Command line: /opt/software/SPAdes/3.15.3-GCC-11.2.0/bin/spades.py	-1	/glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/00_reads/SRR341563_trimmed_1P.fastq.gz	-2	/glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/00_reads/SRR341563_trimmed_2P.fastq.gz	-s	/glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/00_reads/SRR341563_trimmed_U.fastq	-o	/glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome	-t	4	

System information:
  SPAdes version: 3.15.3
  Python version: 3.9.6
  OS: Linux-3.10.0-1160.88.1.el7.x86_64-x86_64-with-glibc2.17

Output dir: /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome
Mode: read error correction and assembling
Debug mode is turned OFF

Dataset parameters:
  Standard mode
  For multi-cell/isolate data we recommend to use '--isolate' option; for single-cell MDA data use '--sc'; for metagenomic data use '--meta'; for RNA-Seq use '--rna'.
  Reads:
    Library number: 1, library type: paired-end
      orientation: fr
      left reads: ['/glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/00_reads/SRR341563_trimmed_1P.fastq.gz']
      right reads: ['/glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/00_reads/SRR341563_trimmed_2P.fastq.gz']
      interlaced reads: not specified
      single reads: ['/glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/00_reads/SRR341563_trimmed_U.fastq']
      merged reads: not specified
Read error correction parameters:
  Iterations: 1
  PHRED offset will be auto-detected
  Corrected reads will be compressed
Assembly parameters:
  k: automatic selection based on read length
  Repeat resolution is enabled
  Mismatch careful mode is turned OFF
  MismatchCorrector will be SKIPPED
  Coverage cutoff is turned OFF
Other parameters:
  Dir for temp files: /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/tmp
  Threads: 4
  Memory limit (in Gb): 125