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: <[email protected]>
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