/opt/software/QUAST/5.2.0-foss-2021b/bin/quast -e -o 01_genome/quast_out_spades -t 36 01_genome/contigs.fasta

Version: 5.2.0

System information:
  OS: Linux-3.10.0-1160.88.1.el7.x86_64-x86_64-with-glibc2.17 (linux_64)
  Python version: 3.9.6
  CPUs number: 36

Started: 2023-04-19 11:21:11

Logging to /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/quast_out_spades/quast.log

CWD: /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training
Main parameters: 
  MODE: default, threads: 36, eukaryotic: true, min contig length: 500, min alignment length: 65, \
  min alignment IDY: 95.0, ambiguity: one, min local misassembly length: 200, min extensive misassembly length: 1000

Contigs:
  Pre-processing...
  01_genome/contigs.fasta ==> contigs

2023-04-19 11:21:16
Running Basic statistics processor...
  Contig files: 
    contigs
  Calculating N50 and L50...
    contigs, N50 = 105392, L50 = 16, auN = 122297.8, Total length = 5238759, GC % = 50.54, # N's per 100 kbp =  0.00
  Drawing Nx plot...
    saved to /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/quast_out_spades/basic_stats/Nx_plot.pdf
  Drawing cumulative plot...
    saved to /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/quast_out_spades/basic_stats/cumulative_plot.pdf
  Drawing GC content plot...
    saved to /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/quast_out_spades/basic_stats/GC_content_plot.pdf
  Drawing contigs GC content plot...
    saved to /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/quast_out_spades/basic_stats/contigs_GC_content_plot.pdf
  Drawing Coverage histogram (bin size: 2x)...
    saved to /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/quast_out_spades/basic_stats/coverage_histogram.pdf
  Drawing contigs coverage histogram (bin size: 2x)...
    saved to /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/quast_out_spades/basic_stats/contigs_coverage_histogram.pdf
Done.

NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.

2023-04-19 11:21:19
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

2023-04-19 11:21:20
RESULTS:
  Text versions of total report are saved to /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/quast_out_spades/report.txt, report.tsv, and report.tex
  Text versions of transposed total report are saved to /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/quast_out_spades/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
  HTML version (interactive tables and plots) is saved to /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/quast_out_spades/report.html
  PDF version (tables and plots) is saved to /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/quast_out_spades/report.pdf
  Icarus (contig browser) is saved to /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/quast_out_spades/icarus.html
  Log is saved to /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/quast_out_spades/quast.log

Finished: 2023-04-19 11:21:21
Elapsed time: 0:00:09.864930
NOTICEs: 1; WARNINGs: 0; non-fatal ERRORs: 0

Thank you for using QUAST!