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Installing latest Mutect1

Hi,

To review a paper, I would need to install MuTect.1.1.7 that I got from the GATK download page.
GATK3.6 is already installed on my machine but I am not sure if it is compatible with MuTect1.
I also followed the installation guide from GitHub but I can only get GATK4 from the repo.

How could I do?
Thanks !

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Answers

  • EADGEADG KielMember ✭✭✭
  • Thanks for the link !
    However, this is version 1.1.4 and I only get a .jar file.
    I think I have to install GATK version ≤ 3.4 at least for MuTect 1 to be compatible with.

  • Mutect1.1.7 available on GATK website (https://software.broadinstitute.org/gatk/download/mutect) is supposed to be a standalone version.
    But when I run:
    java -jar mutect-1.1.7.jar

    I get the following error:

    ERROR ------------------------------------------------------------------------------------------
    ERROR stack trace

    java.lang.ExceptionInInitializerError
    at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.(GenomeAnalysisEngine.java:167)
    at org.broadinstitute.sting.gatk.CommandLineExecutable.(CommandLineExecutable.java:57)
    at org.broadinstitute.sting.gatk.CommandLineGATK.(CommandLineGATK.java:66)
    at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:106)
    Caused by: java.lang.NullPointerException
    at org.reflections.Reflections.scan(Reflections.java:220)
    at org.reflections.Reflections.scan(Reflections.java:166)
    at org.reflections.Reflections.(Reflections.java:94)
    at org.broadinstitute.sting.utils.classloader.PluginManager.(PluginManager.java:79)
    ... 4 more

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 3.1-0-g72492bb):
    ERROR
    ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
    ERROR If not, please post the error message, with stack trace, to the GATK forum.
    ERROR Visit our website and forum for extensive documentation and answers to
    ERROR commonly asked questions http://www.broadinstitute.org/gatk
    ERROR
    ERROR MESSAGE: Code exception (see stack trace for error itself)
    ERROR ------------------------------------------------------------------------------------------

    I then tried to install GATK 3.4 from the GitHub source following these instructions (https://github.com/broadinstitute/mutect).
    But I get a compilation failure for GATK Tools Public:
    [INFO] ------------------------------------------------------------------------
    [INFO] Reactor Summary:
    [INFO]
    [INFO] GATK Root .......................................... SUCCESS [ 0.928 s]
    [INFO] GATK Aggregator .................................... SUCCESS [ 0.660 s]
    [INFO] GATK GSALib ........................................ SUCCESS [ 0.867 s]
    [INFO] GATK Utils ......................................... SUCCESS [ 6.813 s]
    [INFO] GATK Engine ........................................ SUCCESS [ 3.208 s]
    [INFO] GATK Tools Public .................................. FAILURE [ 3.417 s]
    [INFO] External Example ................................... SKIPPED
    [INFO] GATK Aggregator Public ............................. SKIPPED
    [INFO] ------------------------------------------------------------------------
    [INFO] BUILD FAILURE
    [INFO] ------------------------------------------------------------------------
    [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (compile-java) on project gatk-tools-public: Compilation failure

    I don't know anything about how GitHub repo works, any help would be greatly appreciated !
    Or anyone knows where I could get the already built GATK v ≤3.4?

  • user31888user31888 Member
    Accepted Answer

    Wrong java version (need java 7).
    Works with the binary from GATK website.
    Sorry...

  • EADGEADG KielMember ✭✭✭

    Glad you solve this...another option would be the actual genomeInTheCloud-DockerContainer with built in gatk3.4

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