A fix was implemented for HaplotypeCaller but not ported to GenotypeGVCFs nor CombineGVCFs nor CombineVariants. Although user is using v3.7-0-gcfedb67, my understanding is that these types of fixes will only be worked on in GATK4.
The user actually includes a shell script in the test data bundle called JointGenotyping_chr26.sh.
The error shows:
##### ERROR --
##### ERROR stack trace
java.lang.IllegalArgumentException: the number of genotypes is too large for ploidy 20 and allele 16: approx. 3247943160
at org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodCalculators.getInstance(GenotypeLikelihoodCalculators.java:319)
at org.broadinstitute.gatk.tools.walkers.variantutils.ReferenceConfidenceVariantContextMerger.mergeRefConfidenceGenotypes(ReferenceConfidenceVariantContextMerger.java:461)
at org.broadinstitute.gatk.tools.walkers.variantutils.ReferenceConfidenceVariantContextMerger.merge(ReferenceConfidenceVariantContextMerger.java:164)
at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:302)
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: the number of genotypes is too large for ploidy 20 and allele 16: approx. 3247943160
##### ERROR ------------------------------------------------------------------------------------------
A fix was implemented for HaplotypeCaller but not ported to GenotypeGVCFs nor CombineGVCFs nor CombineVariants. Although user is using v3.7-0-gcfedb67, my understanding is that these types of fixes will only be worked on in GATK4.
Test data submitted by user can be found at
/humgen/gsa-scr1/pub/incoming/bugrep_jgeibel_1.tar.gz
This includes chicken reference files.
The command the user uses to generate the error is very long because we have many vcfs:
The user actually includes a shell script in the test data bundle called
JointGenotyping_chr26.sh
.The error shows: