Command line: /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.13.0-Linux/bin/spades.py	-m	512	--plasmid	--pe1-1	/oak/stanford/groups/akundaje/marinovg/Paramecium/2018-10-19-SRA-ciliate-mitogenomes-assemblies/Deviata_sp.-single-cell-SRR6339724/SRR6339724.read1.paired.fastq.gz	--pe1-2	/oak/stanford/groups/akundaje/marinovg/Paramecium/2018-10-19-SRA-ciliate-mitogenomes-assemblies/Deviata_sp.-single-cell-SRR6339724/SRR6339724.read2.paired.fastq.gz	-t	20	-o	/oak/stanford/groups/akundaje/marinovg/Paramecium/2018-10-19-SRA-ciliate-mitogenomes-assemblies/SPAdes-3.13-Deviata_sp.-single-cell-SRR6339724	

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/Paramecium/2018-10-19-SRA-ciliate-mitogenomes-assemblies/SPAdes-3.13-Deviata_sp.-single-cell-SRR6339724
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/Paramecium/2018-10-19-SRA-ciliate-mitogenomes-assemblies/Deviata_sp.-single-cell-SRR6339724/SRR6339724.read1.paired.fastq.gz']
      right reads: ['/oak/stanford/groups/akundaje/marinovg/Paramecium/2018-10-19-SRA-ciliate-mitogenomes-assemblies/Deviata_sp.-single-cell-SRR6339724/SRR6339724.read2.paired.fastq.gz']
      interlaced reads: not specified
      single reads: not specified
      merged reads: not specified
Read error correction parameters:
  Iterations: 1
  PHRED offset will be auto-detected
  Corrected reads will be compressed
Assembly parameters:
  k: automatic selection based on read length
  Plasmid mode is turned ON
  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/Paramecium/2018-10-19-SRA-ciliate-mitogenomes-assemblies/SPAdes-3.13-Deviata_sp.-single-cell-SRR6339724/tmp
  Threads: 20
  Memory limit (in Gb): 512