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niemasd / ViralConsensus

Fast viral consensus genome reconstruction
https://niema.net/ViralConsensus/
GNU General Public License v3.0
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Segmentation Fault - file size? #12

Open VBHerrenC opened 2 weeks ago

VBHerrenC commented 2 weeks ago

Hello,

In my attempts to use ViralConsensus on the command line, I'm having trouble with certain reference fastas. When I provide a reference of 4153 nt, a consensus fasta is outputted properly. When I decrease the size of the reference to something less than 4150 nt, it throws a segmentation fault. The same errors are repeated on the web version. Is it possible there is a minimum size for the reference sequence? Any help would be appreciated!

Thanks, Calleigh

niemasd commented 2 weeks ago

Thank you for reaching out! I don't think there should be a minimum reference genome size, but there could be a bug somewhere (I've mainly tested on SARS-CoV-2). Do you happen to have an example reference genome + SAM/BAM file you would be able to share that triggers the segmentation fault? If you are able to provide one, I can use it to help me debug

VBHerrenC commented 2 weeks ago

Hi,

Sorry, we figured it out! Turns out I was trying to provide a different reference than the one I had used to align the reads to. Thanks for the quick reply though!

niemasd commented 2 weeks ago

Thanks for double checking, and I'm glad to hear you figured it out! If possible, would you be able to share a small example dataset regardless? It would be good for me to add some error-checking to have it output a meaningful error message in this scenario instead of a generic "Segmentation Fault"