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DepthofCoverage Walker

pmudvaripmudvari Washington DCMember
edited June 2013 in Ask the GATK team

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

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