Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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.