IllegalStateException: Genotype has no likelihoods

[aarthi-mohan]

Hi there,

I get the above error while running GenotypeGVCFs on 1000+ samples. GenomicsDB had no issues.

GATK version: v4.4.0.0
command: 
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx84g -Xms84g -DGATK_STACKTRACE_ON_USER_EXCEPTION=true -jar conda-prefix/f3f52f796150d148811f0eadb60aa984_/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar GenotypeGVCFs --variant gendb://genotyped/genomicsdb/genmark_chrY --reference genomes/TCAG/hg38.fa -L chrY:56821510-56887902 --genomicsdb-shared-posixfs-optimizations true --tmp-dir /localhd/19152340 --output genotyped/genotypegvcf/genmark_chrY:56821510-56887902_genotyped.vcf.gz

Error:
11:28:02.761 INFO  GenotypeGVCFs - Shutting down engine
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),5.203697787999986,Cpu time(s),4.1635005660000015
[May 1, 2025 at 11:28:02 a.m. EDT] org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 1.13 minutes.
Runtime.totalMemory()=87187849216
java.lang.IllegalStateException: Genotype has no likelihoods: [21-xxxxx-A-00-00 CATATATATAT*/CAT GQ 42 DP 82 AD 39,17,10,0,0,0 {AF=[0.207, 0.122, 0, 0, 0]>
       	at org.broadinstitute.hellbender.utils.GenotypeUtils.computeDiploidGenotypeCounts(GenotypeUtils.java:89)
       	at org.broadinstitute.hellbender.tools.walkers.annotator.ExcessHet.calculateEH(ExcessHet.java:96)
       	at org.broadinstitute.hellbender.tools.walkers.annotator.ExcessHet.annotate(ExcessHet.java:84)
        at org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine.addInfoAnnotations(VariantAnnotatorEngine.java:390)
       	at org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine.annotateContext(VariantAnnotatorEngine.java:363)
        at org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine.annotateContext(VariantAnnotatorEngine.java:334)
       	at org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFsEngine.regenotypeVC(GenotypeGVCFsEngine.java:188)
        at org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFsEngine.callRegion(GenotypeGVCFsEngine.java:138)
       	at org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs.apply(GenotypeGVCFs.java:316)
        at org.broadinstitute.hellbender.engine.VariantLocusWalker.lambda$traverse$0(VariantLocusWalker.java:135)
       	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
        at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:197)
       	at java.base/java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:179)
        at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:197)
       	at java.base/java.util.Iterator.forEachRemaining(Iterator.java:133)
        at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1845)
       	at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:509)
        at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:499)
       	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
        at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
       	at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
        at java.base/java.util.stream.ReferencePipeline.forEachOrdered(ReferencePipeline.java:601)
       	at org.broadinstitute.hellbender.engine.VariantLocusWalker.traverse(VariantLocusWalker.java:132)
        at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1098)
       	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:149)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:198)
       	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:217)
        at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)

This looks like the same issues reported earlier: https://github.com/broadinstitute/gatk/issues/7933. However, I am using the newer version of GATK, and also running without the --force-output-intervals option.

Is there a fix for this issue? Appreciate your help and feedback!

Thank you, Aarthi