If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra

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error message

i am getting following error message on linux system
Please Check Error:

[email protected]:~/NGS_run_sagar/bwa$ java -Xmx8G
-jar /home/iontorrent/NGS_sofware/GenomeAnalysisTK-3.6/GenomeAnalysisTK.jar
Exception in thread "main" java.lang.UnsupportedClassVersionError:
org/broadinstitute/gatk/engine/CommandLineGATK : Unsupported
major.minor version 52.0
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(
at Method)
at java.lang.ClassLoader.loadClass(
at sun.misc.Launcher$AppClassLoader.loadClass(
at java.lang.ClassLoader.loadClass(
at sun.launcher.LauncherHelper.checkAndLoadMain(


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    You're using the wrong version of Java, you must use Java 8 (jre/jdk 1.8).
  • thank you Geraldine_VdAuwera
    still after updating JAVA new error it is showing as
    Now Error is:

    ERROR ------------------------------------------------------------------------------------------
    ERROR A USER ERROR has occurred (version 3.6-0-g89b7209):
    ERROR This means that one or more arguments or inputs in your command are incorrect.
    ERROR The error message below tells you what is the problem.
    ERROR If the problem is an invalid argument, please check the online documentation guide
    ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
    ERROR Visit our website and forum for extensive documentation and answers to
    ERROR commonly asked questions
    ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
    ERROR MESSAGE: Argument with name '--analysis_type' (-T) is missing.
    ERROR ------------------------------------------------------------------------------------------
  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    Well, now your command line is incomplete or badly formatted. Please read the getting started guide before asking any more questions.
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