": null, "create_time": "2024-11-08T18:45:35.436093", "update_time": "2024-11-08T18:45:41.468705", "galaxy_version": "24.1", "external_id": "gxy-w4vxt", "handler": null, "job_runner_name": null, "command_line": "ln -sf '/galaxy/server/database/objects/6/e/b/dataset_6ebb3cef-bbeb-44d0-a087-5ac77cea1248.dat' 'input.bam' && ln -sf '/galaxy/server/database/objects/_metadata_files/c/e/7/metadata_ce79e776-9d0c-4db3-9bf5-f9f02e668faf.dat' 'input.bam.bai' && umi_tools count '' --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag 'XF' --skip-tags-regex '^[__Unassigned]' --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed='123456789' -I 'input.bam' -S '/galaxy/server/database/objects/6/0/7/dataset_607b7381-aea4-427b-9e0d-2b6e9c81e40e.dat' --log2stderr", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "log": "false", "cond_extra": "{\"__current_case__\": 0, \"prepender\": \"none\"}", "advanced": "{\"random_seed\": \"123456789\"}", "sc": "{\"assigned_status_tag\": null, \"gene_tag\": \"XF\", \"gene_transcript_map\": null, \"per_cell\": false, \"per_contig\": false, \"skip_tags_regex\": \"^[__|Unassigned]\"}", "sambam": "{\"chimeric_pairs\": null, \"chrom\": \"\", \"ignore_tlen\": false, \"ignore_umi\": false, \"mapping_quality\": \"0\", \"paired\": false, \"subset\": \"1.0\", \"unmapped_reads\": \"discard\", \"unpaired_reads\": null}", "umi": "{\"edit_distance_threshold\": \"1\", \"method\": \"directional\", \"read_length\": false, \"soft_clip_threshold\": \"4\", \"spliced_is_unique\": false}", "bc": "{\"__current_case__\": 2, \"extract_umi_method\": \"umis\"}", "wide_format_cell_counts": "false"}, "inputs": {"input": {"id": "eae541d28ead1c6d", "src": "hda", "uuid": "6ebb3cef-bbeb-44d0-a087-5ac77cea1248"}}, "outputs": {"out_counts": {"id": "5868d5d35892214c", "src": "hda", "uuid": "607b7381-aea4-427b-9e0d-2b6e9c81e40e"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "# UMI-tools version: 1.1.2\n# output generated by count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/6/0/7/dataset_607b7381-aea4-427b-9e0d-2b6e9c81e40e.dat --log2stderr\n# job started at Fri Nov 8 18:45:38 2024 on gxy-w4vxt-f9qnc -- 2cd3b257-c856-43a8-9c4a-9f009e9641ab\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XF\n# gene_transcript_map : None\n# get_umi_method : umis\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : directional\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : False\n# per_contig : False\n# per_gene : False\n# random_seed : 123456789\n# read_length : False\n# short_help : None\n# skip_regex : ^[__Unassigned]\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/6/0/7/dataset_607b7381-aea4-427b-9e0d-2b6e9c81e40e.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : False\n2024-11-08 18:45:38,561 INFO command: count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/6/0/7/dataset_607b7381-aea4-427b-9e0d-2b6e9c81e40e.dat --log2stderr\n2024-11-08 18:45:38,589 INFO Input Reads: 1203\n2024-11-08 18:45:38,590 INFO Read skipped - assigned tag matches skip_regex: 120\n2024-11-08 18:45:38,590 INFO Number of (post deduplication) reads counted: 141\n# job finished in 0 seconds at Fri Nov 8 18:45:38 2024 -- 0.90 0.23 0.00 0.00 -- 2cd3b257-c856-43a8-9c4a-9f009e9641ab\n", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "# UMI-tools version: 1.1.2\n# output generated by count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/6/0/7/dataset_607b7381-aea4-427b-9e0d-2b6e9c81e40e.dat --log2stderr\n# job started at Fri Nov 8 18:45:38 2024 on gxy-w4vxt-f9qnc -- 2cd3b257-c856-43a8-9c4a-9f009e9641ab\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XF\n# gene_transcript_map : None\n# get_umi_method : umis\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : directional\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : False\n# per_contig : False\n# per_gene : False\n# random_seed : 123456789\n# read_length : False\n# short_help : None\n# skip_regex : ^[__Unassigned]\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/6/0/7/dataset_607b7381-aea4-427b-9e0d-2b6e9c81e40e.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : False\n2024-11-08 18:45:38,561 INFO command: count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/6/0/7/dataset_607b7381-aea4-427b-9e0d-2b6e9c81e40e.dat --log2stderr\n2024-11-08 18:45:38,589 INFO Input Reads: 1203\n2024-11-08 18:45:38,590 INFO Read skipped - assigned tag matches skip_regex: 120\n2024-11-08 18:45:38,590 INFO Number of (post deduplication) reads counted: 141\n# job finished in 0 seconds at Fri Nov 8 18:45:38 2024 -- 0.90 0.23 0.00 0.00 -- 2cd3b257-c856-43a8-9c4a-9f009e9641ab\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, exit_code: None, stderr: # UMI-tools version: 1.1.2\n# output generated by count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/6/0/7/dataset_607b7381-aea4-427b-9e0d-2b6e9c81e40e.dat --log2stderr\n# job started at Fri Nov 8 18:45:38 2024 on gxy-w4vxt-f9qnc -- 2cd3b257-c856-43a8-9c4a-9f009e9641ab\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XF\n# gene_transcript_map : None\n# get_umi_method : umis\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : directional\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : False\n# per_contig : False\n# per_gene : False\n# random_seed : 123456789\n# read_length : False\n# short_help : None\n# skip_regex : ^[__Unassigned]\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/6/0/7/dataset_607b7381-aea4-427b-9e0d-2b6e9c81e40e.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : False\n2024-11-08 18:45:38,561 INFO command: count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/6/0/7/dataset_607b7381-aea4-427b-9e0d-2b6e9c81e40e.dat --log2stderr\n2024-11-08 18:45:38,589 INFO Input Reads: 1203\n2024-11-08 18:45:38,590 INFO Read skipped - assigned tag matches skip_regex: 120\n2024-11-08 18:45:38,590 INFO Number of (post deduplication) reads counted: 141\n# job finished in 0 seconds at Fri Nov 8 18:45:38 2024 -- 0.90 0.23 0.00 0.00 -- 2cd3b257-c856-43a8-9c4a-9f009e9641ab\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, exit_code: None, stderr: # UMI-tools version: 1.1.2\n# output generated by count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/6/0/7/dataset_607b7381-aea4-427b-9e0d-2b6e9c81e40e.dat --log2stderr\n# job started at Fri Nov 8 18:45:38 2024 on gxy-w4vxt-f9qnc -- 2cd3b257-c856-43a8-9c4a-9f009e9641ab\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XF\n# gene_transcript_map : None\n# get_umi_method : umis\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : directional\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : False\n# per_contig : False\n# per_gene : False\n# random_seed : 123456789\n# read_length : False\n# short_help : None\n# skip_regex : ^[__Unassigned]\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/6/0/7/dataset_607b7381-aea4-427b-9e0d-2b6e9c81e40e.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : False\n2024-11-08 18:45:38,561 INFO command: count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/6/0/7/dataset_607b7381-aea4-427b-9e0d-2b6e9c81e40e.dat --log2stderr\n2024-11-08 18:45:38,589 INFO Input Reads: 1203\n2024-11-08 18:45:38,590 INFO Read skipped - assigned tag matches skip_regex: 120\n2024-11-08 18:45:38,590 INFO Number of (post deduplication) reads counted: 141\n# job finished in 0 seconds at Fri Nov 8 18:45:38 2024 -- 0.90 0.23 0.00 0.00 -- 2cd3b257-c856-43a8-9c4a-9f009e9641ab\n."], "status": "failure"}}, {"id": "umi_tools_count/1.1.2+galaxy2-1", "has_data": true, "data": {"tool_id": "umi_tools_count", "tool_version": "1.1.2+galaxy2", "test_index": 1, "time_seconds": 41.02742624282837, "inputs": {"input": {"src": "hda", "id": "18f545ab1e4ded21"}, "wide_format_cell_counts": false, "bc|extract_umi_method": "umis", "umi|method": "directional", "sc|gene_tag": "XF", "sc|skip_tags_regex": "^[__|Unassigned]", "sc|per_cell": false, "advanced|random_seed": "123456789"}, "job": {"model_class": "Job", "id": "18f545ab1e4ded21", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T18:37:45.958802", "update_time": "2024-11-08T18:38:01.636413", "galaxy_version": "24.1", "external_id": "gxy-kdxrw", "handler": null, "job_runner_name": null, "command_line": "samtools sort --no-PG '/galaxy/server/database/objects/4/e/a/dataset_4ea5c4bb-e494-4880-aad0-2874dbce6a2b.dat' > 'input.bam' && samtools index -b 'input.bam' && umi_tools count '' --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag 'XF' --skip-tags-regex '^[__Unassigned]' --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed='123456789' -I 'input.bam' -S '/galaxy/server/database/objects/7/d/4/dataset_7d46732b-cbf6-4414-8999-d16a224e5423.dat' --log2stderr", "user_email": "tests@fake.org", "command_version": "", "params": {"wide_format_cell_counts": "false", "bc": "{\"__current_case__\": 2, \"extract_umi_method\": \"umis\"}", "umi": "{\"edit_distance_threshold\": \"1\", \"method\": \"directional\", \"read_length\": false, \"soft_clip_threshold\": \"4\", \"spliced_is_unique\": false}", "sambam": "{\"chimeric_pairs\": null, \"chrom\": \"\", \"ignore_tlen\": false, \"ignore_umi\": false, \"mapping_quality\": \"0\", \"paired\": false, \"subset\": \"1.0\", \"unmapped_reads\": \"discard\", \"unpaired_reads\": null}", "sc": "{\"assigned_status_tag\": null, \"gene_tag\": \"XF\", \"gene_transcript_map\": null, \"per_cell\": false, \"per_contig\": false, \"skip_tags_regex\": \"^[__|Unassigned]\"}", "advanced": "{\"random_seed\": \"123456789\"}", "cond_extra": "{\"__current_case__\": 0, \"prepender\": \"none\"}", "log": "false", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"input\""}, "inputs": {"input": {"id": "18f545ab1e4ded21", "src": "hda", "uuid": "4ea5c4bb-e494-4880-aad0-2874dbce6a2b"}}, "outputs": {"out_counts": {"id": "d444d01445fadd22", "src": "hda", "uuid": "7d46732b-cbf6-4414-8999-d16a224e5423"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "# UMI-tools version: 1.1.2\n# output generated by count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/7/d/4/dataset_7d46732b-cbf6-4414-8999-d16a224e5423.dat --log2stderr\n# job started at Fri Nov 8 18:37:49 2024 on gxy-kdxrw-kwxxb -- d4ace035-9164-4138-bf57-71cda01eacf2\n# pid: 26, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XF\n# gene_transcript_map : None\n# get_umi_method : umis\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : directional\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : False\n# per_contig : False\n# per_gene : False\n# random_seed : 123456789\n# read_length : False\n# short_help : None\n# skip_regex : ^[__Unassigned]\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/7/d/4/dataset_7d46732b-cbf6-4414-8999-d16a224e5423.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : False\n2024-11-08 18:37:49,194 INFO command: count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/7/d/4/dataset_7d46732b-cbf6-4414-8999-d16a224e5423.dat --log2stderr\n2024-11-08 18:37:49,222 INFO Input Reads: 1203\n2024-11-08 18:37:49,223 INFO Read skipped - assigned tag matches skip_regex: 120\n2024-11-08 18:37:49,223 INFO Number of (post deduplication) reads counted: 141\n# job finished in 0 seconds at Fri Nov 8 18:37:49 2024 -- 0.90 0.25 0.00 0.00 -- d4ace035-9164-4138-bf57-71cda01eacf2\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "# UMI-tools version: 1.1.2\n# output generated by count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/7/d/4/dataset_7d46732b-cbf6-4414-8999-d16a224e5423.dat --log2stderr\n# job started at Fri Nov 8 18:37:49 2024 on gxy-kdxrw-kwxxb -- d4ace035-9164-4138-bf57-71cda01eacf2\n# pid: 26, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XF\n# gene_transcript_map : None\n# get_umi_method : umis\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : directional\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : False\n# per_contig : False\n# per_gene : False\n# random_seed : 123456789\n# read_length : False\n# short_help : None\n# skip_regex : ^[__Unassigned]\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/7/d/4/dataset_7d46732b-cbf6-4414-8999-d16a224e5423.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : False\n2024-11-08 18:37:49,194 INFO command: count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/7/d/4/dataset_7d46732b-cbf6-4414-8999-d16a224e5423.dat --log2stderr\n2024-11-08 18:37:49,222 INFO Input Reads: 1203\n2024-11-08 18:37:49,223 INFO Read skipped - assigned tag matches skip_regex: 120\n2024-11-08 18:37:49,223 INFO Number of (post deduplication) reads counted: 141\n# job finished in 0 seconds at Fri Nov 8 18:37:49 2024 -- 0.90 0.25 0.00 0.00 -- d4ace035-9164-4138-bf57-71cda01eacf2\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-11-08 18:37:49", "plugin": "core", "name": "end_epoch", "raw_value": "1731091069.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 18:37:47", "plugin": "core", "name": "start_epoch", "raw_value": "1731091067.0000000"}, {"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": "umi_tools_count/1.1.2+galaxy2-1", "has_data": true, "data": {"tool_id": "umi_tools_count", "tool_version": "1.1.2+galaxy2", "test_index": 1, "time_seconds": 41.17427158355713, "inputs": {"input": {"src": "hda", "id": "63e82ac14c91a36d"}, "wide_format_cell_counts": false, "bc|extract_umi_method": "umis", "umi|method": "directional", "sc|gene_tag": "XF", "sc|skip_tags_regex": "^[__|Unassigned]", "sc|per_cell": false, "advanced|random_seed": "123456789"}, "job": {"model_class": "Job", "id": "63e82ac14c91a36d", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T18:41:49.328321", "update_time": "2024-11-08T18:42:05.438328", "galaxy_version": "24.1", "external_id": "gxy-spnvf", "handler": null, "job_runner_name": null, "command_line": "samtools sort --no-PG '/galaxy/server/database/objects/3/f/4/dataset_3f407d25-808f-4ec0-bea1-db140131958a.dat' > 'input.bam' && samtools index -b 'input.bam' && umi_tools count '' --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag 'XF' --skip-tags-regex '^[__Unassigned]' --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed='123456789' -I 'input.bam' -S '/galaxy/server/database/objects/e/9/9/dataset_e9964907-fa86-48ca-810e-fb7cbd0e38d8.dat' --log2stderr", "user_email": "tests@fake.org", "command_version": "", "params": {"wide_format_cell_counts": "false", "bc": "{\"__current_case__\": 2, \"extract_umi_method\": \"umis\"}", "umi": "{\"edit_distance_threshold\": \"1\", \"method\": \"directional\", \"read_length\": false, \"soft_clip_threshold\": \"4\", \"spliced_is_unique\": false}", "sambam": "{\"chimeric_pairs\": null, \"chrom\": \"\", \"ignore_tlen\": false, \"ignore_umi\": false, \"mapping_quality\": \"0\", \"paired\": false, \"subset\": \"1.0\", \"unmapped_reads\": \"discard\", \"unpaired_reads\": null}", "sc": "{\"assigned_status_tag\": null, \"gene_tag\": \"XF\", \"gene_transcript_map\": null, \"per_cell\": false, \"per_contig\": false, \"skip_tags_regex\": \"^[__|Unassigned]\"}", "advanced": "{\"random_seed\": \"123456789\"}", "cond_extra": "{\"__current_case__\": 0, \"prepender\": \"none\"}", "log": "false", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"input\""}, "inputs": {"input": {"id": "63e82ac14c91a36d", "src": "hda", "uuid": "3f407d25-808f-4ec0-bea1-db140131958a"}}, "outputs": {"out_counts": {"id": "f493aa5161845cb8", "src": "hda", "uuid": "e9964907-fa86-48ca-810e-fb7cbd0e38d8"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "# UMI-tools version: 1.1.2\n# output generated by count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/e/9/9/dataset_e9964907-fa86-48ca-810e-fb7cbd0e38d8.dat --log2stderr\n# job started at Fri Nov 8 18:41:52 2024 on gxy-spnvf-vz4t8 -- bdc4883b-52a5-4efd-8af3-5a4d2c0cb28d\n# pid: 26, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XF\n# gene_transcript_map : None\n# get_umi_method : umis\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : directional\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : False\n# per_contig : False\n# per_gene : False\n# random_seed : 123456789\n# read_length : False\n# short_help : None\n# skip_regex : ^[__Unassigned]\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/e/9/9/dataset_e9964907-fa86-48ca-810e-fb7cbd0e38d8.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : False\n2024-11-08 18:41:52,186 INFO command: count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/e/9/9/dataset_e9964907-fa86-48ca-810e-fb7cbd0e38d8.dat --log2stderr\n2024-11-08 18:41:52,214 INFO Input Reads: 1203\n2024-11-08 18:41:52,214 INFO Read skipped - assigned tag matches skip_regex: 120\n2024-11-08 18:41:52,214 INFO Number of (post deduplication) reads counted: 141\n# job finished in 0 seconds at Fri Nov 8 18:41:52 2024 -- 0.90 0.24 0.00 0.00 -- bdc4883b-52a5-4efd-8af3-5a4d2c0cb28d\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "# UMI-tools version: 1.1.2\n# output generated by count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/e/9/9/dataset_e9964907-fa86-48ca-810e-fb7cbd0e38d8.dat --log2stderr\n# job started at Fri Nov 8 18:41:52 2024 on gxy-spnvf-vz4t8 -- bdc4883b-52a5-4efd-8af3-5a4d2c0cb28d\n# pid: 26, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XF\n# gene_transcript_map : None\n# get_umi_method : umis\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : directional\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : False\n# per_contig : False\n# per_gene : False\n# random_seed : 123456789\n# read_length : False\n# short_help : None\n# skip_regex : ^[__Unassigned]\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/e/9/9/dataset_e9964907-fa86-48ca-810e-fb7cbd0e38d8.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : False\n2024-11-08 18:41:52,186 INFO command: count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/e/9/9/dataset_e9964907-fa86-48ca-810e-fb7cbd0e38d8.dat --log2stderr\n2024-11-08 18:41:52,214 INFO Input Reads: 1203\n2024-11-08 18:41:52,214 INFO Read skipped - assigned tag matches skip_regex: 120\n2024-11-08 18:41:52,214 INFO Number of (post deduplication) reads counted: 141\n# job finished in 0 seconds at Fri Nov 8 18:41:52 2024 -- 0.90 0.24 0.00 0.00 -- bdc4883b-52a5-4efd-8af3-5a4d2c0cb28d\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 18:41:50", "plugin": "core", "name": "start_epoch", "raw_value": "1731091310.0000000"}, {"title": "Job End Time", "value": "2024-11-08 18:41:52", "plugin": "core", "name": "end_epoch", "raw_value": "1731091312.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}]}, "status": "success"}}, {"id": "umi_tools_count/1.1.2+galaxy2-1", "has_data": true, "data": {"tool_id": "umi_tools_count", "tool_version": "1.1.2+galaxy2", "test_index": 1, "time_seconds": 40.52311444282532, "inputs": {"input": {"src": "hda", "id": "698da7425e8a10e7"}, "wide_format_cell_counts": false, "bc|extract_umi_method": "umis", "umi|method": "directional", "sc|gene_tag": "XF", "sc|skip_tags_regex": "^[__|Unassigned]", "sc|per_cell": false, "advanced|random_seed": "123456789"}, "job": {"model_class": "Job", "id": "698da7425e8a10e7", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T18:46:05.845020", "update_time": "2024-11-08T18:46:21.887317", "galaxy_version": "24.1", "external_id": "gxy-6x758", "handler": null, "job_runner_name": null, "command_line": "samtools sort --no-PG '/galaxy/server/database/objects/2/0/b/dataset_20bcf657-8094-4ed0-b637-dd6e7a2de2b2.dat' > 'input.bam' && samtools index -b 'input.bam' && umi_tools count '' --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag 'XF' --skip-tags-regex '^[__Unassigned]' --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed='123456789' -I 'input.bam' -S '/galaxy/server/database/objects/b/b/5/dataset_bb58c334-f594-4dc0-9168-510b49b31850.dat' --log2stderr", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "log": "false", "cond_extra": "{\"__current_case__\": 0, \"prepender\": \"none\"}", "advanced": "{\"random_seed\": \"123456789\"}", "sc": "{\"assigned_status_tag\": null, \"gene_tag\": \"XF\", \"gene_transcript_map\": null, \"per_cell\": false, \"per_contig\": false, \"skip_tags_regex\": \"^[__|Unassigned]\"}", "sambam": "{\"chimeric_pairs\": null, \"chrom\": \"\", \"ignore_tlen\": false, \"ignore_umi\": false, \"mapping_quality\": \"0\", \"paired\": false, \"subset\": \"1.0\", \"unmapped_reads\": \"discard\", \"unpaired_reads\": null}", "umi": "{\"edit_distance_threshold\": \"1\", \"method\": \"directional\", \"read_length\": false, \"soft_clip_threshold\": \"4\", \"spliced_is_unique\": false}", "bc": "{\"__current_case__\": 2, \"extract_umi_method\": \"umis\"}", "wide_format_cell_counts": "false"}, "inputs": {"input": {"id": "698da7425e8a10e7", "src": "hda", "uuid": "20bcf657-8094-4ed0-b637-dd6e7a2de2b2"}}, "outputs": {"out_counts": {"id": "42f27ed5246864a9", "src": "hda", "uuid": "bb58c334-f594-4dc0-9168-510b49b31850"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "# UMI-tools version: 1.1.2\n# output generated by count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/b/b/5/dataset_bb58c334-f594-4dc0-9168-510b49b31850.dat --log2stderr\n# job started at Fri Nov 8 18:46:09 2024 on gxy-6x758-9lfsh -- c0acac4b-fdcb-4f67-b212-0204d6fa07b2\n# pid: 26, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XF\n# gene_transcript_map : None\n# get_umi_method : umis\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : directional\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : False\n# per_contig : False\n# per_gene : False\n# random_seed : 123456789\n# read_length : False\n# short_help : None\n# skip_regex : ^[__Unassigned]\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/b/b/5/dataset_bb58c334-f594-4dc0-9168-510b49b31850.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : False\n2024-11-08 18:46:09,070 INFO command: count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/b/b/5/dataset_bb58c334-f594-4dc0-9168-510b49b31850.dat --log2stderr\n2024-11-08 18:46:09,098 INFO Input Reads: 1203\n2024-11-08 18:46:09,099 INFO Read skipped - assigned tag matches skip_regex: 120\n2024-11-08 18:46:09,099 INFO Number of (post deduplication) reads counted: 141\n# job finished in 0 seconds at Fri Nov 8 18:46:09 2024 -- 0.87 0.26 0.00 0.00 -- c0acac4b-fdcb-4f67-b212-0204d6fa07b2\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "# UMI-tools version: 1.1.2\n# output generated by count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/b/b/5/dataset_bb58c334-f594-4dc0-9168-510b49b31850.dat --log2stderr\n# job started at Fri Nov 8 18:46:09 2024 on gxy-6x758-9lfsh -- c0acac4b-fdcb-4f67-b212-0204d6fa07b2\n# pid: 26, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XF\n# gene_transcript_map : None\n# get_umi_method : umis\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : directional\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : False\n# per_contig : False\n# per_gene : False\n# random_seed : 123456789\n# read_length : False\n# short_help : None\n# skip_regex : ^[__Unassigned]\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/b/b/5/dataset_bb58c334-f594-4dc0-9168-510b49b31850.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : False\n2024-11-08 18:46:09,070 INFO command: count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/b/b/5/dataset_bb58c334-f594-4dc0-9168-510b49b31850.dat --log2stderr\n2024-11-08 18:46:09,098 INFO Input Reads: 1203\n2024-11-08 18:46:09,099 INFO Read skipped - assigned tag matches skip_regex: 120\n2024-11-08 18:46:09,099 INFO Number of (post deduplication) reads counted: 141\n# job finished in 0 seconds at Fri Nov 8 18:46:09 2024 -- 0.87 0.26 0.00 0.00 -- c0acac4b-fdcb-4f67-b212-0204d6fa07b2\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 18:46:07", "plugin": "core", "name": "start_epoch", "raw_value": "1731091567.0000000"}, {"title": "Job End Time", "value": "2024-11-08 18:46:09", "plugin": "core", "name": "end_epoch", "raw_value": "1731091569.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}]}, "status": "success"}}, {"id": "umi_tools_count/1.1.2+galaxy2-2", "has_data": true, "data": {"tool_id": "umi_tools_count", "tool_version": "1.1.2+galaxy2", "test_index": 2, "time_seconds": 37.54129242897034, "inputs": {"input": {"src": "hda", "id": "acb6e12e82aa3441"}, "wide_format_cell_counts": false, "bc|extract_umi_method": "umis", "umi|method": "directional", "sc|gene_tag": "XF", "sc|skip_tags_regex": "^[__|Unassigned]", "sc|per_cell": true, "advanced|random_seed": "123456789"}, "job": {"model_class": "Job", "id": "acb6e12e82aa3441", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T18:38:24.178111", "update_time": "2024-11-08T18:38:39.019514", "galaxy_version": "24.1", "external_id": "gxy-cd5rs", "handler": null, "job_runner_name": null, "command_line": "ln -sf '/galaxy/server/database/objects/2/6/f/dataset_26fd6353-6217-43bf-8e8d-3bdae79dd3ea.dat' 'input.bam' && ln -sf '/galaxy/server/database/objects/_metadata_files/3/7/8/metadata_3787ef47-c555-4adf-8f61-66c84d221a18.dat' 'input.bam.bai' && umi_tools count '' --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag 'XF' --skip-tags-regex '^[__Unassigned]' --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed='123456789' -I 'input.bam' -S '/galaxy/server/database/objects/9/2/1/dataset_92189897-a6c8-4bd1-9fa9-6d7dcbdd3a74.dat' --log2stderr", "user_email": "tests@fake.org", "command_version": "", "params": {"wide_format_cell_counts": "false", "bc": "{\"__current_case__\": 2, \"extract_umi_method\": \"umis\"}", "umi": "{\"edit_distance_threshold\": \"1\", \"method\": \"directional\", \"read_length\": false, \"soft_clip_threshold\": \"4\", \"spliced_is_unique\": false}", "sambam": "{\"chimeric_pairs\": null, \"chrom\": \"\", \"ignore_tlen\": false, \"ignore_umi\": false, \"mapping_quality\": \"0\", \"paired\": false, \"subset\": \"1.0\", \"unmapped_reads\": \"discard\", \"unpaired_reads\": null}", "sc": "{\"assigned_status_tag\": null, \"gene_tag\": \"XF\", \"gene_transcript_map\": null, \"per_cell\": true, \"per_contig\": false, \"skip_tags_regex\": \"^[__|Unassigned]\"}", "advanced": "{\"random_seed\": \"123456789\"}", "cond_extra": "{\"__current_case__\": 0, \"prepender\": \"none\"}", "log": "false", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"input\""}, "inputs": {"input": {"id": "acb6e12e82aa3441", "src": "hda", "uuid": "26fd6353-6217-43bf-8e8d-3bdae79dd3ea"}}, "outputs": {"out_counts": {"id": "27ff95f4d71f8569", "src": "hda", "uuid": "92189897-a6c8-4bd1-9fa9-6d7dcbdd3a74"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "# UMI-tools version: 1.1.2\n# output generated by count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/9/2/1/dataset_92189897-a6c8-4bd1-9fa9-6d7dcbdd3a74.dat --log2stderr\n# job started at Fri Nov 8 18:38:26 2024 on gxy-cd5rs-5mx4f -- dff7d8f3-0081-4ea9-b9a5-3b41205b21c9\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XF\n# gene_transcript_map : None\n# get_umi_method : umis\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : directional\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : True\n# per_contig : False\n# per_gene : False\n# random_seed : 123456789\n# read_length : False\n# short_help : None\n# skip_regex : ^[__Unassigned]\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/9/2/1/dataset_92189897-a6c8-4bd1-9fa9-6d7dcbdd3a74.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : False\n2024-11-08 18:38:26,821 INFO command: count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/9/2/1/dataset_92189897-a6c8-4bd1-9fa9-6d7dcbdd3a74.dat --log2stderr\n2024-11-08 18:38:26,849 INFO Input Reads: 1203\n2024-11-08 18:38:26,849 INFO Read skipped - assigned tag matches skip_regex: 120\n2024-11-08 18:38:26,849 INFO Number of (post deduplication) reads counted: 145\n# job finished in 0 seconds at Fri Nov 8 18:38:26 2024 -- 0.86 0.23 0.00 0.00 -- dff7d8f3-0081-4ea9-b9a5-3b41205b21c9\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "# UMI-tools version: 1.1.2\n# output generated by count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/9/2/1/dataset_92189897-a6c8-4bd1-9fa9-6d7dcbdd3a74.dat --log2stderr\n# job started at Fri Nov 8 18:38:26 2024 on gxy-cd5rs-5mx4f -- dff7d8f3-0081-4ea9-b9a5-3b41205b21c9\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XF\n# gene_transcript_map : None\n# get_umi_method : umis\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : directional\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : True\n# per_contig : False\n# per_gene : False\n# random_seed : 123456789\n# read_length : False\n# short_help : None\n# skip_regex : ^[__Unassigned]\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/9/2/1/dataset_92189897-a6c8-4bd1-9fa9-6d7dcbdd3a74.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : False\n2024-11-08 18:38:26,821 INFO command: count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/9/2/1/dataset_92189897-a6c8-4bd1-9fa9-6d7dcbdd3a74.dat --log2stderr\n2024-11-08 18:38:26,849 INFO Input Reads: 1203\n2024-11-08 18:38:26,849 INFO Read skipped - assigned tag matches skip_regex: 120\n2024-11-08 18:38:26,849 INFO Number of (post deduplication) reads counted: 145\n# job finished in 0 seconds at Fri Nov 8 18:38:26 2024 -- 0.86 0.23 0.00 0.00 -- dff7d8f3-0081-4ea9-b9a5-3b41205b21c9\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-08 18:38:26", "plugin": "core", "name": "end_epoch", "raw_value": "1731091106.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 18:38:25", "plugin": "core", "name": "start_epoch", "raw_value": "1731091105.0000000"}, {"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": "umi_tools_count/1.1.2+galaxy2-2", "has_data": true, "data": {"tool_id": "umi_tools_count", "tool_version": "1.1.2+galaxy2", "test_index": 2, "time_seconds": 36.356552600860596, "inputs": {"input": {"src": "hda", "id": "5a76110036291e09"}, "wide_format_cell_counts": false, "bc|extract_umi_method": "umis", "umi|method": "directional", "sc|gene_tag": "XF", "sc|skip_tags_regex": "^[__|Unassigned]", "sc|per_cell": true, "advanced|random_seed": "123456789"}, "job": {"model_class": "Job", "id": "5a76110036291e09", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T18:42:27.060616", "update_time": "2024-11-08T18:42:41.875542", "galaxy_version": "24.1", "external_id": "gxy-sgvgx", "handler": null, "job_runner_name": null, "command_line": "ln -sf '/galaxy/server/database/objects/a/a/3/dataset_aa38a0a6-1e96-47d4-a840-f291d6e515fa.dat' 'input.bam' && ln -sf '/galaxy/server/database/objects/_metadata_files/a/b/2/metadata_ab2cb9b4-172c-442f-b3ab-18fac00846fc.dat' 'input.bam.bai' && umi_tools count '' --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag 'XF' --skip-tags-regex '^[__Unassigned]' --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed='123456789' -I 'input.bam' -S '/galaxy/server/database/objects/d/b/6/dataset_db6bc940-2bdb-4498-ada9-c8694f3b0c66.dat' --log2stderr", "user_email": "tests@fake.org", "command_version": "", "params": {"wide_format_cell_counts": "false", "bc": "{\"__current_case__\": 2, \"extract_umi_method\": \"umis\"}", "umi": "{\"edit_distance_threshold\": \"1\", \"method\": \"directional\", \"read_length\": false, \"soft_clip_threshold\": \"4\", \"spliced_is_unique\": false}", "sambam": "{\"chimeric_pairs\": null, \"chrom\": \"\", \"ignore_tlen\": false, \"ignore_umi\": false, \"mapping_quality\": \"0\", \"paired\": false, \"subset\": \"1.0\", \"unmapped_reads\": \"discard\", \"unpaired_reads\": null}", "sc": "{\"assigned_status_tag\": null, \"gene_tag\": \"XF\", \"gene_transcript_map\": null, \"per_cell\": true, \"per_contig\": false, \"skip_tags_regex\": \"^[__|Unassigned]\"}", "advanced": "{\"random_seed\": \"123456789\"}", "cond_extra": "{\"__current_case__\": 0, \"prepender\": \"none\"}", "log": "false", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"input\""}, "inputs": {"input": {"id": "5a76110036291e09", "src": "hda", "uuid": "aa38a0a6-1e96-47d4-a840-f291d6e515fa"}}, "outputs": {"out_counts": {"id": "69a419b0dfadf9ae", "src": "hda", "uuid": "db6bc940-2bdb-4498-ada9-c8694f3b0c66"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "# UMI-tools version: 1.1.2\n# output generated by count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/d/b/6/dataset_db6bc940-2bdb-4498-ada9-c8694f3b0c66.dat --log2stderr\n# job started at Fri Nov 8 18:42:30 2024 on gxy-sgvgx-fw8q9 -- 7bc01c24-b874-4fdd-b7c5-43521d327377\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XF\n# gene_transcript_map : None\n# get_umi_method : umis\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : directional\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : True\n# per_contig : False\n# per_gene : False\n# random_seed : 123456789\n# read_length : False\n# short_help : None\n# skip_regex : ^[__Unassigned]\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/d/b/6/dataset_db6bc940-2bdb-4498-ada9-c8694f3b0c66.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : False\n2024-11-08 18:42:30,021 INFO command: count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/d/b/6/dataset_db6bc940-2bdb-4498-ada9-c8694f3b0c66.dat --log2stderr\n2024-11-08 18:42:30,051 INFO Input Reads: 1203\n2024-11-08 18:42:30,051 INFO Read skipped - assigned tag matches skip_regex: 120\n2024-11-08 18:42:30,051 INFO Number of (post deduplication) reads counted: 145\n# job finished in 0 seconds at Fri Nov 8 18:42:30 2024 -- 0.91 0.26 0.00 0.00 -- 7bc01c24-b874-4fdd-b7c5-43521d327377\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "# UMI-tools version: 1.1.2\n# output generated by count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/d/b/6/dataset_db6bc940-2bdb-4498-ada9-c8694f3b0c66.dat --log2stderr\n# job started at Fri Nov 8 18:42:30 2024 on gxy-sgvgx-fw8q9 -- 7bc01c24-b874-4fdd-b7c5-43521d327377\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XF\n# gene_transcript_map : None\n# get_umi_method : umis\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : directional\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : True\n# per_contig : False\n# per_gene : False\n# random_seed : 123456789\n# read_length : False\n# short_help : None\n# skip_regex : ^[__Unassigned]\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/d/b/6/dataset_db6bc940-2bdb-4498-ada9-c8694f3b0c66.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : False\n2024-11-08 18:42:30,021 INFO command: count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/d/b/6/dataset_db6bc940-2bdb-4498-ada9-c8694f3b0c66.dat --log2stderr\n2024-11-08 18:42:30,051 INFO Input Reads: 1203\n2024-11-08 18:42:30,051 INFO Read skipped - assigned tag matches skip_regex: 120\n2024-11-08 18:42:30,051 INFO Number of (post deduplication) reads counted: 145\n# job finished in 0 seconds at Fri Nov 8 18:42:30 2024 -- 0.91 0.26 0.00 0.00 -- 7bc01c24-b874-4fdd-b7c5-43521d327377\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 18:42:28", "plugin": "core", "name": "start_epoch", "raw_value": "1731091348.0000000"}, {"title": "Job End Time", "value": "2024-11-08 18:42:30", "plugin": "core", "name": "end_epoch", "raw_value": "1731091350.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}]}, "status": "success"}}, {"id": "umi_tools_count/1.1.2+galaxy2-2", "has_data": true, "data": {"tool_id": "umi_tools_count", "tool_version": "1.1.2+galaxy2", "test_index": 2, "time_seconds": 38.565860748291016, "inputs": {"input": {"src": "hda", "id": "84db50a837b27b27"}, "wide_format_cell_counts": false, "bc|extract_umi_method": "umis", "umi|method": "directional", "sc|gene_tag": "XF", "sc|skip_tags_regex": "^[__|Unassigned]", "sc|per_cell": true, "advanced|random_seed": "123456789"}, "job": {"model_class": "Job", "id": "84db50a837b27b27", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T18:46:45.426213", "update_time": "2024-11-08T18:47:00.500004", "galaxy_version": "24.1", "external_id": "gxy-wwsk9", "handler": null, "job_runner_name": null, "command_line": "ln -sf '/galaxy/server/database/objects/d/f/e/dataset_dfe4e9db-b954-4833-bbdc-c6b53072320f.dat' 'input.bam' && ln -sf '/galaxy/server/database/objects/_metadata_files/2/5/8/metadata_258d58fb-926a-4bc3-90bb-12a20afcd1f0.dat' 'input.bam.bai' && umi_tools count '' --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag 'XF' --skip-tags-regex '^[__Unassigned]' --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed='123456789' -I 'input.bam' -S '/galaxy/server/database/objects/c/c/9/dataset_cc97dc12-c60b-4e58-af17-928850ff5dbd.dat' --log2stderr", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "log": "false", "cond_extra": "{\"__current_case__\": 0, \"prepender\": \"none\"}", "advanced": "{\"random_seed\": \"123456789\"}", "sc": "{\"assigned_status_tag\": null, \"gene_tag\": \"XF\", \"gene_transcript_map\": null, \"per_cell\": true, \"per_contig\": false, \"skip_tags_regex\": \"^[__|Unassigned]\"}", "sambam": "{\"chimeric_pairs\": null, \"chrom\": \"\", \"ignore_tlen\": false, \"ignore_umi\": false, \"mapping_quality\": \"0\", \"paired\": false, \"subset\": \"1.0\", \"unmapped_reads\": \"discard\", \"unpaired_reads\": null}", "umi": "{\"edit_distance_threshold\": \"1\", \"method\": \"directional\", \"read_length\": false, \"soft_clip_threshold\": \"4\", \"spliced_is_unique\": false}", "bc": "{\"__current_case__\": 2, \"extract_umi_method\": \"umis\"}", "wide_format_cell_counts": "false"}, "inputs": {"input": {"id": "84db50a837b27b27", "src": "hda", "uuid": "dfe4e9db-b954-4833-bbdc-c6b53072320f"}}, "outputs": {"out_counts": {"id": "b0b7107b5c1f55d3", "src": "hda", "uuid": "cc97dc12-c60b-4e58-af17-928850ff5dbd"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "# UMI-tools version: 1.1.2\n# output generated by count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/c/c/9/dataset_cc97dc12-c60b-4e58-af17-928850ff5dbd.dat --log2stderr\n# job started at Fri Nov 8 18:46:47 2024 on gxy-wwsk9-n42kd -- 632449aa-b5b7-48f6-9d52-f8b9745ecc04\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XF\n# gene_transcript_map : None\n# get_umi_method : umis\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : directional\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : True\n# per_contig : False\n# per_gene : False\n# random_seed : 123456789\n# read_length : False\n# short_help : None\n# skip_regex : ^[__Unassigned]\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/c/c/9/dataset_cc97dc12-c60b-4e58-af17-928850ff5dbd.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : False\n2024-11-08 18:46:47,795 INFO command: count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/c/c/9/dataset_cc97dc12-c60b-4e58-af17-928850ff5dbd.dat --log2stderr\n2024-11-08 18:46:47,826 INFO Input Reads: 1203\n2024-11-08 18:46:47,826 INFO Read skipped - assigned tag matches skip_regex: 120\n2024-11-08 18:46:47,826 INFO Number of (post deduplication) reads counted: 145\n# job finished in 0 seconds at Fri Nov 8 18:46:47 2024 -- 0.84 0.22 0.00 0.00 -- 632449aa-b5b7-48f6-9d52-f8b9745ecc04\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "# UMI-tools version: 1.1.2\n# output generated by count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/c/c/9/dataset_cc97dc12-c60b-4e58-af17-928850ff5dbd.dat --log2stderr\n# job started at Fri Nov 8 18:46:47 2024 on gxy-wwsk9-n42kd -- 632449aa-b5b7-48f6-9d52-f8b9745ecc04\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XF\n# gene_transcript_map : None\n# get_umi_method : umis\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : directional\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : True\n# per_contig : False\n# per_gene : False\n# random_seed : 123456789\n# read_length : False\n# short_help : None\n# skip_regex : ^[__Unassigned]\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/c/c/9/dataset_cc97dc12-c60b-4e58-af17-928850ff5dbd.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : False\n2024-11-08 18:46:47,795 INFO command: count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/c/c/9/dataset_cc97dc12-c60b-4e58-af17-928850ff5dbd.dat --log2stderr\n2024-11-08 18:46:47,826 INFO Input Reads: 1203\n2024-11-08 18:46:47,826 INFO Read skipped - assigned tag matches skip_regex: 120\n2024-11-08 18:46:47,826 INFO Number of (post deduplication) reads counted: 145\n# job finished in 0 seconds at Fri Nov 8 18:46:47 2024 -- 0.84 0.22 0.00 0.00 -- 632449aa-b5b7-48f6-9d52-f8b9745ecc04\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 18:46:46", "plugin": "core", "name": "start_epoch", "raw_value": "1731091606.0000000"}, {"title": "Job End Time", "value": "2024-11-08 18:46:47", "plugin": "core", "name": "end_epoch", "raw_value": "1731091607.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "umi_tools_count/1.1.2+galaxy2-3", "has_data": true, "data": {"tool_id": "umi_tools_count", "tool_version": "1.1.2+galaxy2", "test_index": 3, "time_seconds": 37.281686782836914, "inputs": {"input": {"src": "hda", "id": "eb41f10a2672178d"}, "wide_format_cell_counts": true, "bc|extract_umi_method": "umis", "umi|method": "directional", "sc|gene_tag": "XF", "sc|skip_tags_regex": "^[__|Unassigned]", "sc|per_cell": true, "advanced|random_seed": "123456789"}, "job": {"model_class": "Job", "id": "eb41f10a2672178d", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T18:39:01.465799", "update_time": "2024-11-08T18:39:16.370803", "galaxy_version": "24.1", "external_id": "gxy-p5v67", "handler": null, "job_runner_name": null, "command_line": "ln -sf '/galaxy/server/database/objects/9/d/a/dataset_9da974b7-8053-41ce-9a20-2e943400cf57.dat' 'input.bam' && ln -sf '/galaxy/server/database/objects/_metadata_files/a/d/c/metadata_adc31c7a-bee9-4b87-9300-d9107df26293.dat' 'input.bam.bai' && umi_tools count '--wide-format-cell-counts' --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag 'XF' --skip-tags-regex '^[__Unassigned]' --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed='123456789' -I 'input.bam' -S '/galaxy/server/database/objects/3/a/3/dataset_3a3e37cb-b9dd-42ae-ba0a-98aff24fbb52.dat' --log2stderr", "user_email": "tests@fake.org", "command_version": "", "params": {"wide_format_cell_counts": "true", "bc": "{\"__current_case__\": 2, \"extract_umi_method\": \"umis\"}", "umi": "{\"edit_distance_threshold\": \"1\", \"method\": \"directional\", \"read_length\": false, \"soft_clip_threshold\": \"4\", \"spliced_is_unique\": false}", "sambam": "{\"chimeric_pairs\": null, \"chrom\": \"\", \"ignore_tlen\": false, \"ignore_umi\": false, \"mapping_quality\": \"0\", \"paired\": false, \"subset\": \"1.0\", \"unmapped_reads\": \"discard\", \"unpaired_reads\": null}", "sc": "{\"assigned_status_tag\": null, \"gene_tag\": \"XF\", \"gene_transcript_map\": null, \"per_cell\": true, \"per_contig\": false, \"skip_tags_regex\": \"^[__|Unassigned]\"}", "advanced": "{\"random_seed\": \"123456789\"}", "cond_extra": "{\"__current_case__\": 0, \"prepender\": \"none\"}", "log": "false", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"input\""}, "inputs": {"input": {"id": "eb41f10a2672178d", "src": "hda", "uuid": "9da974b7-8053-41ce-9a20-2e943400cf57"}}, "outputs": {"out_counts": {"id": "b56b5d5f32c45a36", "src": "hda", "uuid": "3a3e37cb-b9dd-42ae-ba0a-98aff24fbb52"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "# UMI-tools version: 1.1.2\n# output generated by count --wide-format-cell-counts --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/3/a/3/dataset_3a3e37cb-b9dd-42ae-ba0a-98aff24fbb52.dat --log2stderr\n# job started at Fri Nov 8 18:39:04 2024 on gxy-p5v67-xj8xz -- 1490743d-f989-4023-bea6-98ff7d414b90\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XF\n# gene_transcript_map : None\n# get_umi_method : umis\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : directional\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : True\n# per_contig : False\n# per_gene : False\n# random_seed : 123456789\n# read_length : False\n# short_help : None\n# skip_regex : ^[__Unassigned]\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/3/a/3/dataset_3a3e37cb-b9dd-42ae-ba0a-98aff24fbb52.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : True\n2024-11-08 18:39:04,605 INFO command: count --wide-format-cell-counts --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/3/a/3/dataset_3a3e37cb-b9dd-42ae-ba0a-98aff24fbb52.dat --log2stderr\n2024-11-08 18:39:04,634 INFO Input Reads: 1203\n2024-11-08 18:39:04,634 INFO Read skipped - assigned tag matches skip_regex: 120\n2024-11-08 18:39:04,634 INFO Number of (post deduplication) reads counted: 145\n# job finished in 0 seconds at Fri Nov 8 18:39:04 2024 -- 0.93 0.22 0.00 0.00 -- 1490743d-f989-4023-bea6-98ff7d414b90\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "# UMI-tools version: 1.1.2\n# output generated by count --wide-format-cell-counts --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/3/a/3/dataset_3a3e37cb-b9dd-42ae-ba0a-98aff24fbb52.dat --log2stderr\n# job started at Fri Nov 8 18:39:04 2024 on gxy-p5v67-xj8xz -- 1490743d-f989-4023-bea6-98ff7d414b90\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XF\n# gene_transcript_map : None\n# get_umi_method : umis\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : directional\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : True\n# per_contig : False\n# per_gene : False\n# random_seed : 123456789\n# read_length : False\n# short_help : None\n# skip_regex : ^[__Unassigned]\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/3/a/3/dataset_3a3e37cb-b9dd-42ae-ba0a-98aff24fbb52.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : True\n2024-11-08 18:39:04,605 INFO command: count --wide-format-cell-counts --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/3/a/3/dataset_3a3e37cb-b9dd-42ae-ba0a-98aff24fbb52.dat --log2stderr\n2024-11-08 18:39:04,634 INFO Input Reads: 1203\n2024-11-08 18:39:04,634 INFO Read skipped - assigned tag matches skip_regex: 120\n2024-11-08 18:39:04,634 INFO Number of (post deduplication) reads counted: 145\n# job finished in 0 seconds at Fri Nov 8 18:39:04 2024 -- 0.93 0.22 0.00 0.00 -- 1490743d-f989-4023-bea6-98ff7d414b90\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-08 18:39:04", "plugin": "core", "name": "end_epoch", "raw_value": "1731091144.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 18:39:03", "plugin": "core", "name": "start_epoch", "raw_value": "1731091143.0000000"}, {"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": "umi_tools_count/1.1.2+galaxy2-3", "has_data": true, "data": {"tool_id": "umi_tools_count", "tool_version": "1.1.2+galaxy2", "test_index": 3, "time_seconds": 37.28631138801575, "inputs": {"input": {"src": "hda", "id": "562134ea0f434c69"}, "wide_format_cell_counts": true, "bc|extract_umi_method": "umis", "umi|method": "directional", "sc|gene_tag": "XF", "sc|skip_tags_regex": "^[__|Unassigned]", "sc|per_cell": true, "advanced|random_seed": "123456789"}, "job": {"model_class": "Job", "id": "562134ea0f434c69", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T18:43:04.066986", "update_time": "2024-11-08T18:43:19.149120", "galaxy_version": "24.1", "external_id": "gxy-2ww6v", "handler": null, "job_runner_name": null, "command_line": "ln -sf '/galaxy/server/database/objects/3/5/d/dataset_35d52183-25f7-4c35-9d92-54e5160386e1.dat' 'input.bam' && ln -sf '/galaxy/server/database/objects/_metadata_files/f/0/3/metadata_f035e05f-4e1d-4ea7-bb48-3c54ef954695.dat' 'input.bam.bai' && umi_tools count '--wide-format-cell-counts' --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag 'XF' --skip-tags-regex '^[__Unassigned]' --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed='123456789' -I 'input.bam' -S '/galaxy/server/database/objects/9/1/8/dataset_9183442b-26bf-4f17-a97f-1cae902ac8cc.dat' --log2stderr", "user_email": "tests@fake.org", "command_version": "", "params": {"wide_format_cell_counts": "true", "bc": "{\"__current_case__\": 2, \"extract_umi_method\": \"umis\"}", "umi": "{\"edit_distance_threshold\": \"1\", \"method\": \"directional\", \"read_length\": false, \"soft_clip_threshold\": \"4\", \"spliced_is_unique\": false}", "sambam": "{\"chimeric_pairs\": null, \"chrom\": \"\", \"ignore_tlen\": false, \"ignore_umi\": false, \"mapping_quality\": \"0\", \"paired\": false, \"subset\": \"1.0\", \"unmapped_reads\": \"discard\", \"unpaired_reads\": null}", "sc": "{\"assigned_status_tag\": null, \"gene_tag\": \"XF\", \"gene_transcript_map\": null, \"per_cell\": true, \"per_contig\": false, \"skip_tags_regex\": \"^[__|Unassigned]\"}", "advanced": "{\"random_seed\": \"123456789\"}", "cond_extra": "{\"__current_case__\": 0, \"prepender\": \"none\"}", "log": "false", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"input\""}, "inputs": {"input": {"id": "562134ea0f434c69", "src": "hda", "uuid": "35d52183-25f7-4c35-9d92-54e5160386e1"}}, "outputs": {"out_counts": {"id": "9a6057cd21099aeb", "src": "hda", "uuid": "9183442b-26bf-4f17-a97f-1cae902ac8cc"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "# UMI-tools version: 1.1.2\n# output generated by count --wide-format-cell-counts --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/9/1/8/dataset_9183442b-26bf-4f17-a97f-1cae902ac8cc.dat --log2stderr\n# job started at Fri Nov 8 18:43:06 2024 on gxy-2ww6v-zgjgr -- aafbc2f8-a108-47ca-be10-60949276e311\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XF\n# gene_transcript_map : None\n# get_umi_method : umis\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : directional\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : True\n# per_contig : False\n# per_gene : False\n# random_seed : 123456789\n# read_length : False\n# short_help : None\n# skip_regex : ^[__Unassigned]\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/9/1/8/dataset_9183442b-26bf-4f17-a97f-1cae902ac8cc.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : True\n2024-11-08 18:43:06,801 INFO command: count --wide-format-cell-counts --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/9/1/8/dataset_9183442b-26bf-4f17-a97f-1cae902ac8cc.dat --log2stderr\n2024-11-08 18:43:06,830 INFO Input Reads: 1203\n2024-11-08 18:43:06,830 INFO Read skipped - assigned tag matches skip_regex: 120\n2024-11-08 18:43:06,830 INFO Number of (post deduplication) reads counted: 145\n# job finished in 0 seconds at Fri Nov 8 18:43:06 2024 -- 0.87 0.20 0.00 0.00 -- aafbc2f8-a108-47ca-be10-60949276e311\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "# UMI-tools version: 1.1.2\n# output generated by count --wide-format-cell-counts --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/9/1/8/dataset_9183442b-26bf-4f17-a97f-1cae902ac8cc.dat --log2stderr\n# job started at Fri Nov 8 18:43:06 2024 on gxy-2ww6v-zgjgr -- aafbc2f8-a108-47ca-be10-60949276e311\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XF\n# gene_transcript_map : None\n# get_umi_method : umis\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : directional\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : True\n# per_contig : False\n# per_gene : False\n# random_seed : 123456789\n# read_length : False\n# short_help : None\n# skip_regex : ^[__Unassigned]\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/9/1/8/dataset_9183442b-26bf-4f17-a97f-1cae902ac8cc.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : True\n2024-11-08 18:43:06,801 INFO command: count --wide-format-cell-counts --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/9/1/8/dataset_9183442b-26bf-4f17-a97f-1cae902ac8cc.dat --log2stderr\n2024-11-08 18:43:06,830 INFO Input Reads: 1203\n2024-11-08 18:43:06,830 INFO Read skipped - assigned tag matches skip_regex: 120\n2024-11-08 18:43:06,830 INFO Number of (post deduplication) reads counted: 145\n# job finished in 0 seconds at Fri Nov 8 18:43:06 2024 -- 0.87 0.20 0.00 0.00 -- aafbc2f8-a108-47ca-be10-60949276e311\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 18:43:05", "plugin": "core", "name": "start_epoch", "raw_value": "1731091385.0000000"}, {"title": "Job End Time", "value": "2024-11-08 18:43:06", "plugin": "core", "name": "end_epoch", "raw_value": "1731091386.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "umi_tools_count/1.1.2+galaxy2-3", "has_data": true, "data": {"tool_id": "umi_tools_count", "tool_version": "1.1.2+galaxy2", "test_index": 3, "time_seconds": 38.5015184879303, "inputs": {"input": {"src": "hda", "id": "8d099a85f4a8cd09"}, "wide_format_cell_counts": true, "bc|extract_umi_method": "umis", "umi|method": "directional", "sc|gene_tag": "XF", "sc|skip_tags_regex": "^[__|Unassigned]", "sc|per_cell": true, "advanced|random_seed": "123456789"}, "job": {"model_class": "Job", "id": "8d099a85f4a8cd09", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T18:47:23.053093", "update_time": "2024-11-08T18:47:38.895324", "galaxy_version": "24.1", "external_id": "gxy-64tsg", "handler": null, "job_runner_name": null, "command_line": "ln -sf '/galaxy/server/database/objects/f/a/1/dataset_fa1197d8-546b-423c-b1f2-a0d130bbf671.dat' 'input.bam' && ln -sf '/galaxy/server/database/objects/_metadata_files/7/2/5/metadata_725e0d04-4ff8-46dd-82d8-cd66d96c1b5b.dat' 'input.bam.bai' && umi_tools count '--wide-format-cell-counts' --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag 'XF' --skip-tags-regex '^[__Unassigned]' --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed='123456789' -I 'input.bam' -S '/galaxy/server/database/objects/7/1/9/dataset_71949ac5-2c52-4243-a97c-4dddad4757cf.dat' --log2stderr", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "log": "false", "cond_extra": "{\"__current_case__\": 0, \"prepender\": \"none\"}", "advanced": "{\"random_seed\": \"123456789\"}", "sc": "{\"assigned_status_tag\": null, \"gene_tag\": \"XF\", \"gene_transcript_map\": null, \"per_cell\": true, \"per_contig\": false, \"skip_tags_regex\": \"^[__|Unassigned]\"}", "sambam": "{\"chimeric_pairs\": null, \"chrom\": \"\", \"ignore_tlen\": false, \"ignore_umi\": false, \"mapping_quality\": \"0\", \"paired\": false, \"subset\": \"1.0\", \"unmapped_reads\": \"discard\", \"unpaired_reads\": null}", "umi": "{\"edit_distance_threshold\": \"1\", \"method\": \"directional\", \"read_length\": false, \"soft_clip_threshold\": \"4\", \"spliced_is_unique\": false}", "bc": "{\"__current_case__\": 2, \"extract_umi_method\": \"umis\"}", "wide_format_cell_counts": "true"}, "inputs": {"input": {"id": "8d099a85f4a8cd09", "src": "hda", "uuid": "fa1197d8-546b-423c-b1f2-a0d130bbf671"}}, "outputs": {"out_counts": {"id": "dd6d722f839a545f", "src": "hda", "uuid": "71949ac5-2c52-4243-a97c-4dddad4757cf"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "# UMI-tools version: 1.1.2\n# output generated by count --wide-format-cell-counts --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/7/1/9/dataset_71949ac5-2c52-4243-a97c-4dddad4757cf.dat --log2stderr\n# job started at Fri Nov 8 18:47:26 2024 on gxy-64tsg-sc5qn -- 46d064eb-90f2-409c-8263-a43de9c454f7\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XF\n# gene_transcript_map : None\n# get_umi_method : umis\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : directional\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : True\n# per_contig : False\n# per_gene : False\n# random_seed : 123456789\n# read_length : False\n# short_help : None\n# skip_regex : ^[__Unassigned]\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/7/1/9/dataset_71949ac5-2c52-4243-a97c-4dddad4757cf.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : True\n2024-11-08 18:47:26,737 INFO command: count --wide-format-cell-counts --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/7/1/9/dataset_71949ac5-2c52-4243-a97c-4dddad4757cf.dat --log2stderr\n2024-11-08 18:47:26,768 INFO Input Reads: 1203\n2024-11-08 18:47:26,768 INFO Read skipped - assigned tag matches skip_regex: 120\n2024-11-08 18:47:26,768 INFO Number of (post deduplication) reads counted: 145\n# job finished in 0 seconds at Fri Nov 8 18:47:26 2024 -- 0.91 0.23 0.00 0.00 -- 46d064eb-90f2-409c-8263-a43de9c454f7\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "# UMI-tools version: 1.1.2\n# output generated by count --wide-format-cell-counts --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/7/1/9/dataset_71949ac5-2c52-4243-a97c-4dddad4757cf.dat --log2stderr\n# job started at Fri Nov 8 18:47:26 2024 on gxy-64tsg-sc5qn -- 46d064eb-90f2-409c-8263-a43de9c454f7\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XF\n# gene_transcript_map : None\n# get_umi_method : umis\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : directional\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : True\n# per_contig : False\n# per_gene : False\n# random_seed : 123456789\n# read_length : False\n# short_help : None\n# skip_regex : ^[__Unassigned]\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/7/1/9/dataset_71949ac5-2c52-4243-a97c-4dddad4757cf.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : True\n2024-11-08 18:47:26,737 INFO command: count --wide-format-cell-counts --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/7/1/9/dataset_71949ac5-2c52-4243-a97c-4dddad4757cf.dat --log2stderr\n2024-11-08 18:47:26,768 INFO Input Reads: 1203\n2024-11-08 18:47:26,768 INFO Read skipped - assigned tag matches skip_regex: 120\n2024-11-08 18:47:26,768 INFO Number of (post deduplication) reads counted: 145\n# job finished in 0 seconds at Fri Nov 8 18:47:26 2024 -- 0.91 0.23 0.00 0.00 -- 46d064eb-90f2-409c-8263-a43de9c454f7\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 18:47:25", "plugin": "core", "name": "start_epoch", "raw_value": "1731091645.0000000"}, {"title": "Job End Time", "value": "2024-11-08 18:47:26", "plugin": "core", "name": "end_epoch", "raw_value": "1731091646.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "umi_tools_count/1.1.2+galaxy2-4", "has_data": true, "data": {"tool_id": "umi_tools_count", "tool_version": "1.1.2+galaxy2", "test_index": 4, "time_seconds": 36.90284967422485, "inputs": {"input": {"src": "hda", "id": "d2b2f96316a96ccc"}, "umi|method": "unique", "sc|gene_tag": "XT", "sc|per_cell": true, "advanced|random_seed": "0"}, "job": {"model_class": "Job", "id": "d2b2f96316a96ccc", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T18:39:39.061887", "update_time": "2024-11-08T18:39:53.547515", "galaxy_version": "24.1", "external_id": "gxy-w6vlw", "handler": null, "job_runner_name": null, "command_line": "ln -sf '/galaxy/server/database/objects/0/e/3/dataset_0e382b43-0b58-4d41-ae93-cbade31d1b5f.dat' 'input.bam' && ln -sf '/galaxy/server/database/objects/_metadata_files/b/a/5/metadata_ba53ef36-1ed9-4f26-b291-abe17636a409.dat' 'input.bam.bai' && umi_tools count '--wide-format-cell-counts' --extract-umi-method read_id --umi-separator '_' --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag 'XT' --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed='0' -I 'input.bam' -S '/galaxy/server/database/objects/2/c/7/dataset_2c7c9321-c12e-46c2-9a10-1bf9ead756e4.dat' --log2stderr", "user_email": "tests@fake.org", "command_version": "", "params": {"wide_format_cell_counts": "true", "bc": "{\"__current_case__\": 0, \"extract_umi_method\": \"read_id\", \"umi_separator\": \"_\"}", "umi": "{\"edit_distance_threshold\": \"1\", \"method\": \"unique\", \"read_length\": false, \"soft_clip_threshold\": \"4\", \"spliced_is_unique\": false}", "sambam": "{\"chimeric_pairs\": null, \"chrom\": \"\", \"ignore_tlen\": false, \"ignore_umi\": false, \"mapping_quality\": \"0\", \"paired\": false, \"subset\": \"1.0\", \"unmapped_reads\": \"discard\", \"unpaired_reads\": null}", "sc": "{\"assigned_status_tag\": null, \"gene_tag\": \"XT\", \"gene_transcript_map\": null, \"per_cell\": true, \"per_contig\": false, \"skip_tags_regex\": \"\"}", "advanced": "{\"random_seed\": \"0\"}", "cond_extra": "{\"__current_case__\": 0, \"prepender\": \"none\"}", "log": "false", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"input\""}, "inputs": {"input": {"id": "d2b2f96316a96ccc", "src": "hda", "uuid": "0e382b43-0b58-4d41-ae93-cbade31d1b5f"}}, "outputs": {"out_counts": {"id": "a484d048696424a0", "src": "hda", "uuid": "2c7c9321-c12e-46c2-9a10-1bf9ead756e4"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "# UMI-tools version: 1.1.2\n# output generated by count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/2/c/7/dataset_2c7c9321-c12e-46c2-9a10-1bf9ead756e4.dat --log2stderr\n# job started at Fri Nov 8 18:39:41 2024 on gxy-w6vlw-gcc9x -- 05e5321d-dc62-44ae-957f-b3a473cd0546\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XT\n# gene_transcript_map : None\n# get_umi_method : read_id\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : unique\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : True\n# per_contig : False\n# per_gene : False\n# random_seed : 0\n# read_length : False\n# short_help : None\n# skip_regex : ^(__|Unassigned)\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/2/c/7/dataset_2c7c9321-c12e-46c2-9a10-1bf9ead756e4.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : True\n2024-11-08 18:39:41,504 INFO command: count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/2/c/7/dataset_2c7c9321-c12e-46c2-9a10-1bf9ead756e4.dat --log2stderr\n2024-11-08 18:39:41,518 INFO Input Reads: 39\n2024-11-08 18:39:41,518 INFO Number of (post deduplication) reads counted: 12\n# job finished in 0 seconds at Fri Nov 8 18:39:41 2024 -- 0.88 0.24 0.00 0.00 -- 05e5321d-dc62-44ae-957f-b3a473cd0546\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "# UMI-tools version: 1.1.2\n# output generated by count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/2/c/7/dataset_2c7c9321-c12e-46c2-9a10-1bf9ead756e4.dat --log2stderr\n# job started at Fri Nov 8 18:39:41 2024 on gxy-w6vlw-gcc9x -- 05e5321d-dc62-44ae-957f-b3a473cd0546\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XT\n# gene_transcript_map : None\n# get_umi_method : read_id\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : unique\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : True\n# per_contig : False\n# per_gene : False\n# random_seed : 0\n# read_length : False\n# short_help : None\n# skip_regex : ^(__|Unassigned)\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/2/c/7/dataset_2c7c9321-c12e-46c2-9a10-1bf9ead756e4.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : True\n2024-11-08 18:39:41,504 INFO command: count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/2/c/7/dataset_2c7c9321-c12e-46c2-9a10-1bf9ead756e4.dat --log2stderr\n2024-11-08 18:39:41,518 INFO Input Reads: 39\n2024-11-08 18:39:41,518 INFO Number of (post deduplication) reads counted: 12\n# job finished in 0 seconds at Fri Nov 8 18:39:41 2024 -- 0.88 0.24 0.00 0.00 -- 05e5321d-dc62-44ae-957f-b3a473cd0546\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 18:39:40", "plugin": "core", "name": "start_epoch", "raw_value": "1731091180.0000000"}, {"title": "Job End Time", "value": "2024-11-08 18:39:41", "plugin": "core", "name": "end_epoch", "raw_value": "1731091181.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "umi_tools_count/1.1.2+galaxy2-4", "has_data": true, "data": {"tool_id": "umi_tools_count", "tool_version": "1.1.2+galaxy2", "test_index": 4, "time_seconds": 37.23709964752197, "inputs": {"input": {"src": "hda", "id": "1ba321c08a66f6e6"}, "umi|method": "unique", "sc|gene_tag": "XT", "sc|per_cell": true, "advanced|random_seed": "0"}, "job": {"model_class": "Job", "id": "1ba321c08a66f6e6", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T18:43:41.987443", "update_time": "2024-11-08T18:43:56.507865", "galaxy_version": "24.1", "external_id": "gxy-k4dlw", "handler": null, "job_runner_name": null, "command_line": "ln -sf '/galaxy/server/database/objects/3/3/3/dataset_333412d2-ad25-4ba4-b058-8e65b06bde2e.dat' 'input.bam' && ln -sf '/galaxy/server/database/objects/_metadata_files/7/4/f/metadata_74f31431-2057-4259-99f2-2f00a17efbf9.dat' 'input.bam.bai' && umi_tools count '--wide-format-cell-counts' --extract-umi-method read_id --umi-separator '_' --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag 'XT' --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed='0' -I 'input.bam' -S '/galaxy/server/database/objects/0/1/0/dataset_0106d85b-ef63-4314-a0af-e80860a2bd38.dat' --log2stderr", "user_email": "tests@fake.org", "command_version": "", "params": {"wide_format_cell_counts": "true", "bc": "{\"__current_case__\": 0, \"extract_umi_method\": \"read_id\", \"umi_separator\": \"_\"}", "umi": "{\"edit_distance_threshold\": \"1\", \"method\": \"unique\", \"read_length\": false, \"soft_clip_threshold\": \"4\", \"spliced_is_unique\": false}", "sambam": "{\"chimeric_pairs\": null, \"chrom\": \"\", \"ignore_tlen\": false, \"ignore_umi\": false, \"mapping_quality\": \"0\", \"paired\": false, \"subset\": \"1.0\", \"unmapped_reads\": \"discard\", \"unpaired_reads\": null}", "sc": "{\"assigned_status_tag\": null, \"gene_tag\": \"XT\", \"gene_transcript_map\": null, \"per_cell\": true, \"per_contig\": false, \"skip_tags_regex\": \"\"}", "advanced": "{\"random_seed\": \"0\"}", "cond_extra": "{\"__current_case__\": 0, \"prepender\": \"none\"}", "log": "false", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"input\""}, "inputs": {"input": {"id": "1ba321c08a66f6e6", "src": "hda", "uuid": "333412d2-ad25-4ba4-b058-8e65b06bde2e"}}, "outputs": {"out_counts": {"id": "7d230e8f17fedba0", "src": "hda", "uuid": "0106d85b-ef63-4314-a0af-e80860a2bd38"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "# UMI-tools version: 1.1.2\n# output generated by count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/0/1/0/dataset_0106d85b-ef63-4314-a0af-e80860a2bd38.dat --log2stderr\n# job started at Fri Nov 8 18:43:44 2024 on gxy-k4dlw-wd9jg -- 68d00a58-6f8c-402c-9242-7829bfea6a36\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XT\n# gene_transcript_map : None\n# get_umi_method : read_id\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : unique\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : True\n# per_contig : False\n# per_gene : False\n# random_seed : 0\n# read_length : False\n# short_help : None\n# skip_regex : ^(__|Unassigned)\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/0/1/0/dataset_0106d85b-ef63-4314-a0af-e80860a2bd38.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : True\n2024-11-08 18:43:44,568 INFO command: count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/0/1/0/dataset_0106d85b-ef63-4314-a0af-e80860a2bd38.dat --log2stderr\n2024-11-08 18:43:44,584 INFO Input Reads: 39\n2024-11-08 18:43:44,584 INFO Number of (post deduplication) reads counted: 12\n# job finished in 0 seconds at Fri Nov 8 18:43:44 2024 -- 0.89 0.24 0.00 0.00 -- 68d00a58-6f8c-402c-9242-7829bfea6a36\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "# UMI-tools version: 1.1.2\n# output generated by count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/0/1/0/dataset_0106d85b-ef63-4314-a0af-e80860a2bd38.dat --log2stderr\n# job started at Fri Nov 8 18:43:44 2024 on gxy-k4dlw-wd9jg -- 68d00a58-6f8c-402c-9242-7829bfea6a36\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XT\n# gene_transcript_map : None\n# get_umi_method : read_id\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : unique\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : True\n# per_contig : False\n# per_gene : False\n# random_seed : 0\n# read_length : False\n# short_help : None\n# skip_regex : ^(__|Unassigned)\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/0/1/0/dataset_0106d85b-ef63-4314-a0af-e80860a2bd38.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : True\n2024-11-08 18:43:44,568 INFO command: count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/0/1/0/dataset_0106d85b-ef63-4314-a0af-e80860a2bd38.dat --log2stderr\n2024-11-08 18:43:44,584 INFO Input Reads: 39\n2024-11-08 18:43:44,584 INFO Number of (post deduplication) reads counted: 12\n# job finished in 0 seconds at Fri Nov 8 18:43:44 2024 -- 0.89 0.24 0.00 0.00 -- 68d00a58-6f8c-402c-9242-7829bfea6a36\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 18:43:43", "plugin": "core", "name": "start_epoch", "raw_value": "1731091423.0000000"}, {"title": "Job End Time", "value": "2024-11-08 18:43:44", "plugin": "core", "name": "end_epoch", "raw_value": "1731091424.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "umi_tools_count/1.1.2+galaxy2-4", "has_data": true, "data": {"tool_id": "umi_tools_count", "tool_version": "1.1.2+galaxy2", "test_index": 4, "time_seconds": 39.09046459197998, "inputs": {"input": {"src": "hda", "id": "84a6b251d82ff71d"}, "umi|method": "unique", "sc|gene_tag": "XT", "sc|per_cell": true, "advanced|random_seed": "0"}, "job": {"model_class": "Job", "id": "84a6b251d82ff71d", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T18:48:02.517647", "update_time": "2024-11-08T18:48:18.274161", "galaxy_version": "24.1", "external_id": "gxy-k7dqj", "handler": null, "job_runner_name": null, "command_line": "ln -sf '/galaxy/server/database/objects/9/0/d/dataset_90db0758-e6ed-4be1-a9c2-90a725d7e0ae.dat' 'input.bam' && ln -sf '/galaxy/server/database/objects/_metadata_files/8/0/f/metadata_80f196f2-274f-4e1c-9495-343a26f54a84.dat' 'input.bam.bai' && umi_tools count '--wide-format-cell-counts' --extract-umi-method read_id --umi-separator '_' --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag 'XT' --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed='0' -I 'input.bam' -S '/galaxy/server/database/objects/a/d/2/dataset_ad27d980-5c83-44d0-9679-d3208ff349c6.dat' --log2stderr", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "log": "false", "cond_extra": "{\"__current_case__\": 0, \"prepender\": \"none\"}", "advanced": "{\"random_seed\": \"0\"}", "sc": "{\"assigned_status_tag\": null, \"gene_tag\": \"XT\", \"gene_transcript_map\": null, \"per_cell\": true, \"per_contig\": false, \"skip_tags_regex\": \"\"}", "sambam": "{\"chimeric_pairs\": null, \"chrom\": \"\", \"ignore_tlen\": false, \"ignore_umi\": false, \"mapping_quality\": \"0\", \"paired\": false, \"subset\": \"1.0\", \"unmapped_reads\": \"discard\", \"unpaired_reads\": null}", "umi": "{\"edit_distance_threshold\": \"1\", \"method\": \"unique\", \"read_length\": false, \"soft_clip_threshold\": \"4\", \"spliced_is_unique\": false}", "bc": "{\"__current_case__\": 0, \"extract_umi_method\": \"read_id\", \"umi_separator\": \"_\"}", "wide_format_cell_counts": "true"}, "inputs": {"input": {"id": "84a6b251d82ff71d", "src": "hda", "uuid": "90db0758-e6ed-4be1-a9c2-90a725d7e0ae"}}, "outputs": {"out_counts": {"id": "82d06132a0b4a71c", "src": "hda", "uuid": "ad27d980-5c83-44d0-9679-d3208ff349c6"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "# UMI-tools version: 1.1.2\n# output generated by count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/a/d/2/dataset_ad27d980-5c83-44d0-9679-d3208ff349c6.dat --log2stderr\n# job started at Fri Nov 8 18:48:05 2024 on gxy-k7dqj-wb8gk -- 2fb6e12f-ad3a-4329-80a4-37d97a731713\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XT\n# gene_transcript_map : None\n# get_umi_method : read_id\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : unique\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : True\n# per_contig : False\n# per_gene : False\n# random_seed : 0\n# read_length : False\n# short_help : None\n# skip_regex : ^(__|Unassigned)\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/a/d/2/dataset_ad27d980-5c83-44d0-9679-d3208ff349c6.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : True\n2024-11-08 18:48:05,504 INFO command: count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/a/d/2/dataset_ad27d980-5c83-44d0-9679-d3208ff349c6.dat --log2stderr\n2024-11-08 18:48:05,520 INFO Input Reads: 39\n2024-11-08 18:48:05,520 INFO Number of (post deduplication) reads counted: 12\n# job finished in 0 seconds at Fri Nov 8 18:48:05 2024 -- 0.87 0.21 0.00 0.00 -- 2fb6e12f-ad3a-4329-80a4-37d97a731713\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "# UMI-tools version: 1.1.2\n# output generated by count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/a/d/2/dataset_ad27d980-5c83-44d0-9679-d3208ff349c6.dat --log2stderr\n# job started at Fri Nov 8 18:48:05 2024 on gxy-k7dqj-wb8gk -- 2fb6e12f-ad3a-4329-80a4-37d97a731713\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XT\n# gene_transcript_map : None\n# get_umi_method : read_id\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : unique\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : True\n# per_contig : False\n# per_gene : False\n# random_seed : 0\n# read_length : False\n# short_help : None\n# skip_regex : ^(__|Unassigned)\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/a/d/2/dataset_ad27d980-5c83-44d0-9679-d3208ff349c6.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : True\n2024-11-08 18:48:05,504 INFO command: count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/a/d/2/dataset_ad27d980-5c83-44d0-9679-d3208ff349c6.dat --log2stderr\n2024-11-08 18:48:05,520 INFO Input Reads: 39\n2024-11-08 18:48:05,520 INFO Number of (post deduplication) reads counted: 12\n# job finished in 0 seconds at Fri Nov 8 18:48:05 2024 -- 0.87 0.21 0.00 0.00 -- 2fb6e12f-ad3a-4329-80a4-37d97a731713\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 18:48:04", "plugin": "core", "name": "start_epoch", "raw_value": "1731091684.0000000"}, {"title": "Job End Time", "value": "2024-11-08 18:48:05", "plugin": "core", "name": "end_epoch", "raw_value": "1731091685.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "umi_tools_count/1.1.2+galaxy2-5", "has_data": true, "data": {"tool_id": "umi_tools_count", "tool_version": "1.1.2+galaxy2", "test_index": 5, "time_seconds": 38.491920948028564, "inputs": {"input": {"src": "hda", "id": "91a0a57b12e2a1e3"}, "umi|method": "unique", "sc|gene_tag": "XT", "sc|per_cell": true, "advanced|random_seed": "0", "cond_extra|custom_label": "test", "cond_extra|prepender": "string"}, "job": {"model_class": "Job", "id": "91a0a57b12e2a1e3", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T18:40:16.357225", "update_time": "2024-11-08T18:40:32.113391", "galaxy_version": "24.1", "external_id": "gxy-42hpz", "handler": null, "job_runner_name": null, "command_line": "ln -sf '/galaxy/server/database/objects/8/4/f/dataset_84f84dae-5837-46e7-b284-68a192136a98.dat' 'input.bam' && ln -sf '/galaxy/server/database/objects/_metadata_files/1/7/2/metadata_17238bd6-8e1a-4330-87ac-18607fc9dc2e.dat' 'input.bam.bai' && umi_tools count '--wide-format-cell-counts' --extract-umi-method read_id --umi-separator '_' --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag 'XT' --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed='0' -I 'input.bam' -S '/galaxy/server/database/objects/f/7/f/dataset_f7f50908-1a95-4a3c-82c1-95af60f7d8b6.dat' --log2stderr && sed -i -r '1s|\\b([ACGT]+)\\b|'\"test\"'_\\1|g' '/galaxy/server/database/objects/f/7/f/dataset_f7f50908-1a95-4a3c-82c1-95af60f7d8b6.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"wide_format_cell_counts": "true", "bc": "{\"__current_case__\": 0, \"extract_umi_method\": \"read_id\", \"umi_separator\": \"_\"}", "umi": "{\"edit_distance_threshold\": \"1\", \"method\": \"unique\", \"read_length\": false, \"soft_clip_threshold\": \"4\", \"spliced_is_unique\": false}", "sambam": "{\"chimeric_pairs\": null, \"chrom\": \"\", \"ignore_tlen\": false, \"ignore_umi\": false, \"mapping_quality\": \"0\", \"paired\": false, \"subset\": \"1.0\", \"unmapped_reads\": \"discard\", \"unpaired_reads\": null}", "sc": "{\"assigned_status_tag\": null, \"gene_tag\": \"XT\", \"gene_transcript_map\": null, \"per_cell\": true, \"per_contig\": false, \"skip_tags_regex\": \"\"}", "advanced": "{\"random_seed\": \"0\"}", "cond_extra": "{\"__current_case__\": 2, \"custom_label\": \"test\", \"prepender\": \"string\"}", "log": "false", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"input\""}, "inputs": {"input": {"id": "91a0a57b12e2a1e3", "src": "hda", "uuid": "84f84dae-5837-46e7-b284-68a192136a98"}}, "outputs": {"out_counts": {"id": "ed318763576ee756", "src": "hda", "uuid": "f7f50908-1a95-4a3c-82c1-95af60f7d8b6"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "# UMI-tools version: 1.1.2\n# output generated by count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/f/7/f/dataset_f7f50908-1a95-4a3c-82c1-95af60f7d8b6.dat --log2stderr\n# job started at Fri Nov 8 18:40:19 2024 on gxy-42hpz-25dvm -- 2b17ca85-f635-4589-b43a-2aae1ad180b2\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XT\n# gene_transcript_map : None\n# get_umi_method : read_id\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : unique\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : True\n# per_contig : False\n# per_gene : False\n# random_seed : 0\n# read_length : False\n# short_help : None\n# skip_regex : ^(__|Unassigned)\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/f/7/f/dataset_f7f50908-1a95-4a3c-82c1-95af60f7d8b6.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : True\n2024-11-08 18:40:19,583 INFO command: count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/f/7/f/dataset_f7f50908-1a95-4a3c-82c1-95af60f7d8b6.dat --log2stderr\n2024-11-08 18:40:19,598 INFO Input Reads: 39\n2024-11-08 18:40:19,598 INFO Number of (post deduplication) reads counted: 12\n# job finished in 0 seconds at Fri Nov 8 18:40:19 2024 -- 0.90 0.24 0.00 0.00 -- 2b17ca85-f635-4589-b43a-2aae1ad180b2\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "# UMI-tools version: 1.1.2\n# output generated by count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/f/7/f/dataset_f7f50908-1a95-4a3c-82c1-95af60f7d8b6.dat --log2stderr\n# job started at Fri Nov 8 18:40:19 2024 on gxy-42hpz-25dvm -- 2b17ca85-f635-4589-b43a-2aae1ad180b2\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XT\n# gene_transcript_map : None\n# get_umi_method : read_id\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : unique\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : True\n# per_contig : False\n# per_gene : False\n# random_seed : 0\n# read_length : False\n# short_help : None\n# skip_regex : ^(__|Unassigned)\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/f/7/f/dataset_f7f50908-1a95-4a3c-82c1-95af60f7d8b6.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : True\n2024-11-08 18:40:19,583 INFO command: count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/f/7/f/dataset_f7f50908-1a95-4a3c-82c1-95af60f7d8b6.dat --log2stderr\n2024-11-08 18:40:19,598 INFO Input Reads: 39\n2024-11-08 18:40:19,598 INFO Number of (post deduplication) reads counted: 12\n# job finished in 0 seconds at Fri Nov 8 18:40:19 2024 -- 0.90 0.24 0.00 0.00 -- 2b17ca85-f635-4589-b43a-2aae1ad180b2\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 18:40:18", "plugin": "core", "name": "start_epoch", "raw_value": "1731091218.0000000"}, {"title": "Job End Time", "value": "2024-11-08 18:40:19", "plugin": "core", "name": "end_epoch", "raw_value": "1731091219.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "umi_tools_count/1.1.2+galaxy2-5", "has_data": true, "data": {"tool_id": "umi_tools_count", "tool_version": "1.1.2+galaxy2", "test_index": 5, "time_seconds": 37.86532783508301, "inputs": {"input": {"src": "hda", "id": "c38e9d52f41984f4"}, "umi|method": "unique", "sc|gene_tag": "XT", "sc|per_cell": true, "advanced|random_seed": "0", "cond_extra|custom_label": "test", "cond_extra|prepender": "string"}, "job": {"model_class": "Job", "id": "c38e9d52f41984f4", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T18:44:19.593161", "update_time": "2024-11-08T18:44:34.406820", "galaxy_version": "24.1", "external_id": "gxy-lm5wk", "handler": null, "job_runner_name": null, "command_line": "ln -sf '/galaxy/server/database/objects/e/e/2/dataset_ee2e5e41-0daf-4b57-9e04-4a7fbd4f7841.dat' 'input.bam' && ln -sf '/galaxy/server/database/objects/_metadata_files/7/1/6/metadata_716b090b-f29c-4557-b9c5-ad42fc3b6784.dat' 'input.bam.bai' && umi_tools count '--wide-format-cell-counts' --extract-umi-method read_id --umi-separator '_' --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag 'XT' --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed='0' -I 'input.bam' -S '/galaxy/server/database/objects/d/9/7/dataset_d979a622-7e94-4624-81ae-da2d7f772b58.dat' --log2stderr && sed -i -r '1s|\\b([ACGT]+)\\b|'\"test\"'_\\1|g' '/galaxy/server/database/objects/d/9/7/dataset_d979a622-7e94-4624-81ae-da2d7f772b58.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "log": "false", "cond_extra": "{\"__current_case__\": 2, \"custom_label\": \"test\", \"prepender\": \"string\"}", "advanced": "{\"random_seed\": \"0\"}", "sc": "{\"assigned_status_tag\": null, \"gene_tag\": \"XT\", \"gene_transcript_map\": null, \"per_cell\": true, \"per_contig\": false, \"skip_tags_regex\": \"\"}", "sambam": "{\"chimeric_pairs\": null, \"chrom\": \"\", \"ignore_tlen\": false, \"ignore_umi\": false, \"mapping_quality\": \"0\", \"paired\": false, \"subset\": \"1.0\", \"unmapped_reads\": \"discard\", \"unpaired_reads\": null}", "umi": "{\"edit_distance_threshold\": \"1\", \"method\": \"unique\", \"read_length\": false, \"soft_clip_threshold\": \"4\", \"spliced_is_unique\": false}", "bc": "{\"__current_case__\": 0, \"extract_umi_method\": \"read_id\", \"umi_separator\": \"_\"}", "wide_format_cell_counts": "true"}, "inputs": {"input": {"id": "c38e9d52f41984f4", "src": "hda", "uuid": "ee2e5e41-0daf-4b57-9e04-4a7fbd4f7841"}}, "outputs": {"out_counts": {"id": "ed16242a8734824d", "src": "hda", "uuid": "d979a622-7e94-4624-81ae-da2d7f772b58"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "# UMI-tools version: 1.1.2\n# output generated by count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/d/9/7/dataset_d979a622-7e94-4624-81ae-da2d7f772b58.dat --log2stderr\n# job started at Fri Nov 8 18:44:22 2024 on gxy-lm5wk-9tqnp -- 6257156b-c2eb-47a4-bb56-6062de6eaa07\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XT\n# gene_transcript_map : None\n# get_umi_method : read_id\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : unique\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : True\n# per_contig : False\n# per_gene : False\n# random_seed : 0\n# read_length : False\n# short_help : None\n# skip_regex : ^(__|Unassigned)\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/d/9/7/dataset_d979a622-7e94-4624-81ae-da2d7f772b58.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : True\n2024-11-08 18:44:22,602 INFO command: count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/d/9/7/dataset_d979a622-7e94-4624-81ae-da2d7f772b58.dat --log2stderr\n2024-11-08 18:44:22,618 INFO Input Reads: 39\n2024-11-08 18:44:22,618 INFO Number of (post deduplication) reads counted: 12\n# job finished in 0 seconds at Fri Nov 8 18:44:22 2024 -- 0.89 0.24 0.00 0.00 -- 6257156b-c2eb-47a4-bb56-6062de6eaa07\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "# UMI-tools version: 1.1.2\n# output generated by count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/d/9/7/dataset_d979a622-7e94-4624-81ae-da2d7f772b58.dat --log2stderr\n# job started at Fri Nov 8 18:44:22 2024 on gxy-lm5wk-9tqnp -- 6257156b-c2eb-47a4-bb56-6062de6eaa07\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XT\n# gene_transcript_map : None\n# get_umi_method : read_id\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : unique\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : True\n# per_contig : False\n# per_gene : False\n# random_seed : 0\n# read_length : False\n# short_help : None\n# skip_regex : ^(__|Unassigned)\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/d/9/7/dataset_d979a622-7e94-4624-81ae-da2d7f772b58.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : True\n2024-11-08 18:44:22,602 INFO command: count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/d/9/7/dataset_d979a622-7e94-4624-81ae-da2d7f772b58.dat --log2stderr\n2024-11-08 18:44:22,618 INFO Input Reads: 39\n2024-11-08 18:44:22,618 INFO Number of (post deduplication) reads counted: 12\n# job finished in 0 seconds at Fri Nov 8 18:44:22 2024 -- 0.89 0.24 0.00 0.00 -- 6257156b-c2eb-47a4-bb56-6062de6eaa07\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 18:44:21", "plugin": "core", "name": "start_epoch", "raw_value": "1731091461.0000000"}, {"title": "Job End Time", "value": "2024-11-08 18:44:22", "plugin": "core", "name": "end_epoch", "raw_value": "1731091462.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "umi_tools_count/1.1.2+galaxy2-5", "has_data": true, "data": {"tool_id": "umi_tools_count", "tool_version": "1.1.2+galaxy2", "test_index": 5, "time_seconds": 37.90581488609314, "inputs": {"input": {"src": "hda", "id": "351c968571fdaf8f"}, "umi|method": "unique", "sc|gene_tag": "XT", "sc|per_cell": true, "advanced|random_seed": "0", "cond_extra|custom_label": "test", "cond_extra|prepender": "string"}, "job": {"model_class": "Job", "id": "351c968571fdaf8f", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T18:48:40.409399", "update_time": "2024-11-08T18:48:56.156382", "galaxy_version": "24.1", "external_id": "gxy-qrbxz", "handler": null, "job_runner_name": null, "command_line": "ln -sf '/galaxy/server/database/objects/b/8/4/dataset_b8486c99-aebd-4056-8ce0-7ab57e64acdd.dat' 'input.bam' && ln -sf '/galaxy/server/database/objects/_metadata_files/8/0/e/metadata_80ed77ba-3fa1-4b11-a5a8-fc79796ea8f6.dat' 'input.bam.bai' && umi_tools count '--wide-format-cell-counts' --extract-umi-method read_id --umi-separator '_' --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag 'XT' --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed='0' -I 'input.bam' -S '/galaxy/server/database/objects/b/c/f/dataset_bcfc4ac0-af50-4784-a6d4-ae66016b6e41.dat' --log2stderr && sed -i -r '1s|\\b([ACGT]+)\\b|'\"test\"'_\\1|g' '/galaxy/server/database/objects/b/c/f/dataset_bcfc4ac0-af50-4784-a6d4-ae66016b6e41.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "log": "false", "cond_extra": "{\"__current_case__\": 2, \"custom_label\": \"test\", \"prepender\": \"string\"}", "advanced": "{\"random_seed\": \"0\"}", "sc": "{\"assigned_status_tag\": null, \"gene_tag\": \"XT\", \"gene_transcript_map\": null, \"per_cell\": true, \"per_contig\": false, \"skip_tags_regex\": \"\"}", "sambam": "{\"chimeric_pairs\": null, \"chrom\": \"\", \"ignore_tlen\": false, \"ignore_umi\": false, \"mapping_quality\": \"0\", \"paired\": false, \"subset\": \"1.0\", \"unmapped_reads\": \"discard\", \"unpaired_reads\": null}", "umi": "{\"edit_distance_threshold\": \"1\", \"method\": \"unique\", \"read_length\": false, \"soft_clip_threshold\": \"4\", \"spliced_is_unique\": false}", "bc": "{\"__current_case__\": 0, \"extract_umi_method\": \"read_id\", \"umi_separator\": \"_\"}", "wide_format_cell_counts": "true"}, "inputs": {"input": {"id": "351c968571fdaf8f", "src": "hda", "uuid": "b8486c99-aebd-4056-8ce0-7ab57e64acdd"}}, "outputs": {"out_counts": {"id": "0b5bd7178ae007a7", "src": "hda", "uuid": "bcfc4ac0-af50-4784-a6d4-ae66016b6e41"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "# UMI-tools version: 1.1.2\n# output generated by count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/b/c/f/dataset_bcfc4ac0-af50-4784-a6d4-ae66016b6e41.dat --log2stderr\n# job started at Fri Nov 8 18:48:43 2024 on gxy-qrbxz-rnsnm -- b993f077-cb20-458a-92d5-d8ed8defdeb3\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XT\n# gene_transcript_map : None\n# get_umi_method : read_id\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : unique\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : True\n# per_contig : False\n# per_gene : False\n# random_seed : 0\n# read_length : False\n# short_help : None\n# skip_regex : ^(__|Unassigned)\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/b/c/f/dataset_bcfc4ac0-af50-4784-a6d4-ae66016b6e41.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : True\n2024-11-08 18:48:43,407 INFO command: count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/b/c/f/dataset_bcfc4ac0-af50-4784-a6d4-ae66016b6e41.dat --log2stderr\n2024-11-08 18:48:43,423 INFO Input Reads: 39\n2024-11-08 18:48:43,423 INFO Number of (post deduplication) reads counted: 12\n# job finished in 0 seconds at Fri Nov 8 18:48:43 2024 -- 0.90 0.24 0.00 0.00 -- b993f077-cb20-458a-92d5-d8ed8defdeb3\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "# UMI-tools version: 1.1.2\n# output generated by count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/b/c/f/dataset_bcfc4ac0-af50-4784-a6d4-ae66016b6e41.dat --log2stderr\n# job started at Fri Nov 8 18:48:43 2024 on gxy-qrbxz-rnsnm -- b993f077-cb20-458a-92d5-d8ed8defdeb3\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XT\n# gene_transcript_map : None\n# get_umi_method : read_id\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : unique\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : True\n# per_contig : False\n# per_gene : False\n# random_seed : 0\n# read_length : False\n# short_help : None\n# skip_regex : ^(__|Unassigned)\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/b/c/f/dataset_bcfc4ac0-af50-4784-a6d4-ae66016b6e41.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : True\n2024-11-08 18:48:43,407 INFO command: count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/b/c/f/dataset_bcfc4ac0-af50-4784-a6d4-ae66016b6e41.dat --log2stderr\n2024-11-08 18:48:43,423 INFO Input Reads: 39\n2024-11-08 18:48:43,423 INFO Number of (post deduplication) reads counted: 12\n# job finished in 0 seconds at Fri Nov 8 18:48:43 2024 -- 0.90 0.24 0.00 0.00 -- b993f077-cb20-458a-92d5-d8ed8defdeb3\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-08 18:48:43", "plugin": "core", "name": "end_epoch", "raw_value": "1731091723.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 18:48:42", "plugin": "core", "name": "start_epoch", "raw_value": "1731091722.0000000"}, {"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": "umi_tools_count/1.1.2+galaxy2-6", "has_data": true, "data": {"tool_id": "umi_tools_count", "tool_version": "1.1.2+galaxy2", "test_index": 6, "time_seconds": 37.52053165435791, "inputs": {"input": {"src": "hda", "id": "82894f0672bbd4e7"}, "umi|method": "unique", "sc|gene_tag": "XT", "sc|per_cell": true, "advanced|random_seed": "0", "cond_extra|prepender": "dataset name"}, "job": {"model_class": "Job", "id": "82894f0672bbd4e7", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T18:40:53.316748", "update_time": "2024-11-08T18:41:09.472788", "galaxy_version": "24.1", "external_id": "gxy-zqx7k", "handler": null, "job_runner_name": null, "command_line": "ln -sf '/galaxy/server/database/objects/b/4/3/dataset_b43bec0e-5bf3-43a3-bbac-546416cfca1b.dat' 'input.bam' && ln -sf '/galaxy/server/database/objects/_metadata_files/7/1/9/metadata_719bf64f-7880-4efa-87d9-be4579f46156.dat' 'input.bam.bai' && umi_tools count '--wide-format-cell-counts' --extract-umi-method read_id --umi-separator '_' --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag 'XT' --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed='0' -I 'input.bam' -S '/galaxy/server/database/objects/9/a/1/dataset_9a1b1809-af6d-4d41-bc04-f052f3869925.dat' --log2stderr && sed -i -r '1s|\\b([ACGT]+)\\b|'\"fc_ENSDARG00000019692\"'_\\1|g' '/galaxy/server/database/objects/9/a/1/dataset_9a1b1809-af6d-4d41-bc04-f052f3869925.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"wide_format_cell_counts": "true", "bc": "{\"__current_case__\": 0, \"extract_umi_method\": \"read_id\", \"umi_separator\": \"_\"}", "umi": "{\"edit_distance_threshold\": \"1\", \"method\": \"unique\", \"read_length\": false, \"soft_clip_threshold\": \"4\", \"spliced_is_unique\": false}", "sambam": "{\"chimeric_pairs\": null, \"chrom\": \"\", \"ignore_tlen\": false, \"ignore_umi\": false, \"mapping_quality\": \"0\", \"paired\": false, \"subset\": \"1.0\", \"unmapped_reads\": \"discard\", \"unpaired_reads\": null}", "sc": "{\"assigned_status_tag\": null, \"gene_tag\": \"XT\", \"gene_transcript_map\": null, \"per_cell\": true, \"per_contig\": false, \"skip_tags_regex\": \"\"}", "advanced": "{\"random_seed\": \"0\"}", "cond_extra": "{\"__current_case__\": 1, \"prepender\": \"dataset name\"}", "log": "false", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"input\""}, "inputs": {"input": {"id": "82894f0672bbd4e7", "src": "hda", "uuid": "b43bec0e-5bf3-43a3-bbac-546416cfca1b"}}, "outputs": {"out_counts": {"id": "9ec278895232d16d", "src": "hda", "uuid": "9a1b1809-af6d-4d41-bc04-f052f3869925"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "# UMI-tools version: 1.1.2\n# output generated by count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/9/a/1/dataset_9a1b1809-af6d-4d41-bc04-f052f3869925.dat --log2stderr\n# job started at Fri Nov 8 18:40:56 2024 on gxy-zqx7k-vvsqg -- 5ca1a857-45e6-46de-9514-80119ce9d707\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XT\n# gene_transcript_map : None\n# get_umi_method : read_id\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : unique\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : True\n# per_contig : False\n# per_gene : False\n# random_seed : 0\n# read_length : False\n# short_help : None\n# skip_regex : ^(__|Unassigned)\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/9/a/1/dataset_9a1b1809-af6d-4d41-bc04-f052f3869925.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : True\n2024-11-08 18:40:56,456 INFO command: count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/9/a/1/dataset_9a1b1809-af6d-4d41-bc04-f052f3869925.dat --log2stderr\n2024-11-08 18:40:56,472 INFO Input Reads: 39\n2024-11-08 18:40:56,472 INFO Number of (post deduplication) reads counted: 12\n# job finished in 0 seconds at Fri Nov 8 18:40:56 2024 -- 0.89 0.29 0.00 0.00 -- 5ca1a857-45e6-46de-9514-80119ce9d707\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "# UMI-tools version: 1.1.2\n# output generated by count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/9/a/1/dataset_9a1b1809-af6d-4d41-bc04-f052f3869925.dat --log2stderr\n# job started at Fri Nov 8 18:40:56 2024 on gxy-zqx7k-vvsqg -- 5ca1a857-45e6-46de-9514-80119ce9d707\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XT\n# gene_transcript_map : None\n# get_umi_method : read_id\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : unique\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : True\n# per_contig : False\n# per_gene : False\n# random_seed : 0\n# read_length : False\n# short_help : None\n# skip_regex : ^(__|Unassigned)\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/9/a/1/dataset_9a1b1809-af6d-4d41-bc04-f052f3869925.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : True\n2024-11-08 18:40:56,456 INFO command: count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/9/a/1/dataset_9a1b1809-af6d-4d41-bc04-f052f3869925.dat --log2stderr\n2024-11-08 18:40:56,472 INFO Input Reads: 39\n2024-11-08 18:40:56,472 INFO Number of (post deduplication) reads counted: 12\n# job finished in 0 seconds at Fri Nov 8 18:40:56 2024 -- 0.89 0.29 0.00 0.00 -- 5ca1a857-45e6-46de-9514-80119ce9d707\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 18:40:55", "plugin": "core", "name": "start_epoch", "raw_value": "1731091255.0000000"}, {"title": "Job End Time", "value": "2024-11-08 18:40:56", "plugin": "core", "name": "end_epoch", "raw_value": "1731091256.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "umi_tools_count/1.1.2+galaxy2-6", "has_data": true, "data": {"tool_id": "umi_tools_count", "tool_version": "1.1.2+galaxy2", "test_index": 6, "time_seconds": 37.54647970199585, "inputs": {"input": {"src": "hda", "id": "437fd7ddaa458bac"}, "umi|method": "unique", "sc|gene_tag": "XT", "sc|per_cell": true, "advanced|random_seed": "0", "cond_extra|prepender": "dataset name"}, "job": {"model_class": "Job", "id": "437fd7ddaa458bac", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T18:44:56.889021", "update_time": "2024-11-08T18:45:12.019658", "galaxy_version": "24.1", "external_id": "gxy-cnr46", "handler": null, "job_runner_name": null, "command_line": "ln -sf '/galaxy/server/database/objects/b/0/5/dataset_b053392b-12d9-45c5-8c84-07acf75fb486.dat' 'input.bam' && ln -sf '/galaxy/server/database/objects/_metadata_files/6/6/f/metadata_66f6315f-6482-4c50-8a04-bb42bf75db33.dat' 'input.bam.bai' && umi_tools count '--wide-format-cell-counts' --extract-umi-method read_id --umi-separator '_' --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag 'XT' --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed='0' -I 'input.bam' -S '/galaxy/server/database/objects/7/d/0/dataset_7d08569a-221a-4071-a084-092d13ee748f.dat' --log2stderr && sed -i -r '1s|\\b([ACGT]+)\\b|'\"fc_ENSDARG00000019692\"'_\\1|g' '/galaxy/server/database/objects/7/d/0/dataset_7d08569a-221a-4071-a084-092d13ee748f.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "log": "false", "cond_extra": "{\"__current_case__\": 1, \"prepender\": \"dataset name\"}", "advanced": "{\"random_seed\": \"0\"}", "sc": "{\"assigned_status_tag\": null, \"gene_tag\": \"XT\", \"gene_transcript_map\": null, \"per_cell\": true, \"per_contig\": false, \"skip_tags_regex\": \"\"}", "sambam": "{\"chimeric_pairs\": null, \"chrom\": \"\", \"ignore_tlen\": false, \"ignore_umi\": false, \"mapping_quality\": \"0\", \"paired\": false, \"subset\": \"1.0\", \"unmapped_reads\": \"discard\", \"unpaired_reads\": null}", "umi": "{\"edit_distance_threshold\": \"1\", \"method\": \"unique\", \"read_length\": false, \"soft_clip_threshold\": \"4\", \"spliced_is_unique\": false}", "bc": "{\"__current_case__\": 0, \"extract_umi_method\": \"read_id\", \"umi_separator\": \"_\"}", "wide_format_cell_counts": "true"}, "inputs": {"input": {"id": "437fd7ddaa458bac", "src": "hda", "uuid": "b053392b-12d9-45c5-8c84-07acf75fb486"}}, "outputs": {"out_counts": {"id": "c5500d2376344183", "src": "hda", "uuid": "7d08569a-221a-4071-a084-092d13ee748f"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "# UMI-tools version: 1.1.2\n# output generated by count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/7/d/0/dataset_7d08569a-221a-4071-a084-092d13ee748f.dat --log2stderr\n# job started at Fri Nov 8 18:44:59 2024 on gxy-cnr46-n2stk -- e3cf75d3-e016-47d9-a043-7b987acbdb2c\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XT\n# gene_transcript_map : None\n# get_umi_method : read_id\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : unique\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : True\n# per_contig : False\n# per_gene : False\n# random_seed : 0\n# read_length : False\n# short_help : None\n# skip_regex : ^(__|Unassigned)\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/7/d/0/dataset_7d08569a-221a-4071-a084-092d13ee748f.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : True\n2024-11-08 18:44:59,518 INFO command: count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/7/d/0/dataset_7d08569a-221a-4071-a084-092d13ee748f.dat --log2stderr\n2024-11-08 18:44:59,533 INFO Input Reads: 39\n2024-11-08 18:44:59,533 INFO Number of (post deduplication) reads counted: 12\n# job finished in 0 seconds at Fri Nov 8 18:44:59 2024 -- 0.88 0.24 0.00 0.00 -- e3cf75d3-e016-47d9-a043-7b987acbdb2c\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "# UMI-tools version: 1.1.2\n# output generated by count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/7/d/0/dataset_7d08569a-221a-4071-a084-092d13ee748f.dat --log2stderr\n# job started at Fri Nov 8 18:44:59 2024 on gxy-cnr46-n2stk -- e3cf75d3-e016-47d9-a043-7b987acbdb2c\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XT\n# gene_transcript_map : None\n# get_umi_method : read_id\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : unique\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : True\n# per_contig : False\n# per_gene : False\n# random_seed : 0\n# read_length : False\n# short_help : None\n# skip_regex : ^(__|Unassigned)\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/7/d/0/dataset_7d08569a-221a-4071-a084-092d13ee748f.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : True\n2024-11-08 18:44:59,518 INFO command: count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/7/d/0/dataset_7d08569a-221a-4071-a084-092d13ee748f.dat --log2stderr\n2024-11-08 18:44:59,533 INFO Input Reads: 39\n2024-11-08 18:44:59,533 INFO Number of (post deduplication) reads counted: 12\n# job finished in 0 seconds at Fri Nov 8 18:44:59 2024 -- 0.88 0.24 0.00 0.00 -- e3cf75d3-e016-47d9-a043-7b987acbdb2c\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 18:44:58", "plugin": "core", "name": "start_epoch", "raw_value": "1731091498.0000000"}, {"title": "Job End Time", "value": "2024-11-08 18:44:59", "plugin": "core", "name": "end_epoch", "raw_value": "1731091499.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "umi_tools_count/1.1.2+galaxy2-6", "has_data": true, "data": {"tool_id": "umi_tools_count", "tool_version": "1.1.2+galaxy2", "test_index": 6, "time_seconds": 37.691153049468994, "inputs": {"input": {"src": "hda", "id": "0cb54a770db60309"}, "umi|method": "unique", "sc|gene_tag": "XT", "sc|per_cell": true, "advanced|random_seed": "0", "cond_extra|prepender": "dataset name"}, "job": {"model_class": "Job", "id": "0cb54a770db60309", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T18:49:18.696552", "update_time": "2024-11-08T18:49:33.966712", "galaxy_version": "24.1", "external_id": "gxy-v8kvf", "handler": null, "job_runner_name": null, "command_line": "ln -sf '/galaxy/server/database/objects/2/b/0/dataset_2b0c6c61-b6f5-4359-9ce6-b92ceb25e779.dat' 'input.bam' && ln -sf '/galaxy/server/database/objects/_metadata_files/c/5/3/metadata_c5340760-ee42-4230-9840-cf81c4bea07b.dat' 'input.bam.bai' && umi_tools count '--wide-format-cell-counts' --extract-umi-method read_id --umi-separator '_' --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag 'XT' --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed='0' -I 'input.bam' -S '/galaxy/server/database/objects/8/a/d/dataset_8adc2b5b-a32d-4071-b542-1585d58766c5.dat' --log2stderr && sed -i -r '1s|\\b([ACGT]+)\\b|'\"fc_ENSDARG00000019692\"'_\\1|g' '/galaxy/server/database/objects/8/a/d/dataset_8adc2b5b-a32d-4071-b542-1585d58766c5.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "log": "false", "cond_extra": "{\"__current_case__\": 1, \"prepender\": \"dataset name\"}", "advanced": "{\"random_seed\": \"0\"}", "sc": "{\"assigned_status_tag\": null, \"gene_tag\": \"XT\", \"gene_transcript_map\": null, \"per_cell\": true, \"per_contig\": false, \"skip_tags_regex\": \"\"}", "sambam": "{\"chimeric_pairs\": null, \"chrom\": \"\", \"ignore_tlen\": false, \"ignore_umi\": false, \"mapping_quality\": \"0\", \"paired\": false, \"subset\": \"1.0\", \"unmapped_reads\": \"discard\", \"unpaired_reads\": null}", "umi": "{\"edit_distance_threshold\": \"1\", \"method\": \"unique\", \"read_length\": false, \"soft_clip_threshold\": \"4\", \"spliced_is_unique\": false}", "bc": "{\"__current_case__\": 0, \"extract_umi_method\": \"read_id\", \"umi_separator\": \"_\"}", "wide_format_cell_counts": "true"}, "inputs": {"input": {"id": "0cb54a770db60309", "src": "hda", "uuid": "2b0c6c61-b6f5-4359-9ce6-b92ceb25e779"}}, "outputs": {"out_counts": {"id": "0bf0f38e1e757713", "src": "hda", "uuid": "8adc2b5b-a32d-4071-b542-1585d58766c5"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "# UMI-tools version: 1.1.2\n# output generated by count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/8/a/d/dataset_8adc2b5b-a32d-4071-b542-1585d58766c5.dat --log2stderr\n# job started at Fri Nov 8 18:49:21 2024 on gxy-v8kvf-nq9qg -- 0325cc41-5501-4892-b4ab-1b1cafb8c218\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XT\n# gene_transcript_map : None\n# get_umi_method : read_id\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : unique\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : True\n# per_contig : False\n# per_gene : False\n# random_seed : 0\n# read_length : False\n# short_help : None\n# skip_regex : ^(__|Unassigned)\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/8/a/d/dataset_8adc2b5b-a32d-4071-b542-1585d58766c5.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : True\n2024-11-08 18:49:21,109 INFO command: count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/8/a/d/dataset_8adc2b5b-a32d-4071-b542-1585d58766c5.dat --log2stderr\n2024-11-08 18:49:21,126 INFO Input Reads: 39\n2024-11-08 18:49:21,126 INFO Number of (post deduplication) reads counted: 12\n# job finished in 0 seconds at Fri Nov 8 18:49:21 2024 -- 0.86 0.23 0.00 0.00 -- 0325cc41-5501-4892-b4ab-1b1cafb8c218\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "# UMI-tools version: 1.1.2\n# output generated by count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/8/a/d/dataset_8adc2b5b-a32d-4071-b542-1585d58766c5.dat --log2stderr\n# job started at Fri Nov 8 18:49:21 2024 on gxy-v8kvf-nq9qg -- 0325cc41-5501-4892-b4ab-1b1cafb8c218\n# pid: 25, system: Linux 6.1.100+ #1 SMP PREEMPT_DYNAMIC Sat Aug 24 16:19:44 UTC 2024 x86_64\n# assigned_tag : None\n# cell_tag : None\n# cell_tag_delim : None\n# cell_tag_split : -\n# chimeric_pairs : use\n# chrom : None\n# compresslevel : 6\n# filter_umi : None\n# gene_tag : XT\n# gene_transcript_map : None\n# get_umi_method : read_id\n# ignore_tlen : False\n# ignore_umi : False\n# in_sam : False\n# log2stderr : True\n# loglevel : 1\n# mapping_quality : 0\n# method : unique\n# no_sort_output : False\n# out_sam : False\n# output_unmapped : False\n# paired : False\n# per_cell : True\n# per_contig : False\n# per_gene : False\n# random_seed : 0\n# read_length : False\n# short_help : None\n# skip_regex : ^(__|Unassigned)\n# soft_clip_threshold : 4.0\n# spliced : False\n# stderr : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'>\n# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'>\n# stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/8/a/d/dataset_8adc2b5b-a32d-4071-b542-1585d58766c5.dat' mode='w' encoding='UTF-8'>\n# subset : 1.0\n# threshold : 1\n# timeit_file : None\n# timeit_header : None\n# timeit_name : all\n# tmpdir : None\n# umi_sep : _\n# umi_tag : RX\n# umi_tag_delim : None\n# umi_tag_split : None\n# umi_whitelist : None\n# umi_whitelist_paired : None\n# unmapped_reads : discard\n# unpaired_reads : use\n# wide_format_cell_counts : True\n2024-11-08 18:49:21,109 INFO command: count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/8/a/d/dataset_8adc2b5b-a32d-4071-b542-1585d58766c5.dat --log2stderr\n2024-11-08 18:49:21,126 INFO Input Reads: 39\n2024-11-08 18:49:21,126 INFO Number of (post deduplication) reads counted: 12\n# job finished in 0 seconds at Fri Nov 8 18:49:21 2024 -- 0.86 0.23 0.00 0.00 -- 0325cc41-5501-4892-b4ab-1b1cafb8c218\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-11-08 18:49:21", "plugin": "core", "name": "end_epoch", "raw_value": "1731091761.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 18:49:19", "plugin": "core", "name": "start_epoch", "raw_value": "1731091759.0000000"}, {"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": "vcfallelicprimitives/1.0.0_rc3+galaxy0-0", "has_data": true, "data": {"tool_id": "vcfallelicprimitives", "tool_version": "1.0.0_rc3+galaxy0", "test_index": 0, "time_seconds": 44.46969270706177, "inputs": {"input": {"src": "hda", "id": "56885fa78255373a"}}, "job": {"model_class": "Job", "id": "3c8904a39cba5a6b", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:40:02.464947", "update_time": "2024-11-08T19:40:24.258500", "galaxy_version": "24.1", "external_id": "gxy-hwhjm", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/objects/2/6/9/dataset_2699b45b-0019-4a4c-948e-fe4f81d97ade.dat' | vcfallelicprimitives -t 'Split primitives' -L \"200\" > '/galaxy/server/database/objects/e/8/5/dataset_e850dc44-7ee4-4370-8de9-f6d690fe8194.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "keep_geno": "false", "keep_info": "false", "max_length": "\"200\"", "t_option": "\"Split primitives\"", "m_option": "false"}, "inputs": {"input": {"id": "56885fa78255373a", "src": "hda", "uuid": "2699b45b-0019-4a4c-948e-fe4f81d97ade"}}, "outputs": {"out_file1": {"id": "dd1f813fd25574d2", "src": "hda", "uuid": "e850dc44-7ee4-4370-8de9-f6d690fe8194"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-11-08 19:40:10", "plugin": "core", "name": "end_epoch", "raw_value": "1731094810.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:40:10", "plugin": "core", "name": "start_epoch", "raw_value": "1731094810.0000000"}, {"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": "vcfprimers/1.0.0_rc3+galaxy0-0", "has_data": true, "data": {"tool_id": "vcfprimers", "tool_version": "1.0.0_rc3+galaxy0", "test_index": 0, "time_seconds": 36.36902070045471, "inputs": {"input_vcf": {"src": "hda", "id": "c7ce3f1ce57966e8"}, "reference_source|ref_file": {"src": "hda", "id": "828283ee416f5ba9"}, "reference_source|reference_source_selector": "history", "primer_length": "5"}, "job": {"model_class": "Job", "id": "e3071098709962db", "history_id": "da7414b0e37eac28", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc3+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-11-08T19:40:47.269159", "update_time": "2024-11-08T19:41:01.784675", "galaxy_version": "24.1", "external_id": "gxy-mlp54", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/7/6/4/dataset_764569bf-1e20-41b3-b8f2-11f789d0d1be.dat' 'localref.fa' && vcfprimers -f 'localref.fa' -l \"5\" '/galaxy/server/database/objects/2/2/0/dataset_22050ea6-aa25-43f8-8925-c2fca68d7894.dat' > '/galaxy/server/database/objects/4/7/9/dataset_479c4985-5f07-4e4c-930f-fb2b8d9d27b6.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "primer_length": "\"5\"", "reference_source": "{\"__current_case__\": 1, \"ref_file\": {\"values\": [{\"id\": 255, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"input_vcf": {"id": "c7ce3f1ce57966e8", "src": "hda", "uuid": "22050ea6-aa25-43f8-8925-c2fca68d7894"}, "reference_source|ref_file": {"id": "828283ee416f5ba9", "src": "hda", "uuid": "764569bf-1e20-41b3-b8f2-11f789d0d1be"}}, "outputs": {"out_file1": {"id": "f18fba88ddc9d8e4", "src": "hda", "uuid": "479c4985-5f07-4e4c-930f-fb2b8d9d27b6"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "index file localref.fa.fai not found, generating...\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "index file localref.fa.fai not found, generating...\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-11-08 19:40:49", "plugin": "core", "name": "end_epoch", "raw_value": "1731094849.0000000"}, {"title": "Job Start Time", "value": "2024-11-08 19:40:49", "plugin": "core", "name": "start_epoch", "raw_value": "1731094849.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}], "galaxy_url": "http://35.229.39.46:8000/galaxy/"} \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/results.xunit b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/results.xunit new file mode 100644 index 000000000..57fbb3c90 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/results.xunit @@ -0,0 +1,1280 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 times ---- 97 pairs aligned concordantly 0 times; of these: 8 (8.25%) aligned discordantly 1 time ---- 89 pairs aligned 0 times concordantly or discordantly; of these: 178 mates make up the pairs; of these: 153 (85.96%) aligned 0 times 25 (14.04%) aligned exactly 1 time 0 (0.00%) aligned >1 times23.50% overall alignment rate + ]]> + + + + + + + + + + + + + + 1 times ---- 97 pairs aligned concordantly 0 times; of these: 8 (8.25%) aligned discordantly 1 time ---- 89 pairs aligned 0 times concordantly or discordantly; of these: 178 mates make up the pairs; of these: 153 (85.96%) aligned 0 times 25 (14.04%) aligned exactly 1 time 0 (0.00%) aligned >1 times23.50% overall alignment rate + ]]> + + + + + + + + 1 times ---- 97 pairs aligned concordantly 0 times; of these: 8 (8.25%) aligned discordantly 1 time ---- 89 pairs aligned 0 times concordantly or discordantly; of these: 178 mates make up the pairs; of these: 153 (85.96%) aligned 0 times 25 (14.04%) aligned exactly 1 time 0 (0.00%) aligned >1 times23.50% overall alignment rate + ]]> + + + + + + + + 1 times ---- 2 pairs aligned concordantly 0 times; of these: 0 (0.00%) aligned discordantly 1 time ---- 2 pairs aligned 0 times concordantly or discordantly; of these: 4 mates make up the pairs; of these: 3 (75.00%) aligned 0 times 1 (25.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times50.00% overall alignment rate + ]]> + + + + + + + + 1 times ---- 97 pairs aligned concordantly 0 times; of these: 8 (8.25%) aligned discordantly 1 time ---- 89 pairs aligned 0 times concordantly or discordantly; of these: 178 mates make up the pairs; of these: 153 (85.96%) aligned 0 times 25 (14.04%) aligned exactly 1 time 0 (0.00%) aligned >1 times23.50% overall alignment rate + ]]> + + + + + + + + 1 times ---- 97 pairs aligned concordantly 0 times; of these: 8 (8.25%) aligned discordantly 1 time ---- 89 pairs aligned 0 times concordantly or discordantly; of these: 178 mates make up the pairs; of these: 153 (85.96%) aligned 0 times 25 (14.04%) aligned exactly 1 time 0 (0.00%) aligned >1 times23.50% overall alignment rate + ]]> + + + + + + + + 1 times ---- 97 pairs aligned concordantly 0 times; of these: 7 (7.22%) aligned discordantly 1 time ---- 90 pairs aligned 0 times concordantly or discordantly; of these: 180 mates make up the pairs; of these: 156 (86.67%) aligned 0 times 24 (13.33%) aligned exactly 1 time 0 (0.00%) aligned >1 times22.00% overall alignment rate + ]]> + + + + + + + + 1 times ---- 97 pairs aligned concordantly 0 times; of these: 7 (7.22%) aligned discordantly 1 time ---- 90 pairs aligned 0 times concordantly or discordantly; of these: 180 mates make up the pairs; of these: 156 (86.67%) aligned 0 times 24 (13.33%) aligned exactly 1 time 0 (0.00%) aligned >1 times22.00% overall alignment rate + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ' mode='w' encoding='utf-8'># stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'># stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'># stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/b/9/e/dataset_b9e32134-5bc7-4ccb-a6e2-0ac4cd7661c7.dat' mode='w' encoding='UTF-8'># subset : 1.0# threshold : 1# timeit_file : None# timeit_header : None# timeit_name : all# tmpdir : None# umi_sep : _# umi_tag : RX# umi_tag_delim : None# umi_tag_split : None# umi_whitelist : None# umi_whitelist_paired : None# unmapped_reads : discard# unpaired_reads : use# wide_format_cell_counts : False2024-11-08 18:37:04,792 INFO command: count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/b/9/e/dataset_b9e32134-5bc7-4ccb-a6e2-0ac4cd7661c7.dat --log2stderr2024-11-08 18:37:04,821 INFO Input Reads: 12032024-11-08 18:37:04,821 INFO Read skipped - assigned tag matches skip_regex: 1202024-11-08 18:37:04,821 INFO Number of (post deduplication) reads counted: 141# job finished in 0 seconds at Fri Nov 8 18:37:04 2024 -- 0.92 0.27 0.00 0.00 -- 6d88f1e9-b106-4dd4-921f-4cb2f48c723d + ]]> + + + + + + + + + + + + + + + + ' mode='w' encoding='utf-8'># stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'># stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'># stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/6/0/7/dataset_607b7381-aea4-427b-9e0d-2b6e9c81e40e.dat' mode='w' encoding='UTF-8'># subset : 1.0# threshold : 1# timeit_file : None# timeit_header : None# timeit_name : all# tmpdir : None# umi_sep : _# umi_tag : RX# umi_tag_delim : None# umi_tag_split : None# umi_whitelist : None# umi_whitelist_paired : None# unmapped_reads : discard# unpaired_reads : use# wide_format_cell_counts : False2024-11-08 18:45:38,561 INFO command: count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/6/0/7/dataset_607b7381-aea4-427b-9e0d-2b6e9c81e40e.dat --log2stderr2024-11-08 18:45:38,589 INFO Input Reads: 12032024-11-08 18:45:38,590 INFO Read skipped - assigned tag matches skip_regex: 1202024-11-08 18:45:38,590 INFO Number of (post deduplication) reads counted: 141# job finished in 0 seconds at Fri Nov 8 18:45:38 2024 -- 0.90 0.23 0.00 0.00 -- 2cd3b257-c856-43a8-9c4a-9f009e9641ab + ]]> + + + + + + + + ' mode='w' encoding='utf-8'># stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'># stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'># stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/7/d/4/dataset_7d46732b-cbf6-4414-8999-d16a224e5423.dat' mode='w' encoding='UTF-8'># subset : 1.0# threshold : 1# timeit_file : None# timeit_header : None# timeit_name : all# tmpdir : None# umi_sep : _# umi_tag : RX# umi_tag_delim : None# umi_tag_split : None# umi_whitelist : None# umi_whitelist_paired : None# unmapped_reads : discard# unpaired_reads : use# wide_format_cell_counts : False2024-11-08 18:37:49,194 INFO command: count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/7/d/4/dataset_7d46732b-cbf6-4414-8999-d16a224e5423.dat --log2stderr2024-11-08 18:37:49,222 INFO Input Reads: 12032024-11-08 18:37:49,223 INFO Read skipped - assigned tag matches skip_regex: 1202024-11-08 18:37:49,223 INFO Number of (post deduplication) reads counted: 141# job finished in 0 seconds at Fri Nov 8 18:37:49 2024 -- 0.90 0.25 0.00 0.00 -- d4ace035-9164-4138-bf57-71cda01eacf2 + ]]> + + + + + + + + ' mode='w' encoding='utf-8'># stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'># stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'># stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/e/9/9/dataset_e9964907-fa86-48ca-810e-fb7cbd0e38d8.dat' mode='w' encoding='UTF-8'># subset : 1.0# threshold : 1# timeit_file : None# timeit_header : None# timeit_name : all# tmpdir : None# umi_sep : _# umi_tag : RX# umi_tag_delim : None# umi_tag_split : None# umi_whitelist : None# umi_whitelist_paired : None# unmapped_reads : discard# unpaired_reads : use# wide_format_cell_counts : False2024-11-08 18:41:52,186 INFO command: count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/e/9/9/dataset_e9964907-fa86-48ca-810e-fb7cbd0e38d8.dat --log2stderr2024-11-08 18:41:52,214 INFO Input Reads: 12032024-11-08 18:41:52,214 INFO Read skipped - assigned tag matches skip_regex: 1202024-11-08 18:41:52,214 INFO Number of (post deduplication) reads counted: 141# job finished in 0 seconds at Fri Nov 8 18:41:52 2024 -- 0.90 0.24 0.00 0.00 -- bdc4883b-52a5-4efd-8af3-5a4d2c0cb28d + ]]> + + + + + + + + ' mode='w' encoding='utf-8'># stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'># stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'># stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/b/b/5/dataset_bb58c334-f594-4dc0-9168-510b49b31850.dat' mode='w' encoding='UTF-8'># subset : 1.0# threshold : 1# timeit_file : None# timeit_header : None# timeit_name : all# tmpdir : None# umi_sep : _# umi_tag : RX# umi_tag_delim : None# umi_tag_split : None# umi_whitelist : None# umi_whitelist_paired : None# unmapped_reads : discard# unpaired_reads : use# wide_format_cell_counts : False2024-11-08 18:46:09,070 INFO command: count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/b/b/5/dataset_bb58c334-f594-4dc0-9168-510b49b31850.dat --log2stderr2024-11-08 18:46:09,098 INFO Input Reads: 12032024-11-08 18:46:09,099 INFO Read skipped - assigned tag matches skip_regex: 1202024-11-08 18:46:09,099 INFO Number of (post deduplication) reads counted: 141# job finished in 0 seconds at Fri Nov 8 18:46:09 2024 -- 0.87 0.26 0.00 0.00 -- c0acac4b-fdcb-4f67-b212-0204d6fa07b2 + ]]> + + + + + + + + ' mode='w' encoding='utf-8'># stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'># stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'># stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/9/2/1/dataset_92189897-a6c8-4bd1-9fa9-6d7dcbdd3a74.dat' mode='w' encoding='UTF-8'># subset : 1.0# threshold : 1# timeit_file : None# timeit_header : None# timeit_name : all# tmpdir : None# umi_sep : _# umi_tag : RX# umi_tag_delim : None# umi_tag_split : None# umi_whitelist : None# umi_whitelist_paired : None# unmapped_reads : discard# unpaired_reads : use# wide_format_cell_counts : False2024-11-08 18:38:26,821 INFO command: count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/9/2/1/dataset_92189897-a6c8-4bd1-9fa9-6d7dcbdd3a74.dat --log2stderr2024-11-08 18:38:26,849 INFO Input Reads: 12032024-11-08 18:38:26,849 INFO Read skipped - assigned tag matches skip_regex: 1202024-11-08 18:38:26,849 INFO Number of (post deduplication) reads counted: 145# job finished in 0 seconds at Fri Nov 8 18:38:26 2024 -- 0.86 0.23 0.00 0.00 -- dff7d8f3-0081-4ea9-b9a5-3b41205b21c9 + ]]> + + + + + + + + ' mode='w' encoding='utf-8'># stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'># stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'># stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/d/b/6/dataset_db6bc940-2bdb-4498-ada9-c8694f3b0c66.dat' mode='w' encoding='UTF-8'># subset : 1.0# threshold : 1# timeit_file : None# timeit_header : None# timeit_name : all# tmpdir : None# umi_sep : _# umi_tag : RX# umi_tag_delim : None# umi_tag_split : None# umi_whitelist : None# umi_whitelist_paired : None# unmapped_reads : discard# unpaired_reads : use# wide_format_cell_counts : False2024-11-08 18:42:30,021 INFO command: count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/d/b/6/dataset_db6bc940-2bdb-4498-ada9-c8694f3b0c66.dat --log2stderr2024-11-08 18:42:30,051 INFO Input Reads: 12032024-11-08 18:42:30,051 INFO Read skipped - assigned tag matches skip_regex: 1202024-11-08 18:42:30,051 INFO Number of (post deduplication) reads counted: 145# job finished in 0 seconds at Fri Nov 8 18:42:30 2024 -- 0.91 0.26 0.00 0.00 -- 7bc01c24-b874-4fdd-b7c5-43521d327377 + ]]> + + + + + + + + ' mode='w' encoding='utf-8'># stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'># stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'># stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/c/c/9/dataset_cc97dc12-c60b-4e58-af17-928850ff5dbd.dat' mode='w' encoding='UTF-8'># subset : 1.0# threshold : 1# timeit_file : None# timeit_header : None# timeit_name : all# tmpdir : None# umi_sep : _# umi_tag : RX# umi_tag_delim : None# umi_tag_split : None# umi_whitelist : None# umi_whitelist_paired : None# unmapped_reads : discard# unpaired_reads : use# wide_format_cell_counts : False2024-11-08 18:46:47,795 INFO command: count --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/c/c/9/dataset_cc97dc12-c60b-4e58-af17-928850ff5dbd.dat --log2stderr2024-11-08 18:46:47,826 INFO Input Reads: 12032024-11-08 18:46:47,826 INFO Read skipped - assigned tag matches skip_regex: 1202024-11-08 18:46:47,826 INFO Number of (post deduplication) reads counted: 145# job finished in 0 seconds at Fri Nov 8 18:46:47 2024 -- 0.84 0.22 0.00 0.00 -- 632449aa-b5b7-48f6-9d52-f8b9745ecc04 + ]]> + + + + + + + + ' mode='w' encoding='utf-8'># stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'># stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'># stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/3/a/3/dataset_3a3e37cb-b9dd-42ae-ba0a-98aff24fbb52.dat' mode='w' encoding='UTF-8'># subset : 1.0# threshold : 1# timeit_file : None# timeit_header : None# timeit_name : all# tmpdir : None# umi_sep : _# umi_tag : RX# umi_tag_delim : None# umi_tag_split : None# umi_whitelist : None# umi_whitelist_paired : None# unmapped_reads : discard# unpaired_reads : use# wide_format_cell_counts : True2024-11-08 18:39:04,605 INFO command: count --wide-format-cell-counts --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/3/a/3/dataset_3a3e37cb-b9dd-42ae-ba0a-98aff24fbb52.dat --log2stderr2024-11-08 18:39:04,634 INFO Input Reads: 12032024-11-08 18:39:04,634 INFO Read skipped - assigned tag matches skip_regex: 1202024-11-08 18:39:04,634 INFO Number of (post deduplication) reads counted: 145# job finished in 0 seconds at Fri Nov 8 18:39:04 2024 -- 0.93 0.22 0.00 0.00 -- 1490743d-f989-4023-bea6-98ff7d414b90 + ]]> + + + + + + + + ' mode='w' encoding='utf-8'># stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'># stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'># stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/9/1/8/dataset_9183442b-26bf-4f17-a97f-1cae902ac8cc.dat' mode='w' encoding='UTF-8'># subset : 1.0# threshold : 1# timeit_file : None# timeit_header : None# timeit_name : all# tmpdir : None# umi_sep : _# umi_tag : RX# umi_tag_delim : None# umi_tag_split : None# umi_whitelist : None# umi_whitelist_paired : None# unmapped_reads : discard# unpaired_reads : use# wide_format_cell_counts : True2024-11-08 18:43:06,801 INFO command: count --wide-format-cell-counts --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/9/1/8/dataset_9183442b-26bf-4f17-a97f-1cae902ac8cc.dat --log2stderr2024-11-08 18:43:06,830 INFO Input Reads: 12032024-11-08 18:43:06,830 INFO Read skipped - assigned tag matches skip_regex: 1202024-11-08 18:43:06,830 INFO Number of (post deduplication) reads counted: 145# job finished in 0 seconds at Fri Nov 8 18:43:06 2024 -- 0.87 0.20 0.00 0.00 -- aafbc2f8-a108-47ca-be10-60949276e311 + ]]> + + + + + + + + ' mode='w' encoding='utf-8'># stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'># stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'># stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/7/1/9/dataset_71949ac5-2c52-4243-a97c-4dddad4757cf.dat' mode='w' encoding='UTF-8'># subset : 1.0# threshold : 1# timeit_file : None# timeit_header : None# timeit_name : all# tmpdir : None# umi_sep : _# umi_tag : RX# umi_tag_delim : None# umi_tag_split : None# umi_whitelist : None# umi_whitelist_paired : None# unmapped_reads : discard# unpaired_reads : use# wide_format_cell_counts : True2024-11-08 18:47:26,737 INFO command: count --wide-format-cell-counts --extract-umi-method umis --method directional --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XF --skip-tags-regex ^[__Unassigned] --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=123456789 -I input.bam -S /galaxy/server/database/objects/7/1/9/dataset_71949ac5-2c52-4243-a97c-4dddad4757cf.dat --log2stderr2024-11-08 18:47:26,768 INFO Input Reads: 12032024-11-08 18:47:26,768 INFO Read skipped - assigned tag matches skip_regex: 1202024-11-08 18:47:26,768 INFO Number of (post deduplication) reads counted: 145# job finished in 0 seconds at Fri Nov 8 18:47:26 2024 -- 0.91 0.23 0.00 0.00 -- 46d064eb-90f2-409c-8263-a43de9c454f7 + ]]> + + + + + + + + ' mode='w' encoding='utf-8'># stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'># stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'># stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/2/c/7/dataset_2c7c9321-c12e-46c2-9a10-1bf9ead756e4.dat' mode='w' encoding='UTF-8'># subset : 1.0# threshold : 1# timeit_file : None# timeit_header : None# timeit_name : all# tmpdir : None# umi_sep : _# umi_tag : RX# umi_tag_delim : None# umi_tag_split : None# umi_whitelist : None# umi_whitelist_paired : None# unmapped_reads : discard# unpaired_reads : use# wide_format_cell_counts : True2024-11-08 18:39:41,504 INFO command: count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/2/c/7/dataset_2c7c9321-c12e-46c2-9a10-1bf9ead756e4.dat --log2stderr2024-11-08 18:39:41,518 INFO Input Reads: 392024-11-08 18:39:41,518 INFO Number of (post deduplication) reads counted: 12# job finished in 0 seconds at Fri Nov 8 18:39:41 2024 -- 0.88 0.24 0.00 0.00 -- 05e5321d-dc62-44ae-957f-b3a473cd0546 + ]]> + + + + + + + + ' mode='w' encoding='utf-8'># stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'># stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'># stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/0/1/0/dataset_0106d85b-ef63-4314-a0af-e80860a2bd38.dat' mode='w' encoding='UTF-8'># subset : 1.0# threshold : 1# timeit_file : None# timeit_header : None# timeit_name : all# tmpdir : None# umi_sep : _# umi_tag : RX# umi_tag_delim : None# umi_tag_split : None# umi_whitelist : None# umi_whitelist_paired : None# unmapped_reads : discard# unpaired_reads : use# wide_format_cell_counts : True2024-11-08 18:43:44,568 INFO command: count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/0/1/0/dataset_0106d85b-ef63-4314-a0af-e80860a2bd38.dat --log2stderr2024-11-08 18:43:44,584 INFO Input Reads: 392024-11-08 18:43:44,584 INFO Number of (post deduplication) reads counted: 12# job finished in 0 seconds at Fri Nov 8 18:43:44 2024 -- 0.89 0.24 0.00 0.00 -- 68d00a58-6f8c-402c-9242-7829bfea6a36 + ]]> + + + + + + + + ' mode='w' encoding='utf-8'># stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'># stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'># stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/a/d/2/dataset_ad27d980-5c83-44d0-9679-d3208ff349c6.dat' mode='w' encoding='UTF-8'># subset : 1.0# threshold : 1# timeit_file : None# timeit_header : None# timeit_name : all# tmpdir : None# umi_sep : _# umi_tag : RX# umi_tag_delim : None# umi_tag_split : None# umi_whitelist : None# umi_whitelist_paired : None# unmapped_reads : discard# unpaired_reads : use# wide_format_cell_counts : True2024-11-08 18:48:05,504 INFO command: count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/a/d/2/dataset_ad27d980-5c83-44d0-9679-d3208ff349c6.dat --log2stderr2024-11-08 18:48:05,520 INFO Input Reads: 392024-11-08 18:48:05,520 INFO Number of (post deduplication) reads counted: 12# job finished in 0 seconds at Fri Nov 8 18:48:05 2024 -- 0.87 0.21 0.00 0.00 -- 2fb6e12f-ad3a-4329-80a4-37d97a731713 + ]]> + + + + + + + + ' mode='w' encoding='utf-8'># stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'># stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'># stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/f/7/f/dataset_f7f50908-1a95-4a3c-82c1-95af60f7d8b6.dat' mode='w' encoding='UTF-8'># subset : 1.0# threshold : 1# timeit_file : None# timeit_header : None# timeit_name : all# tmpdir : None# umi_sep : _# umi_tag : RX# umi_tag_delim : None# umi_tag_split : None# umi_whitelist : None# umi_whitelist_paired : None# unmapped_reads : discard# unpaired_reads : use# wide_format_cell_counts : True2024-11-08 18:40:19,583 INFO command: count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/f/7/f/dataset_f7f50908-1a95-4a3c-82c1-95af60f7d8b6.dat --log2stderr2024-11-08 18:40:19,598 INFO Input Reads: 392024-11-08 18:40:19,598 INFO Number of (post deduplication) reads counted: 12# job finished in 0 seconds at Fri Nov 8 18:40:19 2024 -- 0.90 0.24 0.00 0.00 -- 2b17ca85-f635-4589-b43a-2aae1ad180b2 + ]]> + + + + + + + + ' mode='w' encoding='utf-8'># stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'># stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'># stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/d/9/7/dataset_d979a622-7e94-4624-81ae-da2d7f772b58.dat' mode='w' encoding='UTF-8'># subset : 1.0# threshold : 1# timeit_file : None# timeit_header : None# timeit_name : all# tmpdir : None# umi_sep : _# umi_tag : RX# umi_tag_delim : None# umi_tag_split : None# umi_whitelist : None# umi_whitelist_paired : None# unmapped_reads : discard# unpaired_reads : use# wide_format_cell_counts : True2024-11-08 18:44:22,602 INFO command: count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/d/9/7/dataset_d979a622-7e94-4624-81ae-da2d7f772b58.dat --log2stderr2024-11-08 18:44:22,618 INFO Input Reads: 392024-11-08 18:44:22,618 INFO Number of (post deduplication) reads counted: 12# job finished in 0 seconds at Fri Nov 8 18:44:22 2024 -- 0.89 0.24 0.00 0.00 -- 6257156b-c2eb-47a4-bb56-6062de6eaa07 + ]]> + + + + + + + + ' mode='w' encoding='utf-8'># stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'># stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'># stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/b/c/f/dataset_bcfc4ac0-af50-4784-a6d4-ae66016b6e41.dat' mode='w' encoding='UTF-8'># subset : 1.0# threshold : 1# timeit_file : None# timeit_header : None# timeit_name : all# tmpdir : None# umi_sep : _# umi_tag : RX# umi_tag_delim : None# umi_tag_split : None# umi_whitelist : None# umi_whitelist_paired : None# unmapped_reads : discard# unpaired_reads : use# wide_format_cell_counts : True2024-11-08 18:48:43,407 INFO command: count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/b/c/f/dataset_bcfc4ac0-af50-4784-a6d4-ae66016b6e41.dat --log2stderr2024-11-08 18:48:43,423 INFO Input Reads: 392024-11-08 18:48:43,423 INFO Number of (post deduplication) reads counted: 12# job finished in 0 seconds at Fri Nov 8 18:48:43 2024 -- 0.90 0.24 0.00 0.00 -- b993f077-cb20-458a-92d5-d8ed8defdeb3 + ]]> + + + + + + + + ' mode='w' encoding='utf-8'># stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'># stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'># stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/9/a/1/dataset_9a1b1809-af6d-4d41-bc04-f052f3869925.dat' mode='w' encoding='UTF-8'># subset : 1.0# threshold : 1# timeit_file : None# timeit_header : None# timeit_name : all# tmpdir : None# umi_sep : _# umi_tag : RX# umi_tag_delim : None# umi_tag_split : None# umi_whitelist : None# umi_whitelist_paired : None# unmapped_reads : discard# unpaired_reads : use# wide_format_cell_counts : True2024-11-08 18:40:56,456 INFO command: count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/9/a/1/dataset_9a1b1809-af6d-4d41-bc04-f052f3869925.dat --log2stderr2024-11-08 18:40:56,472 INFO Input Reads: 392024-11-08 18:40:56,472 INFO Number of (post deduplication) reads counted: 12# job finished in 0 seconds at Fri Nov 8 18:40:56 2024 -- 0.89 0.29 0.00 0.00 -- 5ca1a857-45e6-46de-9514-80119ce9d707 + ]]> + + + + + + + + ' mode='w' encoding='utf-8'># stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'># stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'># stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/7/d/0/dataset_7d08569a-221a-4071-a084-092d13ee748f.dat' mode='w' encoding='UTF-8'># subset : 1.0# threshold : 1# timeit_file : None# timeit_header : None# timeit_name : all# tmpdir : None# umi_sep : _# umi_tag : RX# umi_tag_delim : None# umi_tag_split : None# umi_whitelist : None# umi_whitelist_paired : None# unmapped_reads : discard# unpaired_reads : use# wide_format_cell_counts : True2024-11-08 18:44:59,518 INFO command: count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/7/d/0/dataset_7d08569a-221a-4071-a084-092d13ee748f.dat --log2stderr2024-11-08 18:44:59,533 INFO Input Reads: 392024-11-08 18:44:59,533 INFO Number of (post deduplication) reads counted: 12# job finished in 0 seconds at Fri Nov 8 18:44:59 2024 -- 0.88 0.24 0.00 0.00 -- e3cf75d3-e016-47d9-a043-7b987acbdb2c + ]]> + + + + + + + + ' mode='w' encoding='utf-8'># stdin : <_io.TextIOWrapper name='input.bam' mode='r' encoding='UTF-8'># stdlog : <_io.TextIOWrapper name='' mode='w' encoding='utf-8'># stdout : <_io.TextIOWrapper name='/galaxy/server/database/objects/8/a/d/dataset_8adc2b5b-a32d-4071-b542-1585d58766c5.dat' mode='w' encoding='UTF-8'># subset : 1.0# threshold : 1# timeit_file : None# timeit_header : None# timeit_name : all# tmpdir : None# umi_sep : _# umi_tag : RX# umi_tag_delim : None# umi_tag_split : None# umi_whitelist : None# umi_whitelist_paired : None# unmapped_reads : discard# unpaired_reads : use# wide_format_cell_counts : True2024-11-08 18:49:21,109 INFO command: count --wide-format-cell-counts --extract-umi-method read_id --umi-separator _ --method unique --edit-distance-threshold 1 --soft-clip-threshold 4 --gene-tag XT --per-cell --mapping-quality 0 --unmapped-reads discard --subset 1.0 --random-seed=0 -I input.bam -S /galaxy/server/database/objects/8/a/d/dataset_8adc2b5b-a32d-4071-b542-1585d58766c5.dat --log2stderr2024-11-08 18:49:21,126 INFO Input Reads: 392024-11-08 18:49:21,126 INFO Number of (post deduplication) reads counted: 12# job finished in 0 seconds at Fri Nov 8 18:49:21 2024 -- 0.86 0.23 0.00 0.00 -- 0325cc41-5501-4892-b4ab-1b1cafb8c218 + ]]> + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/tools.yml b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/tools.yml new file mode 100644 index 000000000..7b092be18 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-11-08-18-17-1/tools.yml @@ -0,0 +1,128 @@ +chunk: 9 +tools: +- name: datamash_reverse + owner: iuc + revisions: + - f198773344e4 + tool_panel_section_id: datamash + tool_panel_section_label: Datamash +- name: deeptools_plot_enrichment + owner: bgruening + revisions: + - e65d16fb2724 + tool_panel_section_id: deeptools + tool_panel_section_label: deepTools +- name: umi_tools_count + owner: iuc + revisions: + - 8250ea3a1501 + - b557acca0b56 + - a535cf1e5da4 + tool_panel_section_id: fasta_fastq + tool_panel_section_label: FASTA/FASTQ +- name: bowtie2 + owner: devteam + revisions: + - 09b2cdb7ace5 + tool_panel_section_id: mapping + tool_panel_section_label: Mapping +- name: medaka_consensus_pipeline + owner: iuc + revisions: + - a7228a7ea146 + tool_panel_section_id: nanopore + tool_panel_section_label: Nanopore +- name: poretools_stats + owner: iuc + revisions: + - 4b17acf9b6ab + tool_panel_section_id: nanopore + tool_panel_section_label: Nanopore +- name: stringtie + owner: iuc + revisions: + - 1ebd14235b92 + tool_panel_section_id: rna_seq + tool_panel_section_label: RNA-seq +- name: samtools_markdup + owner: iuc + revisions: + - 83b8e36e9cbe + - b5527cc104ab + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM +- name: bamtools_filter + owner: devteam + revisions: + - cb20f99fd45b + - bd735cae4ce6 + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM +- name: anndata_manipulate + owner: iuc + revisions: + - 9bd945a03d7b + - 3d748954434b + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: salmonquantmerge + owner: bgruening + revisions: + - 88c07fc4024c + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_remove_confounders + owner: iuc + revisions: + - bf2017df9837 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_compute_graph + owner: ebi-gxa + revisions: + - 2401808e20e8 + - a58d4166805b + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: split_file_on_column + owner: bgruening + revisions: + - 37a53100b67e + tool_panel_section_id: text_manipulation + tool_panel_section_label: Text Manipulation +- name: lofreq_indelqual + owner: iuc + revisions: + - 426d707dfc47 + tool_panel_section_id: variant_calling + tool_panel_section_label: Variant Calling +- name: bcftools_norm + owner: iuc + revisions: + - c077f71d351f + tool_panel_section_id: vcf_bcf + tool_panel_section_label: VCF/BCF +- name: bcftools_plugin_fill_tags + owner: iuc + revisions: + - bf7d6acd9884 + tool_panel_section_id: vcf_bcf + tool_panel_section_label: VCF/BCF +- name: vcfallelicprimitives + owner: devteam + revisions: + - 57a16b310fe8 + tool_panel_section_id: vcf_bcf + tool_panel_section_label: VCF/BCF +- name: vcfprimers + owner: devteam + revisions: + - 17096387c0e6 + tool_panel_section_id: vcf_bcf + tool_panel_section_label: VCF/BCF +- name: ivar_filtervariants + owner: iuc + revisions: + - 7fe36019c073 + tool_panel_section_id: virology + tool_panel_section_label: Virology