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java.lang.NullPointerException when running genotypeGVCF on >100 samples
theomarker
qingdaoMember ✭
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 ------------------------------------------------------------------------------------------
Tagged:
Answers
@theomarker
Hi,
I think if you use the latest version of GATK3, this should be fixed.
-Sheila
@Sheila Thanks for your reply. I use GATK3.7, and will change to 3.8 for a try.