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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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run stalling, but no specific error message #340

Closed Jessica1080 closed 1 year ago

Jessica1080 commented 1 year ago

Hello,

I've installed using conda and I successfully get the output from breseq -h. However, when I try to run samples I'm getting the following output without results. No specific error message is supplied. Three folders are produced (01_sequence_conversion, data, and output), but the only file produced is the log.txt file that contains the input code.

================================================================================ ---> bowtie2 :: version 2.5.0 [/opt/conda/envs/env_breseq2/bin/bowtie2] ---> bowtie2 :: NOTE :: breseq output may vary slightly depending on your bowtie2 version ---> bowtie2 :: NOTE :: and occasionally bowtie2 versions may have bugs that cause crashes. ---> bowtie2 :: NOTE :: bowtie2 version 2.4.5 is recommended with this breseq version. ---> R :: version 4.2.2 [/opt/conda/envs/env_breseq2/bin/R] +++ NOW PROCESSING Read and reference sequence file input Backtrace with 8 stack frames. breseq(+0x44cf4) [0x5561acafacf4] breseq(+0x19198f) [0x5561acc4798f] breseq(+0x19ec04) [0x5561acc54c04] breseq(+0x19ee64) [0x5561acc54e64] breseq(+0x6e460) [0x5561acb24460] breseq(+0x36cc4) [0x5561acaeccc4] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7f2b5e91abf7] breseq(+0x40559) [0x5561acaf6559] !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

Thanks! Jessica

jeffreybarrick commented 1 year ago

That's odd. The reference sequence file you provided seems to be causing a hard crash. If you can email that to me at the address in the breseq command-line header, I can take a look.

jeffreybarrick commented 1 year ago

Problem was encountered on a virtual workstation. It seems to have been some kind of misinterpretation of the encoding of the input text files. Reboots and reinstalls using mamba seem to have solved the issue.