see segmentation fault in soapsnp

guoweiguowei@gmail.com · 04-19-2010, 09:29 AM

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 · 04-19-2010, 01:36 PM

sounds like a memory issue...

how much ram do you have?

guoweiguowei@gmail.com · 04-21-2010, 11:10 AM

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 · 04-21-2010, 10:15 PM

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

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04-19-2010, 09:29 AM	#1
guoweiguowei@gmail.com Junior Member Location: ohio Join Date: Apr 2010 Posts: 4	see segmentation fault in soapsnp 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.

04-19-2010, 01:36 PM	#2
jgibbons1 Senior Member Location: Worcester, MA Join Date: Oct 2009 Posts: 133	sounds like a memory issue... how much ram do you have?

04-21-2010, 11:10 AM	#3
guoweiguowei@gmail.com Junior Member Location: ohio Join Date: Apr 2010 Posts: 4	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.

04-21-2010, 10:15 PM	#4
JohnK Senior Member Location: Los Angeles, China. Join Date: Feb 2010 Posts: 106	I get segment faults every now and then. I'd try increasing memory or changing permissions first.