GenotypeGVCFs --max_genotype_count not working?

jogeibjogeib GermanyMember

Hi,
I'm currently trying to call SNPs from a mixture of 42 pooled (a 10 individuas) and 50 individual sequenced chicken, using HaplotypeCaller and GenotypGVCFs (GATK3.7). Using the HaplotypeCaller, the --max_genotype_count argument worked properly and reduced the number of alternative alleles where necessary. But later, using GenotypeGVCFs, it seemed, that it did not work anymore. Even reducing the maximum number of genotypes, writing it as -maxGT and using the latest nightly build of GATK (2017-02-11) did not produce results. Is it possible that there are still bugs within the program or did I mess something up?

Thanks for your answers

Johannes

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 ------------------------------------------------------------------------------------------

Issue · Github
by shlee

Issue Number
1744
State
closed
Last Updated
Assignee
Array
Milestone
Array
Closed By
vdauwera

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