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

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

testing 3.4-0

I've just had GATK upgraded from 3.2.2 to 3.4-0

My input is:


$ -N gatk_test

$ -pe openmp 30

$ -S /bin/sh

$ -cwd

$ -j y

$ -q bioinf.q

. /etc/profile.d/modules.sh

module load jre/1.7.0_25
module load gatk/3.4-0

GenomeAnalysisTK --help \

module unload gatk/3.4-0
module unload jre/1.7.0_25

Unfortunately this returns
/cm/shared/apps/sge/8.2.1/default/spool//node045/job_scripts/6068146: line 15: GenomeAnalysisTK: command not found

I've asked the server admin to check installation but I was wondering if you guys had any suggestions, e.g. Java version


Best Answer


  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    Java version 1.7 should be fine. What happens when you type java -jar GenomeAnalysisTK.jar --help?


  • BlueBlue Member

    Hi @Sheila

    -bash-4.1$ module load gatk/3.4-0
    -bash-4.1$ java -jar GenomeAnalysisTK.jar
    Unable to access jarfile GenomeAnalysisTK.jar

  • BlueBlue Member


    Though note that with my server configuration I omit the java commands, below showing that 3.2 works (with GenomeAnalysisTK --help) but 3.4 doesn't. Note that I haven't used or installed 3.3.

    -bash-4.1$ module load jdk/1.7.0_51_openjdk
    -bash-4.1$ module load gatk/3.4-0
    -bash-4.1$ GenomeAnalysisTK --help
    -bash: GenomeAnalysisTK: command not found
    -bash-4.1$ module unload gatk/3.4-0
    -bash-4.1$ module load gatk/3.2.2

    -bash-4.1$ GenomeAnalysisTK --help

    The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03

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