DepthofCoverage Walker

pmudvari

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

Geraldine_VdAuwera

Ah, there you go -- that's your limit, which you'll need to increase. If you have admin permissions you can edit your /etc/security/limits.conf file to e.g.

me soft nofile 60000 
me hard nofile 60000

If you don't have the permissions, you'll need to ask your systems administrator to do it for you.

Geraldine_VdAuwera

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...

pmudvari

Thanks for your prompt reply.
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:

pmudvari

Oops here's what I got:

open files (-n) 1024

Geraldine_VdAuwera

Ah, there you go -- that's your limit, which you'll need to increase. If you have admin permissions you can edit your /etc/security/limits.conf file to e.g.

me soft nofile 60000 
me hard nofile 60000

If you don't have the permissions, you'll need to ask your systems administrator to do it for you.

pmudvari

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