Mercurial > repos > iuc > quast
diff test-data/test3.log @ 14:3061c8b029e5 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
| author | iuc |
|---|---|
| date | Fri, 05 Aug 2022 15:21:27 +0000 |
| parents | 875d0f36d66f |
| children |
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--- a/test-data/test3.log Fri Mar 25 17:36:59 2022 +0000 +++ b/test-data/test3.log Fri Aug 05 15:21:27 2022 +0000 @@ -1,67 +1,67 @@ -/home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/bin/quast --labels contigs1_fna,contigs2_fna -o outputdir --eukaryote --min-contig 500 --min-alignment 65 --min-identity 95.0 --ambiguity-usage one --ambiguity-score 0.99 --contig-thresholds 0,1000,500 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --skip-unaligned-mis-contigs /tmp/tmpmqu3v_ze/files/c/a/f/dataset_cafcd90b-16e7-46aa-8617-cdefd1766b23.dat /tmp/tmpmqu3v_ze/files/6/4/e/dataset_64ec6db4-a92f-4ec5-b641-96e96830b6b5.dat --threads 1 +/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/bin/quast --labels contigs1_fna,contigs2_fna -o outputdir --eukaryote --min-identity 95.0 --min-contig 500 --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000,500 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --skip-unaligned-mis-contigs --x-for-Nx 90 /tmp/tmphjbhe4x0/files/0/2/b/dataset_02bce539-33f0-4693-bfe9-a92ebf1615f8.dat /tmp/tmphjbhe4x0/files/6/0/2/dataset_60253425-26a2-4019-bae6-07285864be68.dat --threads 1 -Version: 5.0.2 +Version: 5.2.0 System information: - OS: Linux-5.13.0-28-generic-x86_64-with-debian-bullseye-sid (linux_64) - Python version: 3.7.12 + OS: Linux-5.13.0-51-generic-x86_64-with-glibc2.31 (linux_64) + Python version: 3.9.13 CPUs number: 8 -Started: 2022-02-06 19:55:07 +Started: 2022-07-07 16:55:02 -Logging to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/quast.log -NOTICE: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified +Logging to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/quast.log +WARNING: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified -CWD: /tmp/tmpmqu3v_ze/job_working_directory/000/15/working +CWD: /tmp/tmphjbhe4x0/job_working_directory/000/15/working Main parameters: - MODE: default, threads: 1, eukaryotic: true, minimum contig length: 500, minimum alignment length: 65, \ - ambiguity: all, threshold for extensive misassembly size: 1000 + MODE: default, threads: 1, eukaryotic: true, min contig length: 500, min alignment length: 65, \ + min alignment IDY: 95.0, ambiguity: all, min local misassembly length: 200, min extensive misassembly length: 1000 Contigs: Pre-processing... - 1 /tmp/tmpmqu3v_ze/files/c/a/f/dataset_cafcd90b-16e7-46aa-8617-cdefd1766b23.dat ==> contigs1_fna - 2 /tmp/tmpmqu3v_ze/files/6/4/e/dataset_64ec6db4-a92f-4ec5-b641-96e96830b6b5.dat ==> contigs2_fna + 1 /tmp/tmphjbhe4x0/files/0/2/b/dataset_02bce539-33f0-4693-bfe9-a92ebf1615f8.dat ==> contigs1_fna + 2 /tmp/tmphjbhe4x0/files/6/0/2/dataset_60253425-26a2-4019-bae6-07285864be68.dat ==> contigs2_fna -2022-02-06 19:55:10 +2022-07-07 16:55:11 Running Basic statistics processor... Contig files: 1 contigs1_fna 2 contigs2_fna Calculating N50 and L50... - 1 contigs1_fna, N50 = 3980, L50 = 1, Total length = 6710, GC % = 51.28, # N's per 100 kbp = 0.00 - 2 contigs2_fna, N50 = 6650, L50 = 1, Total length = 6650, GC % = 52.00, # N's per 100 kbp = 0.00 + 1 contigs1_fna, N50 = 3980, L50 = 1, auN = 2934.0, Total length = 6710, GC % = 51.28, # N's per 100 kbp = 0.00 + 2 contigs2_fna, N50 = 6650, L50 = 1, auN = 6650.0, Total length = 6650, GC % = 52.00, # N's per 100 kbp = 0.00 Drawing Nx plot... - saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/basic_stats/Nx_plot.pdf + saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/basic_stats/Nx_plot.pdf Drawing cumulative plot... - saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/basic_stats/cumulative_plot.pdf + saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/basic_stats/cumulative_plot.pdf Drawing GC content plot... - saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/basic_stats/GC_content_plot.pdf + saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/basic_stats/GC_content_plot.pdf Drawing contigs1_fna GC content plot... - saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/basic_stats/contigs1_fna_GC_content_plot.pdf + saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/basic_stats/contigs1_fna_GC_content_plot.pdf Drawing contigs2_fna GC content plot... - saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/basic_stats/contigs2_fna_GC_content_plot.pdf + saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/basic_stats/contigs2_fna_GC_content_plot.pdf Done. NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it. -2022-02-06 19:55:11 +2022-07-07 16:55:13 Creating large visual summaries... This may take a while: press Ctrl-C to skip this step.. - 1 of 2: Creating Icarus viewers... - 2 of 2: Creating PDF with all tables and plots... + 1 of 2: Creating PDF with all tables and plots... + 2 of 2: Creating Icarus viewers... Done -2022-02-06 19:55:12 +2022-07-07 16:55:14 RESULTS: - Text versions of total report are saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/report.txt, report.tsv, and report.tex - Text versions of transposed total report are saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex - HTML version (interactive tables and plots) is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/report.html - PDF version (tables and plots) is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/report.pdf - Icarus (contig browser) is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/icarus.html - Log is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/quast.log + Text versions of total report are saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/report.txt, report.tsv, and report.tex + Text versions of transposed total report are saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex + HTML version (interactive tables and plots) is saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/report.html + PDF version (tables and plots) is saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/report.pdf + Icarus (contig browser) is saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/icarus.html + Log is saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/quast.log -Finished: 2022-02-06 19:55:12 -Elapsed time: 0:00:04.673393 -NOTICEs: 2; WARNINGs: 0; non-fatal ERRORs: 0 +Finished: 2022-07-07 16:55:14 +Elapsed time: 0:00:11.737584 +NOTICEs: 1; WARNINGs: 1; non-fatal ERRORs: 0 Thank you for using QUAST!