see segmentation fault in soapsnp

[[email protected]]

When I run the following command in linux
2bwt-builder ref.fasta
soap -a reads.fastq -D ref.fasta.index -o reads.soap
msort -k n9 reads.soap > sort.reads.soap
soapsnp -i sort.reads.soap -d ref.fasta -o reads.soapsnp

soap and msort (or use linux sort command) works well. But when I run soapsnp to call SNPs, I found
'segmentation fault'.

No idea about this.

[jgibbons1]

sounds like a memory issue...

how much ram do you have?

[[email protected]]

I run this in a unix server which have 20GB memory. If soap does not have its own memory limit, I do not think this is caused by it.

[JohnK]

I get segment faults every now and then. I'd try increasing memory or changing permissions first.