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java.lang.NullPointerException when running genotypeGVCF on >100 samples

theomarkertheomarker qingdaoMember
edited January 15 in Ask the GATK team

After processing BAM, I made GVCF for each sample, and use genotypeGVCFs here.
Running the following command in parallel mode (multi-threads) cases an error:

/work/share/software/jre1.8.0_111/bin/java -Xmx60g -jar GenomeAnalysisTK.jar -T GenotypeGVCFs -R /work/home/shilab/exomedata/GATK_boundle/hg19/genome.fa --variant input.list -o GenotypeGVCF.beta.vcf -nt 30

The errror is pasted here:

INFO  11:43:09,914 ProgressMeter -   chr2:26040501   2.52267192E8     2.4 h      33.0 s        8.8%    26.9 h      24.6 h 
INFO  11:44:09,919 ProgressMeter -   chr2:31032901   2.53267192E8     2.4 h      33.0 s        8.9%    26.6 h      24.3 h 
INFO  11:45:09,926 ProgressMeter -   chr2:33019101   2.58267192E8     2.4 h      33.0 s        9.0%    26.6 h      24.2 h 
INFO  11:46:09,975 ProgressMeter -   chr2:38013501   2.61267192E8     2.4 h      33.0 s        9.2%    26.4 h      23.9 h 
INFO  11:47:09,980 ProgressMeter -   chr2:40064501   2.63267192E8     2.4 h      33.0 s        9.2%    26.3 h      23.9 h 
##### ERROR --
##### ERROR stack trace 
java.lang.NullPointerException
        at java.util.LinkedList$ListItr.next(LinkedList.java:893)
        at org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingEngine.coveredByDeletion(GenotypingEngine.java:426)
        at org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingEngine.calculateOutputAlleleSubset(GenotypingEngine.java:387)
        at org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingEngine.calculateGenotypes(GenotypingEngine.java:251)
        at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateGenotypes(UnifiedGenotypingEngine.java:392)
        at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateGenotypes(UnifiedGenotypingEngine.java:375)
        at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateGenotypes(UnifiedGenotypingEngine.java:330)
        at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.regenotypeVC(GenotypeGVCFs.java:326)
        at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:304)
        at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:135)
        at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
        at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
        at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
        at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
        at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
        at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
        at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
        at org.broadinstitute.gatk.engine.executive.ShardTraverser.call(ShardTraverser.java:98)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
        at java.lang.Thread.run(Thread.java:745)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.7-0-gcfedb67):
##### 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://software.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Code exception (see stack trace for error itself)
##### ERROR ------------------------------------------------------------------------------------------

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