output/params.txt

Version 1

Command line: /home/administrator/SPAdes-3.13.0-Linux/bin/spades.py	--rna	-t	32	-o	/DATA/markop/Pcitri_rnaspades/output	--ss-rf	--disable-gzip-output	--pe1-fr	--pe2-fr	--pe3-fr	--pe4-fr	--pe1-1	/FITO_ws/markop/pcitri_trimmed/PRO1976_S1_VF_2_GGAAGAGA-CGAGAGAA_L007_R1_trimmed_paired.R1.fastq.gz	--pe1-2	/FITO_ws/markop/pcitri_trimmed/PRO1976_S1_VF_2_GGAAGAGA-CGAGAGAA_L007_R1_trimmed_paired.R2.fastq.gz	--pe1-s	/FITO_ws/markop/pcitri_trimmed/PRO1976_S1_VF_2_GGAAGAGA-CGAGAGAA_L007_R1_trimmed_orphans.R1.fastq.gz	--pe2-1	/FITO_ws/markop/pcitri_trimmed/PRO1976_S2_VF_3_TCGGATTC-CGCAACTA_L007_R1_trimmed_paired.R1.fastq.gz	--pe2-2	/FITO_ws/markop/pcitri_trimmed/PRO1976_S2_VF_3_TCGGATTC-CGCAACTA_L007_R1_trimmed_paired.R2.fastq.gz	--pe2-s	/FITO_ws/markop/pcitri_trimmed/PRO1976_S2_VF_3_TCGGATTC-CGCAACTA_L007_R1_trimmed_orphans.R1.fastq.gz	--pe3-1	/FITO_ws/markop/pcitri_trimmed/PRO1976_S3_VF_5_CTGTACCA-CACAGACT_L007_R1_trimmed_paired.R1.fastq.gz	--pe3-2	/FITO_ws/markop/pcitri_trimmed/PRO1976_S3_VF_5_CTGTACCA-CACAGACT_L007_R1_trimmed_paired.R2.fastq.gz	--pe3-s	/FITO_ws/markop/pcitri_trimmed/PRO1976_S3_VF_5_CTGTACCA-CACAGACT_L007_R1_trimmed_orphans.R1.fastq.gz	--pe4-1	/FITO_ws/markop/pcitri_trimmed/PRO1976_S4_VF_6_GAGAGTAC-TGGAAGCA_L007_R1_trimmed_paired.R1.fastq.gz	--pe4-2	/FITO_ws/markop/pcitri_trimmed/PRO1976_S4_VF_6_GAGAGTAC-TGGAAGCA_L007_R1_trimmed_paired.R2.fastq.gz	--pe4-s	/FITO_ws/markop/pcitri_trimmed/PRO1976_S4_VF_6_GAGAGTAC-TGGAAGCA_L007_R1_trimmed_orphans.R1.fastq.gz	

System information:
  SPAdes version: 3.13.0
  Python version: 2.7.15
  OS: Linux-4.13.0-41-generic-x86_64-with-debian-stretch-sid

Output dir: /DATA/markop/Pcitri_rnaspades/output
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: ['/FITO_ws/markop/pcitri_trimmed/PRO1976_S1_VF_2_GGAAGAGA-CGAGAGAA_L007_R1_trimmed_paired.R1.fastq.gz']
      right reads: ['/FITO_ws/markop/pcitri_trimmed/PRO1976_S1_VF_2_GGAAGAGA-CGAGAGAA_L007_R1_trimmed_paired.R2.fastq.gz']
      interlaced reads: not specified
      single reads: ['/FITO_ws/markop/pcitri_trimmed/PRO1976_S1_VF_2_GGAAGAGA-CGAGAGAA_L007_R1_trimmed_orphans.R1.fastq.gz']
      merged reads: not specified
    Library number: 2, library type: paired-end
      orientation: fr
      left reads: ['/FITO_ws/markop/pcitri_trimmed/PRO1976_S2_VF_3_TCGGATTC-CGCAACTA_L007_R1_trimmed_paired.R1.fastq.gz']
      right reads: ['/FITO_ws/markop/pcitri_trimmed/PRO1976_S2_VF_3_TCGGATTC-CGCAACTA_L007_R1_trimmed_paired.R2.fastq.gz']
      interlaced reads: not specified
      single reads: ['/FITO_ws/markop/pcitri_trimmed/PRO1976_S2_VF_3_TCGGATTC-CGCAACTA_L007_R1_trimmed_orphans.R1.fastq.gz']
      merged reads: not specified
    Library number: 3, library type: paired-end
      orientation: fr
      left reads: ['/FITO_ws/markop/pcitri_trimmed/PRO1976_S3_VF_5_CTGTACCA-CACAGACT_L007_R1_trimmed_paired.R1.fastq.gz']
      right reads: ['/FITO_ws/markop/pcitri_trimmed/PRO1976_S3_VF_5_CTGTACCA-CACAGACT_L007_R1_trimmed_paired.R2.fastq.gz']
      interlaced reads: not specified
      single reads: ['/FITO_ws/markop/pcitri_trimmed/PRO1976_S3_VF_5_CTGTACCA-CACAGACT_L007_R1_trimmed_orphans.R1.fastq.gz']
      merged reads: not specified
    Library number: 4, library type: paired-end
      orientation: fr
      left reads: ['/FITO_ws/markop/pcitri_trimmed/PRO1976_S4_VF_6_GAGAGTAC-TGGAAGCA_L007_R1_trimmed_paired.R1.fastq.gz']
      right reads: ['/FITO_ws/markop/pcitri_trimmed/PRO1976_S4_VF_6_GAGAGTAC-TGGAAGCA_L007_R1_trimmed_paired.R2.fastq.gz']
      interlaced reads: not specified
      single reads: ['/FITO_ws/markop/pcitri_trimmed/PRO1976_S4_VF_6_GAGAGTAC-TGGAAGCA_L007_R1_trimmed_orphans.R1.fastq.gz']
      merged reads: not specified
Read error correction parameters:
  Iterations: 1
  PHRED offset will be auto-detected
  Corrected reads will NOT 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: /DATA/markop/Pcitri_rnaspades/output/tmp
  Threads: 32
  Memory limit (in Gb): 250