Command line: /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.11.1-Linux/bin/spades.py	--pe1-1	/oak/stanford/groups/akundaje/marinovg/Symbiodinium/2017-10-16-Symbiodinium-assembly/SSA01-SSE01-genomic_HL72T.read1.paired.fastq.gz	--pe1-2	/oak/stanford/groups/akundaje/marinovg/Symbiodinium/2017-10-16-Symbiodinium-assembly/SSA01-SSE01-genomic_HL72T.read2.paired.fastq.gz	-t	16	-o	/oak/stanford/groups/akundaje/marinovg/Symbiodinium/2017-10-16-Symbiodinium-assembly/SCGPM_SSA01-SPAdes-3.11.1-trimmed	

System information:
  SPAdes version: 3.11.1
  Python version: 2.7.13
  OS: Linux-3.10.0-693.el7.x86_64-x86_64-with-centos-7.4.1708-Core

Output dir: /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2017-10-16-Symbiodinium-assembly/SCGPM_SSA01-SPAdes-3.11.1-trimmed
Mode: read error correction and assembling
Debug mode is turned OFF

Dataset parameters:
  Multi-cell mode (you should set '--sc' flag if input data was obtained with MDA (single-cell) technology or --meta flag if processing metagenomic dataset)
  Reads:
    Library number: 1, library type: paired-end
      orientation: fr
      left reads: ['/oak/stanford/groups/akundaje/marinovg/Symbiodinium/2017-10-16-Symbiodinium-assembly/SSA01-SSE01-genomic_HL72T.read1.paired.fastq.gz']
      right reads: ['/oak/stanford/groups/akundaje/marinovg/Symbiodinium/2017-10-16-Symbiodinium-assembly/SSA01-SSE01-genomic_HL72T.read2.paired.fastq.gz']
      interlaced reads: not specified
      single reads: not specified
Read error correction parameters:
  Iterations: 1
  PHRED offset will be auto-detected
  Corrected reads will be compressed (with gzip)
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/Symbiodinium/2017-10-16-Symbiodinium-assembly/SCGPM_SSA01-SPAdes-3.11.1-trimmed/tmp
  Threads: 16
  Memory limit (in Gb): 250