Command line: /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.13.0-Linux/bin/spades.py	-m	256	--pe1-1	/oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run1-AWRI_Rep1_PE1_pf_val_1.fq.gz	--pe1-2	/oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run1-AWRI_Rep1_PE2_pf_val_2.fq.gz	--pe2-1	/oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run1-AWRI_Rep2_PE1_pf_val_1.fq.gz	--pe2-2	/oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run1-AWRI_Rep2_PE2_pf_val_2.fq.gz	--pe3-1	/oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run2-AWRI_Rep1_PE1_pf_val_1.fq.gz	--pe3-2	/oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run2-AWRI_Rep1_PE2_pf_val_2.fq.gz	--pe4-1	/oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run2-AWRI_Rep2_PE1_pf_val_1.fq.gz	--pe4-2	/oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run2-AWRI_Rep2_PE2_pf_val_2.fq.gz	-t	20	-o	/oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-AWRI	

System information:
  SPAdes version: 3.13.0
  Python version: 2.7.14
  OS: Linux-3.10.0-957.1.3.el7.x86_64-x86_64-with-centos-7.6.1810-Core

Output dir: /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-AWRI
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/Yeast-TFs/2019-02-03-datasets-Genomes/Run1-AWRI_Rep1_PE1_pf_val_1.fq.gz']
      right reads: ['/oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run1-AWRI_Rep1_PE2_pf_val_2.fq.gz']
      interlaced reads: not specified
      single reads: not specified
      merged reads: not specified
    Library number: 2, library type: paired-end
      orientation: fr
      left reads: ['/oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run1-AWRI_Rep2_PE1_pf_val_1.fq.gz']
      right reads: ['/oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run1-AWRI_Rep2_PE2_pf_val_2.fq.gz']
      interlaced reads: not specified
      single reads: not specified
      merged reads: not specified
    Library number: 3, library type: paired-end
      orientation: fr
      left reads: ['/oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run2-AWRI_Rep1_PE1_pf_val_1.fq.gz']
      right reads: ['/oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run2-AWRI_Rep1_PE2_pf_val_2.fq.gz']
      interlaced reads: not specified
      single reads: not specified
      merged reads: not specified
    Library number: 4, library type: paired-end
      orientation: fr
      left reads: ['/oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run2-AWRI_Rep2_PE1_pf_val_1.fq.gz']
      right reads: ['/oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run2-AWRI_Rep2_PE2_pf_val_2.fq.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
  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/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-AWRI/tmp
  Threads: 20
  Memory limit (in Gb): 256