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barricklab / breseq

breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA resequencing data. It is intended for haploid microbial genomes (<20 Mb). breseq is a command line tool implemented in C++ and R.
http://barricklab.org/breseq
GNU General Public License v2.0
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Segmentation fault #126

Closed abrozzi closed 6 years ago

abrozzi commented 7 years ago

breseq -r stLMTB11381.fasta -j 8 DNA-4_S4_L001_R1_001.fastq DNA-4_S4_L001_R2_001.fastq

breseq 0.27.1 revision 87c22d663cc3 http://barricklab.org/breseq

Active Developers: Barrick JE, Deatherage DE Contact: jeffrey.e.barrick@gmail.com

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) 2011-2015 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 2.2.4 [/home/ab552791/apps/bowtie2-2.2.4/bowtie2] ---> R :: version 3.2.2 [/projects/GENOMICS/APPLICATIONS/R-3.2.2/bin/R] --- ALREADY COMPLETE Read and reference sequence file input Segmentation fault

Where shall I look at to find what's wrong?

-A

jeffreybarrick commented 7 years ago

I assume this also occurs if you start the output in a clean folder, so that it doesn't have any ALREADY COMPLETE messages?

Can you paste the first few lines of your FASTQ file and reference file you are using so that we can take a look? Something must be unexpected about them.

jeffreybarrick commented 6 years ago

Closing issue. Not enough detail provided to reproduce problem.