a) GATK version used: v4.1.9
b) Exact command used:

/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar \
    VariantEval \
    -R /$PATH_TO_REFERENCE/chm13/t2t-chm13.20200921.withGRCh38chrY.chrEBV.chrYKI270740v1r.fasta \
    --eval /$PATH_TO_VCF/1kgp.chrX.recalibrated.snp_indel.pass.vcf.gz \
    --pedigree /$PATH_TO_PED/1kgp_trios.ped \
    -no-ev -no-st -ST Family \
    -EV MendelianViolationEvaluator \
    -O 1kgp.chrX.recalibrated.snp_indel.pass.MVs.byFamily.table

c) Entire error log:

19:35:29.408 INFO  VariantEval - ------------------------------------------------------------
19:35:29.408 INFO  VariantEval - The Genome Analysis Toolkit (GATK) v4.1.9.0
19:35:29.409 INFO  VariantEval - For support and documentation go to https://software.broadinstitute.org/gatk/
19:35:29.409 INFO  VariantEval - Executing as root@0b79b5044551 on Linux v5.4.104+ amd64
19:35:29.409 INFO  VariantEval - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_152-release-1056-b12
19:35:29.409 INFO  VariantEval - Start Date/Time: May 27, 2021 7:35:29 PM UTC
19:35:29.409 INFO  VariantEval - ------------------------------------------------------------
19:35:29.409 INFO  VariantEval - ------------------------------------------------------------
19:35:29.410 INFO  VariantEval - HTSJDK Version: 2.23.0
19:35:29.410 INFO  VariantEval - Picard Version: 2.23.3
19:35:29.410 INFO  VariantEval - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:35:29.410 INFO  VariantEval - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:35:29.410 INFO  VariantEval - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:35:29.410 INFO  VariantEval - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:35:29.410 INFO  VariantEval - Deflater: IntelDeflater
19:35:29.410 INFO  VariantEval - Inflater: IntelInflater
19:35:29.410 INFO  VariantEval - GCS max retries/reopens: 20
19:35:29.410 INFO  VariantEval - Requester pays: disabled
19:35:29.411 WARN  VariantEval - 

[1m[31m   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

   Warning: VariantEval is a BETA tool and is not yet ready for use in production

   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!![0m


19:35:29.411 INFO  VariantEval - Initializing engine
19:35:29.755 INFO  FeatureManager - Using codec VCFCodec to read file file:///cromwell_root/fc-47de7dae-e8e6-429c-b760-b4ba49136eee/joint_vcfs/recalibrated/PASS/1kgp.chrX.recalibrated.snp_indel.pass.vcf.gz
19:35:29.835 INFO  VariantEval - Done initializing engine
19:35:29.836 INFO  PedReader - Reading PED file /cromwell_root/fc-47de7dae-e8e6-429c-b760-b4ba49136eee/resources/1kgp/1kgp_trios.ped with missing fields: []
19:35:29.854 INFO  PedReader - Phenotype is other? true
19:35:32.686 INFO  VariantEval - Creating 1881 combinatorial stratification states
19:35:32.742 INFO  ProgressMeter - Starting traversal
19:35:32.742 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:36:01.819 INFO  VariantEval - Shutting down engine
[May 27, 2021 7:36:01 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.54 minutes.
Runtime.totalMemory()=4964483072
java.lang.IndexOutOfBoundsException: Index: 1, Size: 1
	at java.util.ArrayList.rangeCheck(ArrayList.java:653)
	at java.util.ArrayList.get(ArrayList.java:429)
	at org.broadinstitute.hellbender.utils.samples.MendelianViolation.isViolation(MendelianViolation.java:180)
	at org.broadinstitute.hellbender.utils.samples.MendelianViolation.updateViolations(MendelianViolation.java:122)
	at org.broadinstitute.hellbender.utils.samples.MendelianViolation.countFamilyViolations(MendelianViolation.java:148)
	at org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator.update1(MendelianViolationEvaluator.java:122)
	at org.broadinstitute.hellbender.tools.walkers.varianteval.util.EvaluationContext.apply(EvaluationContext.java:74)
	at org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval.processComp(VariantEval.java:596)
	at org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval.doApply(VariantEval.java:562)
	at org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval$PositionAggregator.callDoApply(VariantEval.java:497)
	at org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval$PositionAggregator.addVariant(VariantEval.java:478)
	at org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval$PositionAggregator.access$100(VariantEval.java:469)
	at org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval.apply(VariantEval.java:511)
	at org.broadinstitute.hellbender.engine.MultiVariantWalker.lambda$traverse$1(MultiVariantWalker.java:120)
	at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
	at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
	at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
	at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
	at java.util.Iterator.forEachRemaining(Iterator.java:116)
	at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
	at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
	at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
	at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
	at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
	at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
	at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
	at org.broadinstitute.hellbender.engine.MultiVariantWalker.traverse(MultiVariantWalker.java:118)
	at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1049)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
	at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
	at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
	at org.broadinstitute.hellbender.Main.main(Main.java:289)
2021/05/27 19:36:03 Starting delocalization.
2021/05/27 19:36:04 Delocalization script execution started...
2021/05/27 19:36:04 Delocalizing output /cromwell_root/memory_retry_rc -> gs://fc-51aefb1c-4e8e-4dcb-a59c-62e318ea351a/b4b25c64-84dc-4902-ae53-89bff2091e92/mendelian_analysis/fd25ef2c-8ed6-4b2a-9df9-b7287511aee8/call-mendelian_analysis/memory_retry_rc
2021/05/27 19:36:04 Delocalizing output /cromwell_root/rc -> gs://fc-51aefb1c-4e8e-4dcb-a59c-62e318ea351a/b4b25c64-84dc-4902-ae53-89bff2091e92/mendelian_analysis/fd25ef2c-8ed6-4b2a-9df9-b7287511aee8/call-mendelian_analysis/rc
2021/05/27 19:36:05 Delocalizing output /cromwell_root/stdout -> gs://fc-51aefb1c-4e8e-4dcb-a59c-62e318ea351a/b4b25c64-84dc-4902-ae53-89bff2091e92/mendelian_analysis/fd25ef2c-8ed6-4b2a-9df9-b7287511aee8/call-mendelian_analysis/stdout
2021/05/27 19:36:06 Delocalizing output /cromwell_root/stderr -> gs://fc-51aefb1c-4e8e-4dcb-a59c-62e318ea351a/b4b25c64-84dc-4902-ae53-89bff2091e92/mendelian_analysis/fd25ef2c-8ed6-4b2a-9df9-b7287511aee8/call-mendelian_analysis/stderr
2021/05/27 19:36:08 Delocalizing output /cromwell_root/1kgp.chrX.recalibrated.snp_indel.pass.MVs.byFamily.table -> gs://fc-51aefb1c-4e8e-4dcb-a59c-62e318ea351a/b4b25c64-84dc-4902-ae53-89bff2091e92/mendelian_analysis/fd25ef2c-8ed6-4b2a-9df9-b7287511aee8/call-mendelian_analysis/1kgp.chrX.recalibrated.snp_indel.pass.MVs.byFamily.table
Required file output '/cromwell_root/1kgp.chrX.recalibrated.snp_indel.pass.MVs.byFamily.table' does not exist.

I am running VariantEval to detect Mendelian violations in large joint genotyped VCF files, so I'm running it on a per-chromosome basis. This error only occurs for the chromosome X file, and it only occurs with this FASTA file (GRCh38 on chrX does not cause this issue). IndexFeatureFile is run just before this error, which has also led to successful runs in other chromosomes, so that's not the issue. Any insight on this issue would be appreciated.