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memory allocation for DataProcessingPipeline in internal broad network

naarkhoonaarkhoo Member Posts: 38
edited January 2013 in Ask the GATK team

Is there any rule of thumb for allocating memory through "bsub" for running DataProcessingPipeline per bam file or per number of reads ?

Thanks

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,633 admin

    Sorry, we don't provide recommendations at that level. Perhaps other users may want to share their experience in this matter?

    Geraldine Van der Auwera, PhD

  • naarkhoonaarkhoo Member Posts: 38

    and just to add some other aspect to my questions for other users, what could be an efficient way to retrieve the processing; meaning continuing the pipeline from the point that it got terminated.

  • pdexheimerpdexheimer Member, Dev Posts: 544 ✭✭✭✭

    I'm a little confused by what you're asking. Queue automatically checkpoints the steps as it runs them, and will restart from the appropriate point by itself (assuming you don't tell it otherwise).

    As for the memory, that's controlled in the qscript, not from the bsub command. The actual Queue job that you submit doesn't consume much in the way of resources, I think I give it 4GB of RAM, but that's probably way too much

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