jeffreybarrick
commented
1 year ago Hi Marshall, didn't see this until now. Hopefully you figured out that you need to give breseq a valid path to the input files and NC_012967.gbk existed in test_drive but not your current directory.
new to this type of coding on a WSL. Struggled to get everything downloaded this is what I have with the ls command
(base) marshall@DESKTOP-UFJCE8A:~$ ls 01_sequence_conversion anaconda3 miniconda3 planemo test_drive Miniconda3-latest-Linux-x86_64.sh data output 't-Linux-x86_64.sh miniconda3 planemo test_drive tools-iuc' tools-iuc (base) marshall@DESKTOP-UFJCE8A:~$trying to run any breseq command gives me this prompt
breseq` 0.35.5 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 [/home/marshall/anaconda3/bin/bowtie2] ---> R :: version 3.5.3 [/home/marshall/anaconda3/bin/R] +++ NOW PROCESSING Read and reference sequence file input !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!> FATAL ERROR <!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Could not open reference file: NC_012967.gbk FILE: reference_sequence.cpp LINE: 808 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!> STACK TRACE <!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Backtrace with 7 stack frames. breseq(+0x1dc36) [0x7f610b8a2c36] breseq(+0x18d506) [0x7f610ba12506] breseq(+0x18e02c) [0x7f610ba1302c] breseq(+0x4a4ff) [0x7f610b8cf4ff] breseq(+0xe652) [0x7f610b893652] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3) [0x7f610b3540b3] breseq(+0x1cac9) [0x7f610b8a1ac9] !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!`
No sure where to go from here.