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!


adklockoadklocko OregonMember


I'm very new to GATK, and I just got the program unzipped today. When I first went to run it (doing the test on the GATK website), I got this error message:

d139-222:GenomeAnalysisTK-3.1-1 EUS$ java -jar GenomeAnalysisTK.jar -h

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

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 3.1-1-g07a4bf8):
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 MESSAGE: Code exception (see stack trace for error itself)
ERROR ------------------------------------------------------------------------------------------

It's possible I have the wrong version of Java installed. I don't have version 1.7xx; the only thing I could download from Oracle is version 1.8.0_05-b13 (and have installed JDK to make this version available under my Terminal).

Any help, including where to go to get a more stable version(?) would be great.



Best Answer


Sign In or Register to comment.