Command line: /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/2015-06-23-data/pooled-reads/Sample_K12-K12_TCCGCGAA-CAGGACGT_L002_R1_all.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/2015-06-23-data/pooled-reads/Sample_K12-K12_TCCGCGAA-CAGGACGT_L002_R2_all.paired.fastq.gz --mp1-1 GSF816-Doak-K12_S102_R1_001.paired.fastq.gz --mp1-2 GSF816-Doak-K12_S102_R2_001.paired.fastq.gz -t 16 -o Sample_K12-SPAdes-3.5.0-trimmed

System information:
  SPAdes version: 3.5.0
  Python version: 2.6.6
  OS: Linux-2.6.32-573.8.1.el6.x86_64-x86_64-with-redhat-6.7-Santiago

Output dir: /N/dc2/projects/marinovg/2016-01-01-november-data/Sample_K12-SPAdes-3.5.0-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
  Reads:
    Library number: 1, library type: mate-pairs
      orientation: rf
      left reads: ['/N/dc2/projects/marinovg/2016-01-01-november-data/GSF816-Doak-K12_S102_R1_001.paired.fastq.gz']
      right reads: ['/N/dc2/projects/marinovg/2016-01-01-november-data/GSF816-Doak-K12_S102_R2_001.paired.fastq.gz']
      interlaced reads: not specified
      single reads: not specified
    Library number: 2, library type: paired-end
      orientation: fr
      left reads: ['/N/dc2/projects/marinovg/2015-06-23-data/pooled-reads/Sample_K12-K12_TCCGCGAA-CAGGACGT_L002_R1_all.paired.fastq.gz']
      right reads: ['/N/dc2/projects/marinovg/2015-06-23-data/pooled-reads/Sample_K12-K12_TCCGCGAA-CAGGACGT_L002_R2_all.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
  Mismatch careful mode is turned OFF
  Repeat resolution is enabled
  MismatchCorrector will be SKIPPED
  Coverage cutoff is turned OFF
Other parameters:
  Dir for temp files: /N/dc2/projects/marinovg/2016-01-01-november-data/Sample_K12-SPAdes-3.5.0-trimmed/tmp
  Threads: 16
  Memory limit (in Gb): 250