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Thread Tools |
10-13-2009, 07:28 PM
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#1 |
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Member
Location: australia Join Date: Nov 2008
Posts: 20
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soapsnp segmentation fault - help!
i downloaded the latest versions of soapAlign, msort and soapSnp today.
I ran soapAlign and msort (-k n9) no problem. But when i ran SoapSNP on the sorted file, i got a segmentation fault. Any idea???? Thanks Jason |
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04-07-2010, 08:57 PM
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#2 |
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Member
Location: INDIA Join Date: Mar 2009
Posts: 11
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Segmentation fault while using SOAPsnp
Hi,
I am using SOAPsnp for the first time. I tried it with bowtie aligned file and ended up with segmentation fault as mentioned below ------------------------------ Reading Chromosome and dbSNP information Done. Correction Matrix Done! Segmentation fault ------------------------------ I am not sure if SOAPsnp accepts bowtie aligned file or this fault is because of some other reason. Any HELP? ~Vix |
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04-22-2010, 10:15 AM
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#3 | |
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Junior Member
Location: ohio Join Date: Apr 2010
Posts: 4
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did u figure out this problem.
I have the same problem of segmentation fault. Did you figure this out now? Somebody told me it may be caused by memory issue. But the computer administrator in our dep. said it is caused by the soapsnp itself. I am lost.
Thanks. Quote:
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04-22-2010, 12:40 PM
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#4 |
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Member
Location: Ithaca Join Date: Jan 2009
Posts: 19
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I got same problem. Does anyone know how to solve it?
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04-26-2010, 07:47 AM
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#5 |
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Junior Member
Location: Cleveland, OH Join Date: Oct 2009
Posts: 2
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try -L option
soapsnp has a default maximum read length of 45; try using -L to increase this to at least the length of your longest read (e.g. 76).
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04-27-2010, 06:25 AM
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#6 | |
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Member
Location: Ithaca Join Date: Jan 2009
Posts: 19
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Thank you! it works.
I can see the different base between reference and reads, but I can't get the cell line or strain name for every reads? I want to find the SNP between two different strains, how to do it? Quote:
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