Hi all,
I meet some error while call variant with HaplotypeCaller, please help~~ Thanks a lot!
my CMD:
java -Xmx20g -jar GenomeAnalysisTK-3.6.jar -T HaplotypeCaller -R /human_g1k_v37_decoy.fasta -I Human_9.final.bam -nct 4 -ERC GVCF -o Human_9.GATK.var.g.vcf
the ERROR:
WARN 18:07:03,362 HaplotypeCallerGenotypingEngine - location 3:172459286: too many alternative alleles found (7) larger than the maxi
INFO 18:07:48,028 ProgressMeter - 3:176076605 4.92449994E8 2.8 h 20.0 s 21.3% 13.3 h 10.5 h
WARN 18:08:31,543 HaplotypeCallerGenotypingEngine - location 3:179515377-179515384: too many alternative alleles found (7) larger tha
WARN 18:08:47,882 HaplotypeCallerGenotypingEngine - location 3:181236097: too many alternative alleles found (7) larger than the maxi
INFO 18:08:48,029 ProgressMeter - 3:181255828 4.92449994E8 2.9 h 20.0 s 21.5% 13.3 h 10.4 h
INFO 18:09:48,031 ProgressMeter - 3:185512628 4.92449994E8 2.9 h 21.0 s 21.7% 13.3 h 10.4 h
INFO 18:10:48,032 ProgressMeter - 3:189857581 4.92449994E8 2.9 h 21.0 s 21.8% 13.3 h 10.4 h
WARN 18:11:16,309 HaplotypeCallerGenotypingEngine - location 3:191697932: too many alternative alleles found (7) larger than the maxi
WARN 18:11:18,370 HaplotypeCallerGenotypingEngine - location 3:191780770: too many alternative alleles found (12) larger than the max
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.reduceNumberOfAlternativeAllelesBased
at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.assignGenotypeLikelihoods(HaplotypeCa
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$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:70
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:70
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler$ReadMapReduceJob.run(NanoScheduler.java:471)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)