GATK RealignerTargetCreator error

[vdauwera]

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

http://gatkforums.broadinstitute.org/discussion/2055/realignertargetcreator-error#latest

[raj.musunuri]

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!