One out of my 200 samples failed, no matter using single thread more multiple threads. Here is the message:
INFO 15:27:03,632 ProgressMeter - 1:148025863 8.6339635E7 3.5 m 2.0 s 5.7% 61.9 m 58.4 m
INFO 15:27:43,633 ProgressMeter - 1:161087901 1.53300685E8 4.2 m 1.0 s 6.1% 67.9 m 63.8 m
INFO 15:28:23,634 ProgressMeter - 1:183114727 1.83921283E8 4.8 m 1.0 s 7.6% 63.7 m 58.9 m
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(HaplotypeCa llerGenotypingEngine.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$ReadMapReduceJob.run(NanoScheduler.java:471)
at java.util.concurrent.Executors$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)
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 ------------------------------------------------------------------------------------------
my code:
java -Xmx40g -jar picard.jar MarkDuplicates I=TQ24562_Norecur_Base2.bam O=TQ24562_Norecur_Base2.rmdup.bam ASSUME_SORTED=true REMOVE_DUPLICATES=true CREATE_INDEX=true VALIDATION_STRINGENCY=SILENT M=TQ24562_Norecur_Base2.rmdup.bam.metrics
java -Xmx40g -jar GenomeAnalysisTK.jar -T BaseRecalibrator -nct 1 -rf BadCigar -R human_g1k_v37.fasta -I TQ24562_Norecur_Base2.rmdup.bam -knownSites human_GRCh37_v142_16569_MT.vcf -knownSites Mills_and_1000G_gold_standard.indels.b37.vcf -o TQ24562_Norecur_Base2.rmdup.recal.table
java -Xmx40g -jar GenomeAnalysisTK.jar -T PrintReads -nct 1 -rf BadCigar -R human_g1k_v37.fasta -I TQ24562_Norecur_Base2.rmdup.bam -BQSR TQ24562_Norecur_Base2.rmdup.recal.table -o TQ24562_Norecur_Base2.rmdup.recal.bam -simplifyBAM
java -Xmx40G -jar GenomeAnalysisTK.jar -T HaplotypeCaller --emitRefConfidence GVCF -R human_g1k_v37.fasta -I TQ24562_Norecur_Base2.rmdup.recal.bam -nct 8 --out TQ24562_Norecur_Base2.g.vcf -L target.bed
But the HaplotypeCaller was succeed when I used the bwa bam file (without markduplicate and recalibration).