Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!

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.

Error stack trace when I try running GenomeAnalysisTKLite.jar.

Hello, so I know this may sound odd, but I have to use an older version of GATK for my company. We are using 2.3.0 and when I try running it on a new machine I get.

`##### ERROR ------------------------------------------------------------------------------------------

ERROR stack trace

java.lang.ExceptionInInitializerError
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.(GenomeAnalysisEngine.java:160)
at org.broadinstitute.sting.gatk.CommandLineExecutable.(CommandLineExecutable.java:53)
at org.broadinstitute.sting.gatk.CommandLineGATK.(CommandLineGATK.java:54)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:90)
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:77)
... 4 more

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.3-9-gdcdccbb):
ERROR
ERROR Please visit the wiki to see if this is a known problem
ERROR If not, please post the error, 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'm not sure what is causing this because when I run it on my older machine which has BioLinux 14.04, it works. But this is the error I recieve when I try running it on Ubuntu 16.04.

Also, I'm not even inputting any parameters yet..I'm just typing java -jar GenomeAnalysisTKLite.jar

Any ideas?

Comments

Sign In or Register to comment.