I run into a problem when running GenotypeGVCFs for dealig with population gvcfs. my command lines as follows:
/scratch/gkm/software/jdk1.8.0_131/bin/java -Xmx4g -jar /scratch/gkm/software/GATK/GenomeAnalysisTK.jar \
-T GenotypeGVCFs \
-R /newVol/gkm/Project/malus_domestica/reference/GCA_002114115.1_ASM211411v1_genomic.fna \
-nt 12 \
--variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/1/1_raw.g.vcf \
--variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/10/10_raw.g.vcf \
--variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/11/11_raw.g.vcf \
--variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/11-133/11-133_raw.g.vcf \
--variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/11-39/11-39_raw.g.vcf \
--variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/12/12_raw.g.vcf \
--variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/13/13_raw.g.vcf \
--variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/14/14_raw.g.vcf \
--variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/15_merge/15_raw.g.vcf \
--variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/16/16_raw.g.vcf \
--variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/17/17_raw.g.vcf \
--variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/18/18_raw.g.vcf \
--variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/19/19_raw.g.vcf \
--variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/2/2_raw.g.vcf \
--variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/20/20_raw.g.vcf \
--variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/21/21_raw.g.vcf \
--variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/22/22_raw.g.vcf \
--variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/23/23_raw.g.vcf \
--variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/24/24_raw.g.vcf \
--variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/25/25_raw.g.vcf \
--variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/26/26_raw.g.vcf \
--variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/27/27_raw.g.vcf \
--variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/28/28_raw.g.vcf \
--variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/29/29_raw.g.vcf \
--variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/3/3_raw.g.vcf \
--variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/30/30_raw.g.vcf \
--variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/31/31_raw.g.vcf \
--variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/32/32_raw.g.vcf \
--variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/33/33_raw.g.vcf \
--variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/34/34_raw.g.vcf \
--variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/35/35_raw.g.vcf \
-o out.vcf
Get a error:
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:748)
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 ------------------------------------------------------------------------------------------
I look forwards to get a solution, thanks!