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Malformed walker argument

Hello,
I installed GATK package as explained in the documentation, but I am not able to use the "walkers" with go with it. I always this error message:
java -jar GenomeAnalysisTK.jar -T IndelRealigner

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.7-0-gcfedb67):
ERROR
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
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
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions https://software.broadinstitute.org/gatk
ERROR
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR
ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name: IndelRealigner

Any help is more than welcome, I cannot find the problem...
Thank you :)

Best Answer

Answers

  • shleeshlee CambridgeMember, Broadie, Moderator

    Hi @mac,

    Typing java -jar GenomeAnalysisTK.jar -h should list all the tools available and should also list IndelRealigner. This release of GATK (version 3.7-0-gcfedb67) definitely has IndelRealigner as I have used it recently.

    If the problem persists, can you be sure to download the jar afresh and try again.

  • ehschollehscholl Member

    Mac - did you ever find a solution?

    I'm having a similar issue - with ANY tool I try to run
    java -jar /usr/local/bin/GenomeAnalysisTK.jar -T BaseRecalibrator
    Also -T MuTect
    -T IndelRealigner
    -T PrintReads
    -T SplitSamFIle
    -T VariantRecalibrator

    At this point I gave up.
    This is with a downloaded-today version 3.7-0-gcfedb67

    (Also with a version 3.6 and a version 3.5 I've had on my machine....)

    The ONLY thing I can think of is if it's our version of Java, which is on a cluster I'm running on and so out of my control.
    openjdk version "9-internal"
    OpenJDK Runtime Environment (build 9-internal+0-2016-04-14-195246.buildd.src)
    OpenJDK 64-Bit Server VM (build 9-internal+0-2016-04-14-195246.buildd.src, mixed mode)

    Otherwise - why would NOTHING work?

  • shleeshlee CambridgeMember, Broadie, Moderator

    Hi @ehscholl,

    Are you running UNIX or LINUX?

    Can you download the latest GATK4 jar from https://github.com/broadinstitute/gatk/releases, download the gatk-4.beta.1.zip, unzip and run gatk-launch --list? Do you see a list of tools?

  • macmac bodøMember

    Problem was java version. Thanks for your help :)

  • Sheila - see above.
    openjdk version "9-internal"
    OpenJDK Runtime Environment (build 9-internal+0-2016-04-14-195246.buildd.src)
    OpenJDK 64-Bit Server VM (build 9-internal+0-2016-04-14-195246.buildd.src, mixed mode)

    I've downloaded 4.beta.4 and it appears to be running OK now.

    (I wanted to update, for other people who may be having the same issue - version 4 seems to work with java 9)

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @ehscholl
    Hi,

    I am checking with the developers whether it is okay to use Java 9. Sometimes things run, but could cause silent errors/odd results. I will get back to you soon.

    -Sheila

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @ehscholl
    Hi again,

    The developers say they honestly don't know if you can use Java 9 safely. They have not tested it. To be safe, you should stick with using Java 8 which has been tested and is known to be safe to use.

    -Sheila

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