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# DepthofCoverage Walker

Washington DCMember
edited June 2013

Hi I am trying to run the DepthofCoverage walker from GATK for the first time and I am running into stumbling blocks. I am interested in getting coverage info for genes and I downloaded the Refseq genes list and am filtering and sorting according to specifications. I am using the SortByRef.pl script provided in the website. However, I am getting an error saying:

Can not open temporary file 1045: Too many open files at SortByRef.pl line 68, <\$INPUT> line 1021.


I also checked the soft/hard limits for filesystem and it shows that my current system's limit is the following:

ulimit -u :386246
ulimit -S -u: 386246


I am stuck at this point and don't know how to proceed.

Any help is much appreciated.

Thanks

Tagged:

Hi there,

I'm not familiar with the -u flag of ulimit. Can you do ulimit -a | grep open` instead? To be sure what you're getting is the limit on number of open files. Because that number you're showing there seems awfully large...

• Washington DCMember

I was just following instructions from a different post that I found.
open files (-n) 1024
Here's what I get when I ran your command:

• Washington DCMember

Oops here's what I got:

open files (-n) 1024

• Washington DCMember

Thanks a lot. Will have to ask my sys admin to do it. Will let you know how it goes.