Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

gatk4-genome-processing-pipeline fails for 30x-coverage Wholegenome data on default GCP custom machinetype



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    Jason Cerrato

    Hi Priyanka Sebastian,

    Thanks for writing in. Based on your message, I believe you are running these workflows on your own Cromwell instance rather than on Terra, is that correct?

    Even if you are not running on Terra, there is an article about PAPI Error Code 10 that may help:

    If you have any further questions after reading through this, please let us know.

    Kind regards,


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    Brian Wiley

    I get this error below and PAPI is NOT mentioned once in the logs.  I have only seen people post this error and in addition with something to do with PAPI.  Why do I only get this error?  I am running on cromwell-52.

    java.lang.Exception: The
    compute backend terminated the job. If this termination is unexpected, examine likely causes such as preemption, running out of disk or memory on the compute inst
    ance, or exceeding the backend's maximum job duration.


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    Genevieve Brandt (she/her)

    Hi Brian Wiley, our GATK support team is focused on questions involving GATK issues or abnormal results. You can see our support policy here. For questions regarding Cromwell, we encourage other users to help each other find solutions. You can also look at these resources for more information:

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