Hi, Sample is NA12878 and HC runs on this sample routinely as part of our testing. This runtime error seems to be sporadic.
ERROR MESSAGE from HC is below
INFO 14:08:15,398 ProgressMeter - 16:28875483 2.74180703772E11 77.5 m 0.0 s 78.4% 98.8 m 21.3 m
WARN 14:08:24,103 HaplotypeCallerGenotypingEngine - location 16:29677823-29677829: too many alternative alleles found (4) larger than the maximum requested with -maxAltAlleles (3), the following will be dropped: GCT.
WARN 14:08:24,105 HaplotypeCallerGenotypingEngine - location 16:29677839: too many alternative alleles found (4) larger than the maximum requested with -maxAltAlleles (3), the following will be dropped: TCA.
WARN 14:08:24,110 HaplotypeCallerGenotypingEngine - location 16:29677845: too many alternative alleles found (6) larger than the maximum requested with -maxAltAlleles (3), the following will be dropped: TCACACACACA, TCACACACACACA, TCACA.
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)