Mercurial > repos > iuc > quast
diff test-data/test3.log @ 12:875d0f36d66f draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
| author | iuc |
|---|---|
| date | Sun, 06 Feb 2022 21:02:38 +0000 |
| parents | 45924fa8d8c5 |
| children | 3061c8b029e5 |
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--- a/test-data/test3.log Sat Nov 27 09:45:20 2021 +0000 +++ b/test-data/test3.log Sun Feb 06 21:02:38 2022 +0000 @@ -1,27 +1,28 @@ -/usr/local/bin/quast --labels contigs1_fna,contigs2_fna -o outputdir --eukaryote --min-contig 500 --min-alignment 65 --min-identity 95.0 --ambiguity-usage one --contig-thresholds 0,1000,500 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --skip-unaligned-mis-contigs /tmp/tmpfgnwy_vl/files/7/8/2/dataset_78284ced-4f1f-4eb6-a4e0-97cb937c125a.dat /tmp/tmpfgnwy_vl/files/6/b/d/dataset_6bd1949d-014f-47ff-8b78-b609c6a19455.dat --threads 1 +/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 Version: 5.0.2 System information: - OS: Linux-5.11.0-37-generic-x86_64-with-debian-10.9 (linux_64) + OS: Linux-5.13.0-28-generic-x86_64-with-debian-bullseye-sid (linux_64) Python version: 3.7.12 CPUs number: 8 -Started: 2021-11-07 18:59:34 +Started: 2022-02-06 19:55:07 -Logging to /tmp/tmpfgnwy_vl/job_working_directory/000/15/working/outputdir/quast.log +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 -CWD: /tmp/tmpfgnwy_vl/job_working_directory/000/15/working +CWD: /tmp/tmpmqu3v_ze/job_working_directory/000/15/working Main parameters: MODE: default, threads: 1, eukaryotic: true, minimum contig length: 500, minimum alignment length: 65, \ - ambiguity: one, threshold for extensive misassembly size: 1000 + ambiguity: all, threshold for extensive misassembly size: 1000 Contigs: Pre-processing... - 1 /tmp/tmpfgnwy_vl/files/7/8/2/dataset_78284ced-4f1f-4eb6-a4e0-97cb937c125a.dat ==> contigs1_fna - 2 /tmp/tmpfgnwy_vl/files/6/b/d/dataset_6bd1949d-014f-47ff-8b78-b609c6a19455.dat ==> contigs2_fna + 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 -2021-11-07 18:59:34 +2022-02-06 19:55:10 Running Basic statistics processor... Contig files: 1 contigs1_fna @@ -30,37 +31,37 @@ 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 Drawing Nx plot... - saved to /tmp/tmpfgnwy_vl/job_working_directory/000/15/working/outputdir/basic_stats/Nx_plot.pdf + saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/basic_stats/Nx_plot.pdf Drawing cumulative plot... - saved to /tmp/tmpfgnwy_vl/job_working_directory/000/15/working/outputdir/basic_stats/cumulative_plot.pdf + saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/basic_stats/cumulative_plot.pdf Drawing GC content plot... - saved to /tmp/tmpfgnwy_vl/job_working_directory/000/15/working/outputdir/basic_stats/GC_content_plot.pdf + saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/basic_stats/GC_content_plot.pdf Drawing contigs1_fna GC content plot... - saved to /tmp/tmpfgnwy_vl/job_working_directory/000/15/working/outputdir/basic_stats/contigs1_fna_GC_content_plot.pdf + saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/basic_stats/contigs1_fna_GC_content_plot.pdf Drawing contigs2_fna GC content plot... - saved to /tmp/tmpfgnwy_vl/job_working_directory/000/15/working/outputdir/basic_stats/contigs2_fna_GC_content_plot.pdf + saved to /tmp/tmpmqu3v_ze/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. -2021-11-07 18:59:35 +2022-02-06 19:55:11 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... Done -2021-11-07 18:59:36 +2022-02-06 19:55:12 RESULTS: - Text versions of total report are saved to /tmp/tmpfgnwy_vl/job_working_directory/000/15/working/outputdir/report.txt, report.tsv, and report.tex - Text versions of transposed total report are saved to /tmp/tmpfgnwy_vl/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/tmpfgnwy_vl/job_working_directory/000/15/working/outputdir/report.html - PDF version (tables and plots) is saved to /tmp/tmpfgnwy_vl/job_working_directory/000/15/working/outputdir/report.pdf - Icarus (contig browser) is saved to /tmp/tmpfgnwy_vl/job_working_directory/000/15/working/outputdir/icarus.html - Log is saved to /tmp/tmpfgnwy_vl/job_working_directory/000/15/working/outputdir/quast.log + 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 -Finished: 2021-11-07 18:59:36 -Elapsed time: 0:00:02.245904 -NOTICEs: 1; WARNINGs: 0; non-fatal ERRORs: 0 +Finished: 2022-02-06 19:55:12 +Elapsed time: 0:00:04.673393 +NOTICEs: 2; WARNINGs: 0; non-fatal ERRORs: 0 Thank you for using QUAST!