Segmentation fault with larger sequences (on Desktop and HPC)

[CMWbio]

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]

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]

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

[CMWbio]

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