If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

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.
We will be out of the office on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.

LSF job resource allocation with Queue

Greetings GATK Team,

I am working with Queue for the GATK and am having some difficulties getting the resource allocation aspect to work on our cluster using LSF. I have used the command line options -memLimit, -resMemLimit and -jobNative to allocate the memory needed for the jobs spurred by Queue. When looking at the jobs after their submission, they do not seem to have requested the resources I specified.

Likewise, I would like to specify how many cores to reserve for each job and assume I do that with -jobNative (-n 4,4, for instance). Again, the allocation doesn't seem to show up in the job description as being requested and watching the job indicates that Queue ignores it.

Can you help me to work through this?

thanks for the great toolkit,



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