Hi GATK Team,
I am running HaplotypeCaller on my BAM file, command line:
... variants calling by gatk with multi sample is start ~...
2016-07-03 00:13:44: java -XX:ParallelGCThreads=5 -Xmx50g -Djava.io.tmpdir=/home/fubaiqi/project/BnXFS/Callsnp_Analysis/SNP/tmp -jar /home/fubaiqi/biosoft/GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -R /home/fubaiqi/project/BnXFS/Callsnp_Analysis/Ref/Brassica_napus_v4.1.chromosomes.fa --genotyping_mode DISCOVERY -stand_emit_conf 10 -stand_call_conf 30 -o /home/fubaiqi/project/BnXFS/Callsnp_Analysis/SNP/first/gatk.raw.vcf
-I /home/fubaiqi/project/BnXFS/Callsnp_Analysis/Mapping/bwa/sort/001.sort.bam
-I /home/fubaiqi/project/BnXFS/Callsnp_Analysis/Mapping/bwa/sort/002.sort.bam
-I /home/fubaiqi/project/BnXFS/Callsnp_Analysis/Mapping/bwa/sort/003.sort.bam ......
error information:
INFO 06:10:36,672 ProgressMeter - chrA03:22489680 4.8061593E7 29.9 h 37.4 m 8.3% 15.0 d 13.8 d
INFO 06:11:36,673 ProgressMeter - chrA03:22611608 4.8061593E7 30.0 h 37.4 m 8.3% 15.0 d 13.8 d
INFO 06:12:36,675 ProgressMeter - chrA03:22709288 4.8061593E7 30.0 h 37.4 m 8.3% 15.0 d 13.8 d
INFO 06:13:36,676 ProgressMeter - chrA03:22784541 4.8061593E7 30.0 h 37.4 m 8.3% 15.0 d 13.8 d
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)
ERROR ------------------------------------------------------------------------------------------
Thanks in advance for your help.
Best Wishes,
Baiqi Fu