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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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std::bad_alloc #292

Closed khoriba closed 2 years ago

khoriba commented 2 years ago

Hi, My analysis on breseq (0.36.0) was stopped in the step of making html report by the following error.

...
Creating evidence file: SNP_5778.html
Creating read alignment for region: NZ_KB944666.1:843349.0-843349.0
Creating evidence file: SNP_5779.html
Creating read alignment for region: NZ_KB944666.1:843352.0-843352.0
terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc

Can this problem be solved? Is there a way to rescue this failed process?

jeffreybarrick commented 2 years ago

Can you share the read and reference files and the command you used to run breseq with me?

Email me at the address in the breseq header and I can share a folder for you to upload the large files. Without the input files, I won't be able to diagnose what is going on. It seems there must be a bug around some edge case in creating the HTML alignments.

The machine-readable output files (ex: output/output.gd) for this run should still be complete/fine at the point in the pipeline where it died.

khoriba commented 2 years ago

Thank you for your reply. I can share my fastq and ref data. Unfortunately, I can not found your email address for breseq. where is it ? I'm sorry....

jeffreybarrick commented 2 years ago

When you run breseq at the command line it is in the header.

khoriba commented 2 years ago

I found it. I sent an email to you. Thank you!

jeffreybarrick commented 2 years ago

Issue could not be reproduced. Closing for now.