Hi, I'm running Breseq v0.33.2 and getting the following error during the initial alignment step to a core genome produced using the Spine tool (250 contigs). The sample reads are Illumina 250bp paired-end trimmed using Trimmomatic. When I manually run the first Breseq Bowtie2 command I don't get any errors, so I'm not sure what could be causing the problem. I will send you the relevant files if needed if you link me your preferred email.

Here's the error:

breseq 0.33.2 revision caddc01d3be9 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.

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.

+++ NOW PROCESSING Read and reference sequence file input READ FILE::A12_GTAGAGGA-GCGTAAGA_L002_R1_trimmed Converting/filtering FASTQ file... Original base quality format: SANGER New format: SANGER Original reads: 1516694 bases: 217752639 Filtered reads: none Analyzed reads: 1516694 bases: 217752639 READ FILE::A12_GTAGAGGA-GCGTAAGA_L002_R2_trimmed Converting/filtering FASTQ file... Original base quality format: SANGER New format: SANGER Original reads: 1516694 bases: 179680949 Filtered reads: 2 bases: 196 (≥90.0% same base) Analyzed reads: 1516692 bases: 179680753 ::TOTAL:: Original reads: 3033388 bases: 397433588 Analyzed reads: 3033386 bases: 397433392 REFERENCE: backbone_0001_length_17251 LENGTH: 17251 REFERENCE: backbone_0002_length_23547 LENGTH: 23547 REFERENCE: backbone_0003_length_14094 LENGTH: 14094 REFERENCE: backbone_0004_length_3156 LENGTH: 3156 REFERENCE: backbone_0005_length_108 LENGTH: 108 REFERENCE: backbone_0006_length_589 LENGTH: 589 REFERENCE: backbone_0007_length_536 LENGTH: 536 REFERENCE: backbone_0008_length_10096 LENGTH: 10096 REFERENCE: backbone_0009_length_27306 LENGTH: 27306 REFERENCE: backbone_0010_length_22520 LENGTH: 22520 REFERENCE: backbone_0011_length_3657 LENGTH: 3657 REFERENCE: backbone_0012_length_26992 LENGTH: 26992 REFERENCE: backbone_0013_length_14541 LENGTH: 14541 REFERENCE: backbone_0014_length_5372 LENGTH: 5372 REFERENCE: 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backbone_0249_length_18137 LENGTH: 18137 REFERENCE: backbone_0250_length_4260 LENGTH: 4260 +++ NOW PROCESSING Read alignment to reference genome [system] bowtie2-build -q /data/pseudomonas/sequencing_run_16_pl74_CFtypeStrains_Archaea/pipeline_runs/PA_CoreGenome1/Sample_A12_GTAGAGGA-GCGTAAGA_L002/breseq_Paeruginosa_CoreGenome1//data/reference.fasta /data/pseudomonas/sequencing_run_16_pl74_CFtypeStrains_Archaea/pipeline_runs/PA_CoreGenome1/Sample_A12_GTAGAGGA-GCGTAAGA_L002/breseq_Paeruginosa_CoreGenome1//02_reference_alignment/reference !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!> FATAL ERROR <!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Segmentation Fault !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!> STACK TRACE <!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Segmentation fault (core dumped)

barricklab / breseq

Segmentation Error during read alignment stage #201

Here's the error:

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.