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Old 04-19-2010, 09:29 AM   #1
guoweiguowei@gmail.com
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Location: ohio

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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.
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Old 04-19-2010, 01:36 PM   #2
jgibbons1
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sounds like a memory issue...

how much ram do you have?
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Old 04-21-2010, 11:10 AM   #3
guoweiguowei@gmail.com
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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.
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Old 04-21-2010, 10:15 PM   #4
JohnK
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I get segment faults every now and then. I'd try increasing memory or changing permissions first.
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