Command line: /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.15.4-Linux/bin/spades.py	--pe1-1	/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-gDNA/L2786-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_cloudy/L2786-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_cloudy.230413_NB551514_0043_AHN7TGBGXN.end1.fastq.gz	--pe1-2	/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-gDNA/L2786-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_cloudy/L2786-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_cloudy.230413_NB551514_0043_AHN7TGBGXN.end2.fastq.gz	--pe2-1	/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-gDNA/L2787-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_clear1/L2787-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_clear1.230413_NB551514_0043_AHN7TGBGXN.end1.fastq.gz	--pe2-2	/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-gDNA/L2787-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_clear1/L2787-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_clear1.230413_NB551514_0043_AHN7TGBGXN.end2.fastq.gz	--pe3-1	/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-gDNA/L2788-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_clear2/L2788-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_clear2.230413_NB551514_0043_AHN7TGBGXN.end1.fastq.gz	--pe3-2	/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-gDNA/L2788-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_clear2/L2788-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_clear2.230413_NB551514_0043_AHN7TGBGXN.end2.fastq.gz	--nanopore	/oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2023-04-20-gDNA-Flongle/2023-04-19-B_b_gDNA_check.pass.fastq	-o	/oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2023-04-20-gDNA-Flongle/SPAdes-3.15.4-2023-04-19-B_b_gDNA_check.pass	

System information:
  SPAdes version: 3.15.4
  Python version: 2.7.13
  OS: Linux-4.15.0-189-generic-x86_64-with-debian-buster-sid

Output dir: /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2023-04-20-gDNA-Flongle/SPAdes-3.15.4-2023-04-19-B_b_gDNA_check.pass
Mode: read error correction and assembling
Debug mode is turned OFF

Dataset parameters:
  Standard mode
  For multi-cell/isolate data we recommend to use '--isolate' option; for single-cell MDA data use '--sc'; for metagenomic data use '--meta'; for RNA-Seq use '--rna'.
  Reads:
    Library number: 1, library type: nanopore
      left reads: not specified
      right reads: not specified
      interlaced reads: not specified
      single reads: ['/oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2023-04-20-gDNA-Flongle/2023-04-19-B_b_gDNA_check.pass.fastq']
      merged reads: not specified
    Library number: 2, library type: paired-end
      orientation: fr
      left reads: ['/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-gDNA/L2786-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_cloudy/L2786-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_cloudy.230413_NB551514_0043_AHN7TGBGXN.end1.fastq.gz']
      right reads: ['/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-gDNA/L2786-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_cloudy/L2786-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_cloudy.230413_NB551514_0043_AHN7TGBGXN.end2.fastq.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/ENCODE4/datasets-gDNA/L2787-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_clear1/L2787-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_clear1.230413_NB551514_0043_AHN7TGBGXN.end1.fastq.gz']
      right reads: ['/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-gDNA/L2787-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_clear1/L2787-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_clear1.230413_NB551514_0043_AHN7TGBGXN.end2.fastq.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/ENCODE4/datasets-gDNA/L2788-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_clear2/L2788-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_clear2.230413_NB551514_0043_AHN7TGBGXN.end1.fastq.gz']
      right reads: ['/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-gDNA/L2788-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_clear2/L2788-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_clear2.230413_NB551514_0043_AHN7TGBGXN.end2.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
  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/ENCODE4/Chromatin-nanopores/2023-04-20-gDNA-Flongle/SPAdes-3.15.4-2023-04-19-B_b_gDNA_check.pass/tmp
  Threads: 16
  Memory limit (in Gb): 250