Gatk Depthofcoverage Sortbyref.Pl Error

Question

[pm2013]

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

Any help is much appreciated.

Thanks

Answer 1

[pablo.riesgo]

Your problem is solved here: http://gatkforums.broadinstitute.org/discussion/1328/script-for-sorting-an-input-file-based-on-a-reference-sortbyref-pl

Be sure you restart your computer after modifying the indicated configuration files.

Cheers, Pablo.