/srlab/programs/miniforge3-24.7.1-0/lib/python3.12/site-packages/quast-5.3.0-py3.12.egg/EGG-INFO/scripts/quast.py ../output/13.1-genome-assembly-lean/snam-lean-pb-flye-assembly.fasta ../output/13.1-hifiasm-genome-assembly-lean/pb-hifiasm-lean-assembly.fa ../output/13.1-genome-assembly-siscowet/snam-siscowet-pb-flye-assembly.fasta ../output/13.1-hifiasm-genome-assembly-siscowet/pb-hifiasm-siscowet-assembly.fa --output-dir ../output/13.2-genome-assembly-comparisons --threads 40 --labels lean_flye, lean_hifiasm, siscowet_flye, siscowet_hifiasm

Version: 5.3.0

System information:
  OS: Linux-4.18.0-513.18.1.el8_9.x86_64-x86_64-with-glibc2.39 (linux_64)
  Python version: 3.12.5
  CPUs number: 192

Started: 2026-04-10 12:49:08

Logging to /mmfs1/gscratch/scrubbed/samwhite/gitrepos/RobertsLab/project-lake-trout/output/13.2-genome-assembly-comparisons/quast.log

CWD: /mmfs1/gscratch/scrubbed/samwhite/gitrepos/RobertsLab/project-lake-trout/code
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  ../output/13.1-genome-assembly-lean/snam-lean-pb-flye-assembly.fasta ==> lean_flye
  2  ../output/13.1-hifiasm-genome-assembly-lean/pb-hifiasm-lean-assembly.fa ==> lean_hifiasm
  3  ../output/13.1-genome-assembly-siscowet/snam-siscowet-pb-flye-assembly.fasta ==> siscowet_flye
  4  ../output/13.1-hifiasm-genome-assembly-siscowet/pb-hifiasm-siscowet-assembly.fa ==> siscowet_hifiasm

2026-04-10 12:51:06
Running Basic statistics processor...
  Contig files: 
    1  lean_flye
    2  lean_hifiasm
    3  siscowet_flye
    4  siscowet_hifiasm
  Calculating N50 and L50...
    1  lean_flye, N50 = 74514, L50 = 10897, auN = 172736.7, Total length = 4046355081, GC % = 42.89, # N's per 100 kbp =  0.00
    2  lean_hifiasm, N50 = 325701, L50 = 2542, auN = 608980.5, Total length = 3733314870, GC % = 42.57, # N's per 100 kbp =  0.00
    3  siscowet_flye, N50 = 78564, L50 = 10934, auN = 189833.9, Total length = 4336770215, GC % = 43.17, # N's per 100 kbp =  0.00
    4  siscowet_hifiasm, N50 = 514031, L50 = 1844, auN = 874464.1, Total length = 4008351139, GC % = 42.84, # N's per 100 kbp =  0.00
Done.

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

2026-04-10 12:56:51
Creating large visual summaries...
This may take a while: press Ctrl-C to skip this step..
  1 of 1: Creating Icarus viewers...
Done

2026-04-10 12:58:19
RESULTS:
  Text versions of total report are saved to /mmfs1/gscratch/scrubbed/samwhite/gitrepos/RobertsLab/project-lake-trout/output/13.2-genome-assembly-comparisons/report.txt, report.tsv, and report.tex
  Text versions of transposed total report are saved to /mmfs1/gscratch/scrubbed/samwhite/gitrepos/RobertsLab/project-lake-trout/output/13.2-genome-assembly-comparisons/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
  HTML version (interactive tables and plots) is saved to /mmfs1/gscratch/scrubbed/samwhite/gitrepos/RobertsLab/project-lake-trout/output/13.2-genome-assembly-comparisons/report.html
  Icarus (contig browser) is saved to /mmfs1/gscratch/scrubbed/samwhite/gitrepos/RobertsLab/project-lake-trout/output/13.2-genome-assembly-comparisons/icarus.html
  Log is saved to /mmfs1/gscratch/scrubbed/samwhite/gitrepos/RobertsLab/project-lake-trout/output/13.2-genome-assembly-comparisons/quast.log

Finished: 2026-04-10 12:58:19
Elapsed time: 0:09:10.519647
NOTICEs: 1; WARNINGs: 1; non-fatal ERRORs: 0

Thank you for using QUAST!