search

sanger-pathogens / snp-sites

Finds SNP sites from a multi-FASTA alignment file
http://sanger-pathogens.github.io/snp-sites/
Other
233 stars 50 forks source link

segmentation fault with `-b` option #58

Closed kwongj closed 7 years ago

kwongj commented 7 years ago

Version: 

$ snp-sites -V
snp-sites 2.3.2

No problems with standard usage e.g. outputting variant sites only.

On Linux:

$ snp-sites -b -o monomorphic.fa full.aln 
Segmentation fault (core dumped)

On MacOS:

$ snp-sites -b -o monomorphic.fa full.aln
Segmentation fault: 11

Is there a way to turn on a verbose or debugging mode? I can supply the alignment file (multifasta) if needed. 13 sequences, each 1.89Mbp in length.

Thanks for your help.

andrewjpage commented 7 years ago

Hi Jason, It would be great to get a look at the alignment file. Thanks, Andrew

kwongj commented 7 years ago

Thanks Andrew, have sent it to you on slack.

andrewjpage commented 7 years ago

I have fixed the issue in https://github.com/sanger-pathogens/snp-sites/pull/59 so pull down version 2.3.3

kwongj commented 7 years ago

Amazingly efficient! Thanks Andrew.