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hsinnan75 / GSAlign

GSAlign: an ultra-fast sequence alignment algorithm for intra-species genome comparison
MIT License
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Segmentation fault on alignment #4

Closed salanova-elliott closed 4 years ago

salanova-elliott commented 4 years ago

Hello,

I'm running GenAlign v1.0.21 installed through Bioconda on a machine running Ubuntu18.04. I was trying to align some chloroplast genomes and around half have been successfully processed through GSAlign, but the others are producing a Segmentation fault (core dumped) error. I can't see any obvious differences between files that are working and those that aren't. Attached are two genomes that are producing the error.

chloros.zip

Any ideas on what could be causing the problem?

Thanks!

hsinnan75 commented 4 years ago

Thank you for reporting this issue. I'll find the bugs with the two files and let you know asap.

hsinnan75 commented 4 years ago

The headers of the two sequences are too long to load to memory. If you use a much shorter header, the error won't happen. But I still fixed the bug and you can update GSAlign if you don't want to modify the sequence headers. Thank you!

salanova-elliott commented 4 years ago

Great, thank you so much for the incredibly fast response time!

yassineS commented 3 years ago

Thanks for the great support!

I just wanted to note that this issue is resolved when working with fast, but persists when working with an indexed target (-i).