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'Cannot allocate memory' when I try to run gatk4-data-processing use whole genome data of one person

I have tried to run gatk4-data-processing with the test data you provide, with no error tips, finally I got the outputs.
Then ,I tried to run this workflow with whole genome data of one person,however,it always reported some error like this:
OpenJDK 64-Bit Server VM warning: INFO: os::commit_memory(0x000000079af80000, 1695023104, 0) failed; error='Cannot allocate memory'
(errno=12)
I read the processing-for-variant-discovery-gatk4.wdl, and guess that the reason may be I do not have enough memory to support it.
However, I can not get more memory or change another better mechine, may I do something else to run this workflow with my data?
When It call this task:BaseRecalibrator,it will been shut down:

Is there any method to change the scatter function?
Thank u very much to give me some suggestions,I will be appricate for your suggestions.

Best Answer

  • bhanuGandhambhanuGandham Cambridge MA admin
    Accepted Answer

    Hi @2tong

    Would you please send me your machine specifications, because my best guess is that the machine you are using is unable to handle the basic memory requirements of the BaseRecalibrator.

    One option is to try firecloud, which is an open platform for secure and scalable analysis on the cloud. Firecloud has a free credits program, which you use to see if it fits your purpose. Firecloud is provided by GATK developers. For more information please follow this link: https://software.broadinstitute.org/firecloud/documentation/freecredits

    I hope this helps.

    Regards
    Bhanu

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