Command line: /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.15.4-Linux/bin/spades.py	-s	/oak/stanford/groups/akundaje/marinovg/ENCODE4/single-cell/2024-11-15-RNA-assembly/all_reads.end1.fastq.gz	-t	60	--rna	-o	/oak/stanford/groups/akundaje/marinovg/ENCODE4/single-cell/2024-11-15-RNA-assembly/all_reads-SPAdes-3.15.4-rna	

System information:
  SPAdes version: 3.15.4
  Python version: 3.10.9
  OS: Linux-5.4.0-190-generic-x86_64-with-glibc2.31

Output dir: /oak/stanford/groups/akundaje/marinovg/ENCODE4/single-cell/2024-11-15-RNA-assembly/all_reads-SPAdes-3.15.4-rna
Debug mode is turned OFF

Dataset parameters:
  RNA-seq mode
  Reads:
    Library number: 1, library type: single
      left reads: not specified
      right reads: not specified
      interlaced reads: not specified
      single reads: ['/oak/stanford/groups/akundaje/marinovg/ENCODE4/single-cell/2024-11-15-RNA-assembly/all_reads.end1.fastq.gz']
      merged reads: not specified
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: /oak/stanford/groups/akundaje/marinovg/ENCODE4/single-cell/2024-11-15-RNA-assembly/all_reads-SPAdes-3.15.4-rna/tmp
  Threads: 60
  Memory limit (in Gb): 250