ERROR MESSAGE: com/sun/javadoc/ProgramElementDoc
Posted in Ask the GATK team | Last updated on 2013-01-07 19:17:35


Comments (10)

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

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