Segmentation fault with larger sequences (on Desktop and HPC)

sanger-pathogens / snp-sites

Finds SNP sites from a multi-FASTA alignment file

http://sanger-pathogens.github.io/snp-sites/

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Segmentation fault with larger sequences (on Desktop and HPC) #57

Closed CMWbio closed 7 years ago

CMWbio commented 7 years ago

Hi,

I am running into a segmentation fault when calling the variants on a fasta with genome size > approx 9Mb (8Mb of the same fasta works fine). Any thoughts as to why this is the case? I couldn't see a hard maximum genome length in the code.

edit: generating some test fastas with the included perl script reveals that it is an issue with the number of variants in the alignment, which makes sense.

Cheers

Chris

andrewjpage commented 7 years ago

Hi Chris, There is no hardcoded maximum genome length. The largest I have ever passed in are 6Mbase genomes. The most number of samples has been about 10,000.
I'm afraid I can't see your attached perl script?
Regards, Andrew

andrewjpage commented 7 years ago

Hi Chris, I think I have identified the issue. Could you try out the latest version (2.3.3)? Regards, Andrew

CMWbio commented 7 years ago

Hi Andrew Thank you for the speedy reply, I have tested and the bug is solved (tested up to 50Mb total genome size).

Thanks

Chris