Bug: GenotypeGVCFs --max_genotype_count needs to handle large ploidy

[droazen]

@sooheelee commented on Fri Feb 17 2017

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.

• Previous discussion of HaplotypeCaller fix
  https://github.com/broadinstitute/gsa-unstable/issues/855#issuecomment-278478318

---

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:

Program Args: -T GenotypeGVCFs -R /usr/users/geibel/chicken/chickenrefgen/galGal5_Dec2015/galGal5.fa --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_WL_72631_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_WL_72632_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_WL_72633_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_WL_72634_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_WL_72635_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_WL_72636_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_WL_72637_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_WL_72638_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_WL_72639_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_WL_72640_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_WL_72641_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_WL_72642_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_WL_72643_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_WL_72644_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_WL_72645_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_WL_72646_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_WL_72647_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_WL_72648_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_WL_72649_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_WL_72650_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_WL_72651_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_WL_72652_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_WL_72653_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_WL_72654_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_WL_72655_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_BL_72656_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_BL_72657_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_BL_72658_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_BL_72659_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_BL_72660_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_BL_72661_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_BL_72662_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_BL_72663_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_BL_72664_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_BL_72665_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_BL_72666_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_BL_72667_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_BL_72668_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_BL_72669_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_BL_72670_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_BL_72671_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_BL_72672_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_BL_72673_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_BL_72674_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_BL_72675_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_BL_72676_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_BL_72678_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_BL_72680_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_BL_72682_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/i_BL_72683_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_AB_0001_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_AR_0002_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_AS_0003_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_BA_0004_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_BK_0005_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_BH_0006_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_CG_0007_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_CS_0008_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_DG_0009_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_FG_0010_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_HO_0011_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_GG_0012_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_GS_0013_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_KW_0014_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_IT_0015_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_KA_0016_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_KG_0017_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_PA_0018_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_LE_0019_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_MA_0020_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_MR_0021_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_OH_0022_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_OR_0023_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_OM_0024_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_NH_0025_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_SB_0026_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_SE_0027_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_SH_0028_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_SA_0029_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_SN_0030_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_TO_0031_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_WT_0032_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_WY_0033_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_YO_0034_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_ZC_0035_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_GV_0036_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_CW_0037_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_DL_0038_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_KS_0039_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_OF_0040_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_WR_0041_chr26.raw.g.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/gVCF/pl_RI_0042_chr26.raw.g.vcf -nt 10 --max_genotype_count 1024 -L chr26 --dbsnp /usr/users/geibel/chicken/chickenrefgen/ENSEMBL_20170106/Gallus_gallus.updated.vcf -o /usr/users/geibel/chicken/pool_sequence_nov2016/data/rawVCF/IndandPool_chr26.raw.vcf 

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

---

• Original discussion with user
  http://gatkforums.broadinstitute.org/gatk/discussion/comment/36309#Comment_36309
• related dsde-docs issue
  https://github.com/broadinstitute/dsde-docs/issues/1744