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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

MarkDuplicatesSpark crash

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5 comments

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    David Gómez-Sánchez

    Sorry, exact command was: gatk MarkDuplicatesSpark -I 1.bam -O MD_Spark_1.bam

     
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    Derek Caetano-Anolles

    The issue doesn't seem to be originating from MarkDuplicatesSpark; it's coming from Java. You're trying to load a Java class file that is unsupported in the version of Java that you are running.

    If I had to guess I'd say that the version of JDK you are running is older than the version MarkDuplicatesSpark was designed to run under.

    Can you please update your dependencies and try again?

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    David Gómez-Sánchez

    Hi Derek. 

    When typing "java --version" on the console I get this:


    openjdk 11.0.5 2019-10-15
    OpenJDK Runtime Environment (build 11.0.5+10-post-Ubuntu-0ubuntu1.118.04)
    OpenJDK 64-Bit Server VM (build 11.0.5+10-post-Ubuntu-0ubuntu1.118.04, mixed mode, sharing)

     

    Which java version do I need to install?

    Thanks,
    David.

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    Derek Caetano-Anolles

    Thank you, David. So the issue is definitely related to your version of Java, it's not that your Java is too old, but that it is too new.

    You're running OpenJDK 11, but you're going to need to try running it under OpenJDK 8 instead. Try installing this version and you should not have the error anymore.

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    Louis Bergelson

    We have beta support for running with java 11 but you have to build gatk yourself with some special flags enabled.  If you're interested I can try to walk you through it. 

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