How to run Breseq. FASTQ sequence record does not begin with @NAME line error.

Question

[taffners]

I running breseq. I'm getting the error: FASTQ sequence record does not begin with @NAME line. I'm exactly sure what this means.

I can't find anything about @NAME and FASTQ files.

I was thinking it meant add a line to the top of the file to identify the fastq file. So I added @NAME 8_cre_urmc_002 to the first line of the file

This resulted in this error:

  FASTQ sequence record does not contain +NAME line.

This part of the new file:

  @NAME 8_cre_urmc_002
  @M04837:64:000000000-BB5KR:1:1101:15481:1036 1:N:0:NAGAGAGG+NTAAGCCT
  CATCGGTACGGCTTCTTCTATCTACGTCGCGTCCGCGCTGGNNNNGANNCTNNNNNNGANNCGCGAGCANNNGATCCAGCAGNNNNNNNNAAAANAAGGGGCGGNNCNGCCNTNNATNCTGCCGTNNNNGGNTNNNNNGAGATAAANNNNNNNNGGCCTTGTNNNCGGGATTTTTTTTGCCNNNNAGAAACCTGCNNACNNNNNGCNNNNAGNAGNCCNNNNNTACACTGCTTCTGAACTCACTAACGANNNGGAGGAAGTATGANCAACGCTGTCTCTTATACACNNNNNCCNNNNNNNC

Here's the original fastq file:

  @M04837:64:000000000-BB5KR:1:1101:15481:1036 1:N:0:NAGAGAGG+NTAAGCCT
  CATCGGTACGGCTTCTTCTATCTACGTCGCGTCCGCGCTGGNNNNGANNCTNNNNNNGANNCGCGAGCANNNGATCCAGCAGNNNNNNNNAAAANAAGGGGCGGNNCNGCCNTNNATNCTGCCGTNNNNGGNTNNNNNGAGATAAANNNNNNNNGGCCTTGTNNNCGGGATTTTTTTTGCCNNNNAGAAACCTGCNNACNNNNNGCNNNNAGNAGNCCNNNNNTACACTGCTTCTGAACTCACTAACGANNNGGAGGAAGTATGANCAACGCTGTCTCTTATACACNNNNNCCNNNNNNNC
  +
  CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG####::##::######::##:CFGGGGG###::FGGGGGGG########::DF#:BFGGGGGG##:#::D#:##8:#:BFFGGF####:6#6#####66@FGGGG########66=FGGGE###66=CCGGGGGGGGDGG####/22@EFGGCF##/2#####2/####22#21#29#####119CDGGGGFGGFGFFC@FFFF?GF)###007:?>@BFBFF6#(-4?FF?FFF<A9>2>AB>)#####-(#######(
  @M04837:64:000000000-BB5KR:1:1101:15562:1037 1:N:0:NAGAGAGG+NTAAGCCT
  CCATTACCCTGATTGAAATGATCCAGCAGCATGAAGCCGGTNNNNGCNNGANNNNNNTGNNGCATATCANNNAACAGTTTGGNNNNNNNNTCGCNATTGGTCTTNNCNGCGNCNNTTNGCTGCTGNNNNTGNTNNNNNGTATTGTCNNNNNNNNCGGGCTCTNNNCGCTACTGGCGCTAAGNNNNGGGATCATGANNTTNNNNNTCNNNNCCNCTNTTNNNNNTAGCGGTATCCTCGCGGTCTATCTCTNCNGTTTCCTGCTCGGNAATAAACCCATTCGCAACCCNNNNNGCNNNNNNNC
  +

Here's the original output (without @NAME added):

  breseq -r Enterobacter_aerogenes_KCTC_2190_uid66537/CP002824.gbk \
    -o aerogenes/mapping/breseq_gbk/ \
    Sample_8_cre_urmc_002/8_cre_urmc_002_S8_L001_R1_001.fastq.gz \
    Sample_8_cre_urmc_002 /8_cre_urmc_002_S8_L001_R2_001.fastq.gz
  ================================================================================
  breseq 0.31.0  revision 69e7c3c0fa11   http://barricklab.org/breseq

  Active Developers: Barrick JE, Deatherage DE
  Contact:           <[e-mail]>

  breseq is free software; you can redistribute it and/or modify it under the
  terms the GNU General Public License as published by the Free Software 
  Foundation; either version 2, or (at your option) any later version.

  Copyright (c) 2008-2010 Michigan State University
  Copyright (c) 2011-2017 The University of Texas at Austin

  If you use breseq in your research, please cite:

    Deatherage, D.E., Barrick, J.E. (2014) Identification of mutations
    in laboratory-evolved microbes from next-generation sequencing
    data using breseq. Methods Mol. Biol. 1151: 165–188.

  If you use structural variation (junction) predictions, please cite:

    Barrick, J.E., Colburn, G., Deatherage D.E., Traverse, C.C.,
    Strand, M.D., Borges, J.J., Knoester, D.B., Reba, A., Meyer, A.G. 
    (2014) Identifying structural variation in haploid microbial genomes 
    from short-read resequencing data using breseq. BMC Genomics 15:1039.
  ================================================================================
  ---> bowtie2  :: version 2.2.9 [/software/bowtie2/2.2.9/bowtie2]
  ---> R        :: version 3.4.1 [/software/r/3.4.1/b1/bin/R]
  +++   NOW PROCESSING Read and reference sequence file input
    READ FILE::8_cre_urmc_002_S8_L001_R1_001
      Converting/filtering FASTQ file...
      Original base quality format: SANGER New format: SANGER
      Original reads: 1078545 bases: 324642045
      Filtered reads:       1 bases:       301 (≥90.0% same base)
      Analyzed reads: 1078544 bases: 324641744
    READ FILE::Sample_8_cre_urmc_002
      Converting/filtering FASTQ file...
  FASTQ sequence record does not begin with @NAME line.
  File /scratch/staffner/test_micro_pipeline/orginal/2017_aerogenes_outbreak_pecora080117/Sample_8_cre_urmc_002
  Line: 1
​

Answer 1

[h.mon]

There is a space after the folder path on you R2 filename (Sample_8_cre_urmc_002 /8_cre_urmc_002_S8_L001_R2_001.fastq.gz), so breseq thinks the name of the file is:

/scratch/staffner/test_micro_pipeline/orginal/2017_aerogenes_outbreak_pecora080117/Sample_8_cre_urmc_002