Command line: /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.13.0-Linux/bin/spades.py	--rna	--pe1-1	/oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Phaeodarea_Illumina_W-ERX2094047.read1.paired.fastq.gz	--pe1-2	/oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Phaeodarea_Illumina_W-ERX2094047.read2.paired.fastq.gz	--s1	/oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Phaeodarea_Illumina_W-ERX2094047.read1.unpaired.fastq.gz	--s2	/oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Phaeodarea_Illumina_W-ERX2094047.read2.unpaired.fastq.gz	-t	20	-o	/oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Phaeodarea_Illumina_W-ERX2094047	

System information:
  SPAdes version: 3.13.0
  Python version: 2.7.15
  OS: Linux-3.10.0-957.10.1.el7.x86_64-x86_64-with-centos-7.6.1810-Core

Output dir: /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Phaeodarea_Illumina_W-ERX2094047
Mode: read error correction and assembling
Debug mode is turned OFF

Dataset parameters:
  RNA-seq mode
  Reads:
    Library number: 1, library type: paired-end
      orientation: fr
      left reads: ['/oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Phaeodarea_Illumina_W-ERX2094047.read1.paired.fastq.gz']
      right reads: ['/oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Phaeodarea_Illumina_W-ERX2094047.read2.paired.fastq.gz']
      interlaced reads: not specified
      single reads: not specified
      merged reads: not specified
    Library number: 2, library type: single
      left reads: not specified
      right reads: not specified
      interlaced reads: not specified
      single reads: ['/oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Phaeodarea_Illumina_W-ERX2094047.read1.unpaired.fastq.gz']
      merged reads: not specified
    Library number: 3, library type: single
      left reads: not specified
      right reads: not specified
      interlaced reads: not specified
      single reads: ['/oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Phaeodarea_Illumina_W-ERX2094047.read2.unpaired.fastq.gz']
      merged reads: not specified
Read error correction parameters:
  Iterations: 1
  PHRED offset will be auto-detected
  Corrected reads will be compressed
Assembly parameters:
  k: auto
  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/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Phaeodarea_Illumina_W-ERX2094047/tmp
  Threads: 20
  Memory limit (in Gb): 250