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  • GATK RealignerTargetCreator error

    Hello All, I am working with some Illumina FASTQ files. I used Mosaik to align the data. I then sorted, indexed and marked the bam file for PCR duplicates using picard. And then in order to realign around the indels, I used the RealignerTargetCreator. Here is the error I go from it:
    ERROR ------------------------------------------------------------------------------------------
    ERROR stack trace

    java.lang.NoClassDefFoundError: com/sun/javadoc/ProgramElementDoc at org.broadinstitute.sting.utils.exceptions.UserException$LexicographicallySortedSequenceDictionary.(UserException.java:354) at org.broadinstitute.sting.utils.SequenceDictionaryUtils.validateDictionaries(SequenceDictionaryUtils.java:128) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.validateSourcesAgainstReference(GenomeAnalysisEngine.java:823) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.getReferenceOrderedDataSources(GenomeAnalysisEngine.java:907) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.initializeDataSources(GenomeAnalysisEngine.java:765) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:259) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:237) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:147) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:94) Caused by: java.lang.ClassNotFoundException: com.sun.javadoc.ProgramElementDoc at java.net.URLClassLoader$1.run(URLClassLoader.java:366) at java.net.URLClassLoader$1.run(URLClassLoader.java:355) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:354) at java.lang.ClassLoader.loadClass(ClassLoader.java:423) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308) at java.lang.ClassLoader.loadClass(ClassLoader.java:356) ... 10 more
    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 2.3-0-g9593e74):
    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: com/sun/javadoc/ProgramElementDoc
    ERROR ------------------------------------------------------------------------------------------

    Any help is welcome. Thanks in advance!

  • #2
    This problem has been solved on the GATK forum at this address:

    Comment

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