Command line: /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --careful --pe1-1 IB0001_1.paired.fastq.gz --pe1-2 IB0001_2.paired.fastq.gz -t 16 -o IB0001-Haemophilus_ducreyi-SPAdes-3.5.0-2x250mers-trimmed

System information:
  SPAdes version: 3.5.0
  Python version: 2.6.6
  OS: Linux-2.6.32-573.7.1.el6.x86_64-x86_64-with-redhat-6.7-Santiago

Output dir: /N/dc2/projects/marinovg/2015-10-29-Haemophilus_ducreyi/IB0001-Haemophilus_ducreyi-SPAdes-3.5.0-2x250mers-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: paired-end
      orientation: fr
      left reads: ['/N/dc2/projects/marinovg/2015-10-29-Haemophilus_ducreyi/IB0001_1.paired.fastq.gz']
      right reads: ['/N/dc2/projects/marinovg/2015-10-29-Haemophilus_ducreyi/IB0001_2.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 ON
  Repeat resolution is enabled
  MismatchCorrector will be used
  Coverage cutoff is turned OFF
Other parameters:
  Dir for temp files: /N/dc2/projects/marinovg/2015-10-29-Haemophilus_ducreyi/IB0001-Haemophilus_ducreyi-SPAdes-3.5.0-2x250mers-trimmed/tmp
  Threads: 16
  Memory limit (in Gb): 250