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RealignerTargetCreator Bug

Hi there,

I'm running GATK (version 3.1-1-g07a4bf8).
I already ran RealignerTargerCreator and IndelRealigner without any problem on my computer.
However, today, RealignerTargetcreator no longer works and I got this error message:

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 ------------------------------------------------------------------------------------------

Yesterday, I updated my setting from Ubuntu 13.10 to 14.04 and java from 1.7 to "1.8.0_05".
Reading the error stack trace (notably "Caused by: java.lang.NullPointerException"), could it be that this last java update is causing this error?

But after I upgraded java, I have been successfully using 2 programs running with java: picard (MarkDuplicates.jar or BuildBamIndex.jar tools) or Qualimap_v0.8.

Would you have any idea to help me solve this issue?
Many thanks !


Best Answers


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