Hi,GATK term
I have set up a bwa + gatk best pratices pipeline for variant calling on WES data (50 samples ).
I use the haplotype caller in gvcf mode.When I joint gvcf to vcf with the following commands:
java -Xmx60g -jar GenomeAnalysisTK.jar \
-T GenotypeGVCFs \
-R human_g1k_v37_decoy.fasta \
-nt 6 \
-V *g.vcf \
......
-o All.WES.raw.vcf
After running this commands, I got the error message is as follows:
ERROR stack trace
java.lang.NullPointerException
at java.util.LinkedList$ListItr.next(LinkedList.java:893)
at org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingEngine.coveredByDeletion(GenotypingEngine.java:426)
at org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingEngine.calculateOutputAlleleSubset(GenotypingEngine.java:387)
at org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingEngine.calculateGenotypes(GenotypingEngine.java:251)
at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateGenotypes(UnifiedGenotypingEngine.java:392)
at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateGenotypes(UnifiedGenotypingEngine.java:375)
at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateGenotypes(UnifiedGenotypingEngine.java:330)
at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.regenotypeVC(GenotypeGVCFs.java:311)
at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:289)
at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:132)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$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 nightly-2016-09-23-gfade77f):
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 a lot !
Best !
May