Command line: /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.13.0-Linux/bin/spades.py	-m	512	--s1	/oak/stanford/groups/akundaje/marinovg/Symbiodinium/2017-10-16-Symbiodinium-assembly/SSBO1.read1.unpaired.fastq.gz	--s2	/oak/stanford/groups/akundaje/marinovg/Symbiodinium/2017-10-16-Symbiodinium-assembly/SSBO1.read2.unpaired.fastq.gz	--nanopore	/oak/stanford/groups/akundaje/marinovg/Symbiodinium/2018-11-22-SSBO1-nanopore-assembly/20181115_Symbiodinium.albacore.fastq.gz	--nanopore	/oak/stanford/groups/akundaje/marinovg/Symbiodinium/2018-11-22-SSBO1-nanopore-assembly/20180731_Symbiodinium.albacore.fastq.gz	--trusted-contigs	/oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/sequence/symbB.v1.0.genome.fa	-t	20	-o	/oak/stanford/groups/akundaje/marinovg/Symbiodinium/2018-11-22-SSBO1-nanopore-assembly/SPAdes-3.13-Symbiodinium_minutum_SSBO1-nanopore-contigs	

System information:
  SPAdes version: 3.13.0
  Python version: 2.7.14
  OS: Linux-3.10.0-862.14.4.el7.x86_64-x86_64-with-centos-7.5.1804-Core

Output dir: /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2018-11-22-SSBO1-nanopore-assembly/SPAdes-3.13-Symbiodinium_minutum_SSBO1-nanopore-contigs
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: single
      left reads: not specified
      right reads: not specified
      interlaced reads: not specified
      single reads: ['/oak/stanford/groups/akundaje/marinovg/Symbiodinium/2017-10-16-Symbiodinium-assembly/SSBO1.read1.unpaired.fastq.gz']
      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/Symbiodinium/2017-10-16-Symbiodinium-assembly/SSBO1.read2.unpaired.fastq.gz']
      merged reads: not specified
    Library number: 3, library type: nanopore
      left reads: not specified
      right reads: not specified
      interlaced reads: not specified
      single reads: ['/oak/stanford/groups/akundaje/marinovg/Symbiodinium/2018-11-22-SSBO1-nanopore-assembly/20181115_Symbiodinium.albacore.fastq.gz', '/oak/stanford/groups/akundaje/marinovg/Symbiodinium/2018-11-22-SSBO1-nanopore-assembly/20180731_Symbiodinium.albacore.fastq.gz']
      merged reads: not specified
    Library number: 4, library type: trusted-contigs
      left reads: not specified
      right reads: not specified
      interlaced reads: not specified
      single reads: ['/oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/sequence/symbB.v1.0.genome.fa']
      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
  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/2018-11-22-SSBO1-nanopore-assembly/SPAdes-3.13-Symbiodinium_minutum_SSBO1-nanopore-contigs/tmp
  Threads: 20
  Memory limit (in Gb): 512