Mercurial > repos > iuc > quast
diff test-data/test3.log @ 16:a3b35edea53a draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
| author | iuc |
|---|---|
| date | Tue, 12 Nov 2024 12:46:19 +0000 |
| parents | 3061c8b029e5 |
| children |
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--- a/test-data/test3.log Thu Mar 02 10:38:54 2023 +0000 +++ b/test-data/test3.log Tue Nov 12 12:46:19 2024 +0000 @@ -1,67 +1,62 @@ -/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 +/usr/local/bin/quast --labels contigs1_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/tmplvd_uy2v/files/9/3/d/dataset_93dcca11-36ea-4b55-9eac-980009de363e.dat --threads 1 -Version: 5.2.0 +Version: 5.3.0 System information: - OS: Linux-5.13.0-51-generic-x86_64-with-glibc2.31 (linux_64) - Python version: 3.9.13 - CPUs number: 8 + OS: Linux-6.8.0-107047-tuxedo-x86_64-with-glibc2.36 (linux_64) + Python version: 3.12.3 + CPUs number: 12 -Started: 2022-07-07 16:55:02 +Started: 2024-11-12 11:22:10 -Logging to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/quast.log +Logging to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/quast.log WARNING: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified -CWD: /tmp/tmphjbhe4x0/job_working_directory/000/15/working +CWD: /tmp/tmplvd_uy2v/job_working_directory/000/14/working Main parameters: 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/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 + /tmp/tmplvd_uy2v/files/9/3/d/dataset_93dcca11-36ea-4b55-9eac-980009de363e.dat ==> contigs1_fna -2022-07-07 16:55:11 +2024-11-12 11:22:11 Running Basic statistics processor... Contig files: - 1 contigs1_fna - 2 contigs2_fna + contigs1_fna Calculating N50 and L50... - 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 + contigs1_fna, N50 = 3980, L50 = 1, auN = 2934.0, Total length = 6710, GC % = 51.28, # N's per 100 kbp = 0.00 Drawing Nx plot... - saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/basic_stats/Nx_plot.pdf + saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/basic_stats/Nx_plot.pdf Drawing cumulative plot... - saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/basic_stats/cumulative_plot.pdf + saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/basic_stats/cumulative_plot.pdf Drawing GC content plot... - saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/basic_stats/GC_content_plot.pdf + saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/basic_stats/GC_content_plot.pdf Drawing contigs1_fna GC content plot... - 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/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/basic_stats/contigs2_fna_GC_content_plot.pdf + saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/basic_stats/contigs1_fna_GC_content_plot.pdf Done. NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it. -2022-07-07 16:55:13 +2024-11-12 11:22:11 Creating large visual summaries... This may take a while: press Ctrl-C to skip this step.. 1 of 2: Creating PDF with all tables and plots... 2 of 2: Creating Icarus viewers... Done -2022-07-07 16:55:14 +2024-11-12 11:22:11 RESULTS: - 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 + Text versions of total report are saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/report.txt, report.tsv, and report.tex + Text versions of transposed total report are saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex + HTML version (interactive tables and plots) is saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/report.html + PDF version (tables and plots) is saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/report.pdf + Icarus (contig browser) is saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/icarus.html + Log is saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/quast.log -Finished: 2022-07-07 16:55:14 -Elapsed time: 0:00:11.737584 +Finished: 2024-11-12 11:22:11 +Elapsed time: 0:00:01.104288 NOTICEs: 1; WARNINGs: 1; non-fatal ERRORs: 0 Thank you for using QUAST!