/srlab/programs/miniforge3-24.7.1-0/bin/quast.py:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  __import__('pkg_resources').run_script('quast==5.3.0', 'quast.py')
/srlab/programs/miniforge3-24.7.1-0/lib/python3.12/site-packages/quast-5.3.0-py3.12.egg/EGG-INFO/scripts/quast.py /mmfs1/gscratch/scrubbed/samwhite/outputs/20260519-crog-hembra-genome_assembly-hifiasm/crog-hembra-pb-hifiasm-assembly.fa /mmfs1/gscratch/scrubbed/samwhite/outputs/20260519-crog-macho-genome_assembly-hifiasm/crog-macho-pb-hifiasm-assembly.fa --output-dir /mmfs1/gscratch/scrubbed/samwhite/outputs/20260520-crog-quast --threads 40 --labels hembra_hifiasm, macho_hifiasm

Version: 5.3.0

System information:
  OS: Linux-4.18.0-553.123.1.el8_10.x86_64-x86_64-with-glibc2.39 (linux_64)
  Python version: 3.12.5
  CPUs number: 192

Started: 2026-05-20 09:48:44

Logging to /mmfs1/gscratch/scrubbed/samwhite/outputs/20260520-crog-quast/quast.log

CWD: /mmfs1/gscratch/scrubbed/samwhite/gitrepos/RobertsLab/sams-notebook/posts/2026/2026-05-20-Genome-Comparisons---C.rogercresseyi-Hembra-and-Macho-PacBio-hifiasm-Assemblies-Using-QUAST-on-Hyak
Main parameters: 
  MODE: default, threads: 40, 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

WARNING: Can't draw plots: python-matplotlib is missing or corrupted.

Contigs:
  Pre-processing...
  1  /mmfs1/gscratch/scrubbed/samwhite/outputs/20260519-crog-hembra-genome_assembly-hifiasm/crog-hembra-pb-hifiasm-assembly.fa ==> hembra_hifiasm
  2  /mmfs1/gscratch/scrubbed/samwhite/outputs/20260519-crog-macho-genome_assembly-hifiasm/crog-macho-pb-hifiasm-assembly.fa ==> macho_hifiasm

2026-05-20 09:49:06
Running Basic statistics processor...
  Contig files: 
    1  hembra_hifiasm
    2  macho_hifiasm
  Calculating N50 and L50...
    1  hembra_hifiasm, N50 = 29880, L50 = 6795, auN = 263844.4, Total length = 965132142, GC % = 35.50, # N's per 100 kbp =  0.00
    2  macho_hifiasm, N50 = 52326, L50 = 3979, auN = 315728.2, Total length = 1039559438, GC % = 36.26, # N's per 100 kbp =  0.00
Done.

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

2026-05-20 09:49:45
Creating large visual summaries...
This may take a while: press Ctrl-C to skip this step..
  1 of 1: Creating Icarus viewers...
Done

2026-05-20 09:49:53
RESULTS:
  Text versions of total report are saved to /mmfs1/gscratch/scrubbed/samwhite/outputs/20260520-crog-quast/report.txt, report.tsv, and report.tex
  Text versions of transposed total report are saved to /mmfs1/gscratch/scrubbed/samwhite/outputs/20260520-crog-quast/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
  HTML version (interactive tables and plots) is saved to /mmfs1/gscratch/scrubbed/samwhite/outputs/20260520-crog-quast/report.html
  Icarus (contig browser) is saved to /mmfs1/gscratch/scrubbed/samwhite/outputs/20260520-crog-quast/icarus.html
  Log is saved to /mmfs1/gscratch/scrubbed/samwhite/outputs/20260520-crog-quast/quast.log

Finished: 2026-05-20 09:49:53
Elapsed time: 0:01:09.254529
NOTICEs: 1; WARNINGs: 1; non-fatal ERRORs: 0

Thank you for using QUAST!