Mercurial > repos > iuc > quast
view test-data/test3.log @ 9:45924fa8d8c5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
| author | iuc |
|---|---|
| date | Mon, 08 Nov 2021 09:03:00 +0000 |
| parents | |
| children | 875d0f36d66f |
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/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 Version: 5.0.2 System information: OS: Linux-5.11.0-37-generic-x86_64-with-debian-10.9 (linux_64) Python version: 3.7.12 CPUs number: 8 Started: 2021-11-07 18:59:34 Logging to /tmp/tmpfgnwy_vl/job_working_directory/000/15/working/outputdir/quast.log CWD: /tmp/tmpfgnwy_vl/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 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 2021-11-07 18:59:34 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 Drawing Nx plot... saved to /tmp/tmpfgnwy_vl/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 Drawing GC content plot... saved to /tmp/tmpfgnwy_vl/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 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 Done. NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it. 2021-11-07 18:59:35 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 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 Finished: 2021-11-07 18:59:36 Elapsed time: 0:00:02.245904 NOTICEs: 1; WARNINGs: 0; non-fatal ERRORs: 0 Thank you for using QUAST!