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java.lang.ExceptionInInitializerError in java.lang.ExceptionInInitializerError

Hello,
We are trying to Run RealignerTargetCreator for 102 Bam files.Out of 102 bam files 14 files are showing the following error.I just want to know that the below issue is because of bam file or with GATK .

Command : java -Xmx8g -jar GenomeAnalysisTKLite.jar -T RealignerTargetCreator -I RISE00.hg19.flt.sort.rmdup.realign.md.bam -R hg19.fa -o RISE00_Interval.intervals -known Mills_and_1000G_gold_standard.indels.hg19.sites.vcf

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

java.lang.ExceptionInInitializerError
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.(GenomeAnalysisEngine.java:160)
at org.broadinstitute.sting.gatk.CommandLineExecutable.a(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 ------------------------------------------------------------------------------------------

Error in the realignment of sample RISE00

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    It's impossible to seay based on this. You can run Picard ValidateSamFile to find out if there's anything wrong with the bam.

    I understand you're probably stuck using that version of GATK, but keep in mind that it is very old and unsupported.
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