Mercurial > repos > greg > quast
diff test-data/test3.log @ 0:5367786dc871 draft default tip
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| author | greg |
|---|---|
| date | Tue, 14 Mar 2023 15:21:14 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test3.log Tue Mar 14 15:21:14 2023 +0000 @@ -0,0 +1,67 @@ +/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: 5.2.0 + +System information: + OS: Linux-5.13.0-51-generic-x86_64-with-glibc2.31 (linux_64) + Python version: 3.9.13 + CPUs number: 8 + +Started: 2022-07-07 16:55:02 + +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/tmphjbhe4x0/job_working_directory/000/15/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 + +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, 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/tmphjbhe4x0/job_working_directory/000/15/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 + Drawing GC content plot... + 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/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 +Done. + +NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it. + +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 PDF with all tables and plots... + 2 of 2: Creating Icarus viewers... +Done + +2022-07-07 16:55:14 +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 + +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!