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missing ProgramElementDoc


I'm trying to run the depth of coverage analysis with the following command:

java -jar /usr/local/gatk/GenomeAnalysisTK.jar -T DepthOfCoverage -I 6293-BRCA_S7.bam -R hg19.fasta

I get this trace:

INFO 10:52:31,682 HelpFormatter - --------------------------------------------------------------------------------
INFO 10:52:31,683 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-4-g57ea19f, Compiled 2012/12/20 15:09:50
INFO 10:52:31,683 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 10:52:31,683 HelpFormatter - For support and documentation go to
INFO 10:52:31,686 HelpFormatter - Program Args: -T DepthOfCoverage -I 6293-BRCA_S7.bam -R hg19.fasta
INFO 10:52:31,686 HelpFormatter - Date/Time: 2012/12/27 10:52:31
INFO 10:52:31,686 HelpFormatter - --------------------------------------------------------------------------------
INFO 10:52:31,686 HelpFormatter - --------------------------------------------------------------------------------
INFO 10:52:31,696 GenomeAnalysisEngine - Strictness is SILENT
INFO 10:52:31,786 GenomeAnalysisEngine - Downsampling Settings: No downsampling
INFO 10:52:31,790 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 10:52:31,799 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01

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

java.lang.NoClassDefFoundError: com/sun/javadoc/ProgramElementDoc
at org.broadinstitute.sting.utils.exceptions.UserException$LexicographicallySortedSequenceDictionary.(
at org.broadinstitute.sting.utils.SequenceDictionaryUtils.validateDictionaries(
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.validateSourcesAgainstReference(
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.getReferenceOrderedDataSources(
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.initializeDataSources(
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(
at org.broadinstitute.sting.commandline.CommandLineProgram.start(
at org.broadinstitute.sting.commandline.CommandLineProgram.start(
at org.broadinstitute.sting.gatk.CommandLineGATK.main(
Caused by: java.lang.ClassNotFoundException: com.sun.javadoc.ProgramElementDoc
at Method)
at java.lang.ClassLoader.loadClass(
at sun.misc.Launcher$AppClassLoader.loadClass(
at java.lang.ClassLoader.loadClass(
... 10 more

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.3-4-g57ea19f):

I'm in debian wheezy, I've tried with:


and also with the java-sun binary.
Maybe the problem is due to my lack of experience with java. Any advice?
Best regards,

Jose Blanca

Best Answer


  • jblancajblanca Member

    Thanks for the answer, it really helps.
    I was using your precompiled GATK.
    I tried with OpenJDK and with the sun java and in both had the same problem. I think I'll give up for the time being because I completely ignore everything about the java ecosystem. I was trying to compare GATK with bedtools.
    Best regards, and thanks again for you answer.

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