ERROR MESSAGE: com/sun/javadoc/ProgramElementDoc

Jinyan

Dear expert,

When I run gatk with fellow command,

java -Xmx10g -Xms10g -jar ~/bin/GenomeAnalysisTK-2.3-4-g57ea19f/GenomeAnalysisTK.jar \ -T BaseRecalibrator \ -R Homo_sapiens.GRCh37.63/bak/Homo_sapiens.GRCh37.63.dna.chromosome.fa \ -knownSites ~/bin/GenomeAnalysisTK-2.3-4-g57ea19f/dbsnp_137.hg19.vcf \ -I input_4.bam \ -o mySample_CovarTable_Recal.grp

I got this error:

INFO 22:25:22,825 RMDTrackBuilder - Creating Tribble index in memory for file ~/bin/GenomeAnalysisTK-2.3-4-g57ea19f/dbsnp_137.hg19.vcf

ERROR ------------------------------------------------------------------------------------------

ERROR stack trace

java.lang.NoClassDefFoundError: com/sun/javadoc/ProgramElementDoc ... ... ...

ERROR MESSAGE: com/sun/javadoc/ProgramElementDoc

Jinyan

Here the bam file is RNA-seq.

pdexheimer

Hmm, this looks like exactly the same error as was reported here: http://gatkforums.broadinstitute.org/discussion/2013/missing-programelementdoc Same version, same error message. Are you by any chance running OpenJDK as well (check the output of "java -version")?

ramma

I just got this same error with RNA-seq samples using OpenJDK. I am running the RealignerTargetCreator as opposed to the BaseRecalibrator though.

If I get time I'll test with Sun Java instead. I'm also running GATK on an Ubuntu 12.04 server if that matters.

Geraldine_VdAuwera

Hey folks, the 'ProgramElementDoc' part of the error seems to be due to a bug in pulling out the exception details. The actual error varies from case to case. We'll fix this in the next release, but in the meantime if you get one of these, please post the entire stack trace so we can help you diagnose the problem.

droazen

This should be fixed in the latest GATK release (2.3-5) -- if those experiencing this problem could try out that version and let us know whether the issue is resolved, it would be helpful.

David

droazen

I take it back -- after reviewing the 2.3-5 patch, I think the issue is likely not resolved after all. We'll probably push out another patch shortly to fix the "ProgramElementDoc" issue.

droazen

The ProgramElementDoc issue should be fixed in version 2.3-6, which should be released in a few hours.