Mercurial > repos > greg > quast
comparison test-data/test3.log @ 0:5367786dc871 draft default tip
Uploaded
| author | greg |
|---|---|
| date | Tue, 14 Mar 2023 15:21:14 +0000 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:5367786dc871 |
|---|---|
| 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 | |
| 2 | |
| 3 Version: 5.2.0 | |
| 4 | |
| 5 System information: | |
| 6 OS: Linux-5.13.0-51-generic-x86_64-with-glibc2.31 (linux_64) | |
| 7 Python version: 3.9.13 | |
| 8 CPUs number: 8 | |
| 9 | |
| 10 Started: 2022-07-07 16:55:02 | |
| 11 | |
| 12 Logging to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/quast.log | |
| 13 WARNING: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified | |
| 14 | |
| 15 CWD: /tmp/tmphjbhe4x0/job_working_directory/000/15/working | |
| 16 Main parameters: | |
| 17 MODE: default, threads: 1, eukaryotic: true, min contig length: 500, min alignment length: 65, \ | |
| 18 min alignment IDY: 95.0, ambiguity: all, min local misassembly length: 200, min extensive misassembly length: 1000 | |
| 19 | |
| 20 Contigs: | |
| 21 Pre-processing... | |
| 22 1 /tmp/tmphjbhe4x0/files/0/2/b/dataset_02bce539-33f0-4693-bfe9-a92ebf1615f8.dat ==> contigs1_fna | |
| 23 2 /tmp/tmphjbhe4x0/files/6/0/2/dataset_60253425-26a2-4019-bae6-07285864be68.dat ==> contigs2_fna | |
| 24 | |
| 25 2022-07-07 16:55:11 | |
| 26 Running Basic statistics processor... | |
| 27 Contig files: | |
| 28 1 contigs1_fna | |
| 29 2 contigs2_fna | |
| 30 Calculating N50 and L50... | |
| 31 1 contigs1_fna, N50 = 3980, L50 = 1, auN = 2934.0, Total length = 6710, GC % = 51.28, # N's per 100 kbp = 0.00 | |
| 32 2 contigs2_fna, N50 = 6650, L50 = 1, auN = 6650.0, Total length = 6650, GC % = 52.00, # N's per 100 kbp = 0.00 | |
| 33 Drawing Nx plot... | |
| 34 saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/basic_stats/Nx_plot.pdf | |
| 35 Drawing cumulative plot... | |
| 36 saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/basic_stats/cumulative_plot.pdf | |
| 37 Drawing GC content plot... | |
| 38 saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/basic_stats/GC_content_plot.pdf | |
| 39 Drawing contigs1_fna GC content plot... | |
| 40 saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/basic_stats/contigs1_fna_GC_content_plot.pdf | |
| 41 Drawing contigs2_fna GC content plot... | |
| 42 saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/basic_stats/contigs2_fna_GC_content_plot.pdf | |
| 43 Done. | |
| 44 | |
| 45 NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it. | |
| 46 | |
| 47 2022-07-07 16:55:13 | |
| 48 Creating large visual summaries... | |
| 49 This may take a while: press Ctrl-C to skip this step.. | |
| 50 1 of 2: Creating PDF with all tables and plots... | |
| 51 2 of 2: Creating Icarus viewers... | |
| 52 Done | |
| 53 | |
| 54 2022-07-07 16:55:14 | |
| 55 RESULTS: | |
| 56 Text versions of total report are saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/report.txt, report.tsv, and report.tex | |
| 57 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 | |
| 58 HTML version (interactive tables and plots) is saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/report.html | |
| 59 PDF version (tables and plots) is saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/report.pdf | |
| 60 Icarus (contig browser) is saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/icarus.html | |
| 61 Log is saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/quast.log | |
| 62 | |
| 63 Finished: 2022-07-07 16:55:14 | |
| 64 Elapsed time: 0:00:11.737584 | |
| 65 NOTICEs: 1; WARNINGs: 1; non-fatal ERRORs: 0 | |
| 66 | |
| 67 Thank you for using QUAST! |