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tseemann / snp-dists

Pairwise SNP distance matrix from a FASTA sequence alignment
GNU General Public License v3.0
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Segmentation fault (core dumped) #14

Closed luciagrami closed 6 years ago

luciagrami commented 6 years ago

Hello, I am trying to run snp-dist (thank you very much for this tool!) in Ubintu 14.04, and i'm getting this error:

This is snp-dists 0.4 Segmentation fault (core dumped)

Apparently it could mean the software tries to access memory and it has no permission, so i tried to solve this with: ulimit -c unlimited but the problem persists.

Can you help me with this? Could it be an instalation problem? Thanks

andersgs commented 6 years ago

Hi @luciagrami. It would help if you could provide us with an example dataset in order to reproduce the problem.

Thank you.

Anders.

luciagrami commented 6 years ago

Ok, I am trying to create the SNP distances matrix from this concatenated alignment of core genes from a set of closley related bacterial isolates. Thanks!

ConcaAlignSGF.fasta.tar.gz

andersgs commented 6 years ago

Hi @luciagrami. Looking into it, thank you. In the meantime, I was able to generate the SNP matrix with the stable release (https://github.com/tseemann/snp-dists/releases/tag/v0.2). Give that one a go, if you can. A.

luciagrami commented 6 years ago

stable release worked! Thanks

kloetzl commented 6 years ago

I would say, this is a duplicate of #9.

tseemann commented 6 years ago

Agreed.