Hi,
Following "best practice", I am running haplotypecaller for each individual with the command
java -Xmx131072m -jar GenomeAnalysisTK.jar \
-T HaplotypeCaller \
-I bam \
-o g.vcf \
-R GRCh38_full_analysis_set_plus_decoy_hla.fa \
--emitRefConfidence GVCF
There are more than 30 individual's WGS, 8 out of which report the error. The rest are good.
"##### ERROR --
ERROR stack trace
java.util.NoSuchElementException
at java.util.HashMap$HashIterator.nextNode(HashMap.java:1431)
at java.util.HashMap$KeyIterator.next(HashMap.java:1453)
at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.reduceNumberOfAlternativeAllelesBasedOnLikelihoods(HaplotypeCallerGenotypingEngine.java:336)
at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.assignGenotypeLikelihoods(HaplotypeCallerGenotypingEngine.java:264)
at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:964)
at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:251)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:709)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:705)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:274)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:78)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:311)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:255)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:157)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)
ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.6-0-g89b7209):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions https://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Code exception (see stack trace for error itself)
"
Then I repeat HaplotypeCaller for these 8 bad bams again. The same errors are reported, and the outputed gvcf terminate at the same place.
Then I checked the a good input bam for HaplotypeCaller and a bad input bam for HaplotypeCaller with picard "ValidateSamFile". Both of them have "MATE_NOT_FOUND" error.
Could you suggest how to fix this problem?
Thanks!
best,
Peter