We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

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 ✭✭✭✭✭


    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

Sign In or Register to comment.