dannagifford
commented
5 years ago Check the filename and path of your reference genome "ChAd-Genome2.gbk". Perhaps try specifying the full path.
Closed trangthuypham closed 5 years ago
dannagifford
commented
5 years ago Check the filename and path of your reference genome "ChAd-Genome2.gbk". Perhaps try specifying the full path.
trangthuypham
commented
5 years ago Hi,
Thank you for getting back to me. I was able to run it (and yes the issue was the path to the reference and data files).
Trang Pham, PhD. Research Associate Turnstone Biologics 401 Smyth Road, Ottawa, ON K1H 8L1 Email: trang.pham@turnstonebio.com Mobile: 613-617-4541
On Fri, Jun 7, 2019 at 6:56 AM Danna Gifford notifications@github.com wrote:
Check the filename and path of your reference genome "ChAd-Genome2.gbk". Perhaps try specifying the full path.
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Hi, I am trying to install and run Breseq on my NGS data. However, this is what I did and got
Last login: Thu Jun 6 21:13:45 on ttys000 TPhams-MacBook-Pro:~ tpham$ export PATH=$PATH:/Applications/bowtie2-2.3.5.1-macos-x86_64 TPhams-MacBook-Pro:~ tpham$ export PATH=$PATH:/Applications/R TPhams-MacBook-Pro:~ tpham$ /Applications/breseq-0.33.2-MacOSX-10.9+/bin/breseq -r ChAd-Genome2.gbk ChAd-Genome-Clone-3_S1_L001_R1_001.fastq ChAd-Genome-Clone-3_S1_L001_R2_001.fastq -o clone3_breseq
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.
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 2.3.5.1 [/Applications/bowtie2-2.3.5.1-macos-x86_64/bowtie2] ---> R :: version 3.6.0 [/usr/local/bin/R] +++ NOW PROCESSING Read and reference sequence file input !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!> FATAL ERROR <!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Could not open reference file: ChAd-Genome2.gbk FILE: reference_sequence.cpp LINE: 807 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!> STACK TRACE <!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Backtrace with 6 stack frames. 0 breseq 0x000000010a261c15 _ZN6breseq16my_error_handlerEbbbPKcS1_iRKNSt3112basic_stringIcNS2_11char_traitsIcEENS2_9allocatorIcEEEE + 1253 1 breseq 0x000000010a4c1e0c _ZN6breseq19cReferenceSequences15PrivateLoadFileERKNSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEE + 380 2 breseq 0x000000010a4c11bc _ZN6breseq19cReferenceSequences9LoadFilesERKNSt316vectorINS1_12basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEENS6_IS8_EEEE + 140 3 breseq 0x000000010a278ea5 _Z21breseq_default_actioniPPc + 1525 4 breseq 0x000000010a287f66 main + 1718 5 libdyld.dylib 0x000000010a72a235 start + 1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! TPhams-MacBook-Pro:~ tpham$
Any suggestion on how to solve the problem? Thank you! Trang