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Old 04-19-2010, 09:29 AM   #1
Junior Member
Location: ohio

Join Date: Apr 2010
Posts: 4
Question 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. is offline   Reply With Quote
Old 04-19-2010, 01:36 PM   #2
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Location: Worcester, MA

Join Date: Oct 2009
Posts: 133

sounds like a memory issue...

how much ram do you have?
jgibbons1 is offline   Reply With Quote
Old 04-21-2010, 11:10 AM   #3
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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. is offline   Reply With Quote
Old 04-21-2010, 10:15 PM   #4
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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.
JohnK is offline   Reply With Quote


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