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Old 10-13-2009, 07:28 PM   #1
jtjli
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Location: australia

Join Date: Nov 2008
Posts: 21
Question 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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Old 04-07-2010, 08:57 PM   #2
VIX_Z
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Location: INDIA

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Default 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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Old 04-22-2010, 10:15 AM   #3
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Location: ohio

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Default 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:
Originally Posted by jtjli View Post
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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Old 04-22-2010, 12:40 PM   #4
kentnf
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Location: Ithaca

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Default

I got same problem. Does anyone know how to solve it?
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Old 04-26-2010, 07:47 AM   #5
mdachoh
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Default 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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Old 04-27-2010, 06:25 AM   #6
kentnf
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Default

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?

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Originally Posted by mdachoh View Post
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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