REQUIRED for all errors and issues:
a) GATK version used: v4.5.0.0

b) Exact command used: 

gatk FilterFuncotations --allele-frequency-data-source exac -O filter_funcotations.vcf.gz --ref-version hg38 -V merged.funcotated.vcf.gz

c) Entire program log:

Using GATK jar /gpfs0/home1/gdbakerlab/nxr042/research/setups/gatk-4.5.0.0/gatk-package-4.5.0.0-local.jar

Running:

    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 -jar /gpfs0/home1/gdbakerlab/nxr042/research/setups/gatk-4.5.0.0/gatk-package-4.5.0.0-local.jar FilterFuncotations --allele-frequency-data-source exac -O filter_funcotations.vcf.gz --ref-version hg38 -V merged_analysis_ready.funcotated.check.vcf.gz

02:29:14.741 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gpfs0/home1/gdbakerlab/nxr042/research/setups/gatk-4.5.0.0/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so

02:29:14.870 INFO  FilterFuncotations - ------------------------------------------------------------

02:29:14.872 INFO  FilterFuncotations - The Genome Analysis Toolkit (GATK) v4.5.0.0

02:29:14.873 INFO  FilterFuncotations - For support and documentation go to https://software.broadinstitute.org/gatk/

02:29:14.873 INFO  FilterFuncotations - Executing as nxr042@r1pl-hpcf-log01 on Linux v4.18.0-372.32.1.el8_6.x86_64 amd64

02:29:14.873 INFO  FilterFuncotations - Java runtime: OpenJDK 64-Bit Server VM v17.0.2+8-86

02:29:14.873 INFO  FilterFuncotations - Start Date/Time: January 14, 2024 at 2:29:14 AM EST

02:29:14.873 INFO  FilterFuncotations - ------------------------------------------------------------

02:29:14.873 INFO  FilterFuncotations - ------------------------------------------------------------

02:29:14.874 INFO  FilterFuncotations - HTSJDK Version: 4.1.0

02:29:14.874 INFO  FilterFuncotations - Picard Version: 3.1.1

02:29:14.874 INFO  FilterFuncotations - Built for Spark Version: 3.5.0

02:29:14.874 INFO  FilterFuncotations - HTSJDK Defaults.COMPRESSION_LEVEL : 2

02:29:14.874 INFO  FilterFuncotations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false

02:29:14.875 INFO  FilterFuncotations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true

02:29:14.875 INFO  FilterFuncotations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false

02:29:14.875 INFO  FilterFuncotations - Deflater: IntelDeflater

02:29:14.875 INFO  FilterFuncotations - Inflater: IntelInflater

02:29:14.875 INFO  FilterFuncotations - GCS max retries/reopens: 20

02:29:14.875 INFO  FilterFuncotations - Requester pays: disabled

02:29:14.875 WARN  FilterFuncotations - 

   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

   Warning: FilterFuncotations is an EXPERIMENTAL tool and should not be used for production

   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

02:29:14.876 INFO  FilterFuncotations - Initializing engine

02:29:14.997 INFO  FeatureManager - Using codec VCFCodec to read file file:///gpfs0/home1/gdbakerlab/nxr042/research/exome/mullarian_abnormality/analysis/results/F036P1/new/varCal/merged_analysis_ready.funcotated.check.vcf.gz

02:29:15.212 INFO  FilterFuncotations - Done initializing engine

02:29:15.262 INFO  ProgressMeter - Starting traversal

02:29:15.262 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute

02:29:15.263 INFO  FilterFuncotations - Starting pass 0 through the variants

02:29:15.796 ERROR FuncotationMap - Keys:  Gencode_43_hugoSymbol, Gencode_43_ncbiBuild, Gencode_43_chromosome, Gencode_43_start, Gencode_43_end, Gencode_43_variantClassification, Gencode_43_secondaryVariantClassification, Gencode_43_variantType, Gencode_43_refAllele, Gencode_43_tumorSeqAllele1, Gencode_43_tumorSeqAllele2, Gencode_43_genomeChange, Gencode_43_annotationTranscript, Gencode_43_transcriptStrand, Gencode_43_transcriptExon, Gencode_43_transcriptPos, Gencode_43_cDnaChange, Gencode_43_codonChange, Gencode_43_proteinChange, Gencode_43_gcContent, Gencode_43_referenceContext, Gencode_43_otherTranscripts, ACMGLMMLof_LOF_Mechanism, ACMGLMMLof_Mode_of_Inheritance, ACMGLMMLof_Notes, ACMG_recommendation_Disease_Name, ClinVar_VCF_AF_ESP, ClinVar_VCF_AF_EXAC, ClinVar_VCF_AF_TGP, ClinVar_VCF_ALLELEID, ClinVar_VCF_CLNDISDB, ClinVar_VCF_CLNDISDBINCL, ClinVar_VCF_CLNDN, ClinVar_VCF_CLNDNINCL, ClinVar_VCF_CLNHGVS, ClinVar_VCF_CLNREVSTAT, ClinVar_VCF_CLNSIG, ClinVar_VCF_CLNSIGCONF, ClinVar_VCF_CLNSIGINCL, ClinVar_VCF_CLNVC, ClinVar_VCF_CLNVCSO, ClinVar_VCF_CLNVI, ClinVar_VCF_DBVARID, ClinVar_VCF_GENEINFO, ClinVar_VCF_MC, ClinVar_VCF_ORIGIN, ClinVar_VCF_RS, ClinVar_VCF_ID, ClinVar_VCF_FILTER, LMMKnown_LMM_FLAGGED, LMMKnown_ID, LMMKnown_FILTER, gnomAD_exome_AF, gnomAD_exome_AF_afr, gnomAD_exome_AF_afr_female, gnomAD_exome_AF_afr_male, gnomAD_exome_AF_amr, gnomAD_exome_AF_amr_female, gnomAD_exome_AF_amr_male, gnomAD_exome_AF_asj, gnomAD_exome_AF_asj_female, gnomAD_exome_AF_asj_male, gnomAD_exome_AF_eas, gnomAD_exome_AF_eas_female, gnomAD_exome_AF_eas_jpn, gnomAD_exome_AF_eas_kor, gnomAD_exome_AF_eas_male, gnomAD_exome_AF_eas_oea, gnomAD_exome_AF_female, gnomAD_exome_AF_fin, gnomAD_exome_AF_fin_female, gnomAD_exome_AF_fin_male, gnomAD_exome_AF_male, gnomAD_exome_AF_nfe, gnomAD_exome_AF_nfe_bgr, gnomAD_exome_AF_nfe_est, gnomAD_exome_AF_nfe_female, gnomAD_exome_AF_nfe_male, gnomAD_exome_AF_nfe_nwe, gnomAD_exome_AF_nfe_onf, gnomAD_exome_AF_nfe_seu, gnomAD_exome_AF_nfe_swe, gnomAD_exome_AF_oth, gnomAD_exome_AF_oth_female, gnomAD_exome_AF_oth_male, gnomAD_exome_AF_popmax, gnomAD_exome_AF_raw, gnomAD_exome_AF_sas, gnomAD_exome_AF_sas_female, gnomAD_exome_AF_sas_male, gnomAD_exome_ID, gnomAD_exome_FILTER, gnomAD_genome_AF, gnomAD_genome_AF_afr, gnomAD_genome_AF_afr_female, gnomAD_genome_AF_afr_male, gnomAD_genome_AF_amr, gnomAD_genome_AF_amr_female, gnomAD_genome_AF_amr_male, gnomAD_genome_AF_asj, gnomAD_genome_AF_asj_female, gnomAD_genome_AF_asj_male, gnomAD_genome_AF_eas, gnomAD_genome_AF_eas_female, gnomAD_genome_AF_eas_male, gnomAD_genome_AF_female, gnomAD_genome_AF_fin, gnomAD_genome_AF_fin_female, gnomAD_genome_AF_fin_male, gnomAD_genome_AF_male, gnomAD_genome_AF_nfe, gnomAD_genome_AF_nfe_est, gnomAD_genome_AF_nfe_female, gnomAD_genome_AF_nfe_male, gnomAD_genome_AF_nfe_nwe, gnomAD_genome_AF_nfe_onf, gnomAD_genome_AF_nfe_seu, gnomAD_genome_AF_oth, gnomAD_genome_AF_oth_female, gnomAD_genome_AF_oth_male, gnomAD_genome_AF_popmax, gnomAD_genome_AF_raw, gnomAD_genome_OriginalAlleles, gnomAD_genome_OriginalContig, gnomAD_genome_OriginalStart, gnomAD_genome_ReverseComplementedAlleles, gnomAD_genome_SwappedAlleles, gnomAD_genome_ID, gnomAD_genome_FILTER

02:29:15.797 ERROR FuncotationMap - Values:  , , , , , , , , , , , , , , , , , , , , , , , , , , , false, , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , false, false, , 

02:29:15.807 INFO  FilterFuncotations - Shutting down engine

[January 14, 2024 at 2:29:15 AM EST] org.broadinstitute.hellbender.tools.funcotator.FilterFuncotations done. Elapsed time: 0.02 minutes.

Runtime.totalMemory()=267386880

org.broadinstitute.hellbender.exceptions.GATKException$ShouldNeverReachHereException: Cannot parse the funcotation attribute.  Num values: 107   Num keys: 129

at org.broadinstitute.hellbender.tools.funcotator.FuncotationMap.createAsAllTableFuncotationsFromVcf(FuncotationMap.java:224)

at org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils.lambda$createAlleleToFuncotationMapFromFuncotationVcfAttribute$5(FuncotatorUtils.java:2261)

at java.base/java.util.stream.Collectors.lambda$uniqKeysMapAccumulator$1(Collectors.java:180)

at java.base/java.util.stream.ReduceOps$3ReducingSink.accept(ReduceOps.java:169)

at java.base/java.util.stream.IntPipeline$1$1.accept(IntPipeline.java:180)

at java.base/java.util.stream.Streams$RangeIntSpliterator.forEachRemaining(Streams.java:104)

at java.base/java.util.Spliterator$OfInt.forEachRemaining(Spliterator.java:711)

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.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:921)

at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)

at java.base/java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:682)

at org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils.createAlleleToFuncotationMapFromFuncotationVcfAttribute(FuncotatorUtils.java:2260)

at org.broadinstitute.hellbender.tools.funcotator.filtrationRules.ArHetvarFilter.buildArHetByGene(ArHetvarFilter.java:77)

at org.broadinstitute.hellbender.tools.funcotator.filtrationRules.ArHetvarFilter.firstPassApply(ArHetvarFilter.java:50)

at org.broadinstitute.hellbender.tools.funcotator.FilterFuncotations.firstPassApply(FilterFuncotations.java:161)

at org.broadinstitute.hellbender.engine.TwoPassVariantWalker.nthPassApply(TwoPassVariantWalker.java:17)

at org.broadinstitute.hellbender.engine.MultiplePassVariantWalker.lambda$traverse$0(MultiplePassVariantWalker.java:40)

at org.broadinstitute.hellbender.engine.MultiplePassVariantWalker.lambda$traverseVariants$1(MultiplePassVariantWalker.java:77)

at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)

at java.base/java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:179)

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.forEach(ReferencePipeline.java:596)

at org.broadinstitute.hellbender.engine.MultiplePassVariantWalker.traverseVariants(MultiplePassVariantWalker.java:75)

at org.broadinstitute.hellbender.engine.MultiplePassVariantWalker.traverse(MultiplePassVariantWalker.java:40)

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:166)

at org.broadinstitute.hellbender.Main.mainEntry(Main.java:209)

at org.broadinstitute.hellbender.Main.main(Main.java:306)