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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

Java exception: index 65 is CONSTANT_MethodRef and should be CONSTANT_InterfaceMethodRef

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    Anthony Dias-Ciarla

    Hi Julián García-Abadillo,

    Thank you for writing to the GATK forum! We hope that we can help you sort this out.

    BQSR, in itself, cannot change the Java version. What appears to be happening is that you are starting GATK on Java 8, and your cluster environment is substituting Java 11 at runtime, causing this error. So the problem is related to your cluster environment.

    We suggest you talk to the admin of your cluster and show them this error. Try asking them if there is anything in the cluster setup that could cause the Java version to change like this. You could also try running BQSR using our official Docker image, which would be isolated from the external cluster environment.

    I hope this helps! Please let me know if this leads you to success. In the meantime, if any other questions arise, please do not hesitate to reach out.

    Best,
    Anthony

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    Anthony Dias-Ciarla

    Hi Julián García-Abadillo,

    We haven't heard from you in a while so we're going to close out this ticket. If you still require assistance, simply respond to this email and we'll be happy to pick up where we left off!

    Kind regards,

    Anthony​

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