comparison test-data/test3.log @ 9:45924fa8d8c5 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"

9:45924fa8d8c5

/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!