Hi,

I've downloaded manually this source file: https://storage.googleapis.com/broad-public-datasets/funcotator/funcotator_dataSources.v1.8.hg19.20230908g.tar.gz and unpacked.

Then, I've typed the command line below and got the error: java.lang.IllegalArgumentException: Unexpected value: Ensembl_canonical

Ensembl_canonical seems to be a TAG within the "gencode.v43lift37.annotation.REORDERED.gtf" file located within the source folder just downloaded,

I've no idea why this is a problem. Anybody can help?

thanks, tom

p.s. If I download the hg38 source file/folder (funcotator_dataSources.v1.8.hg38.20230908g.tar.gz) and try to annotate hg38 variants, I get a similar problem:

java.lang.IllegalArgumentException: Unexpected value: overlaps_pseudogene

p.p.s. Same problems if I use "somatic" source files...

-----
a) GATK version used:  v4.3.0.0
b) Exact command used: gatk Funcotator -R PATH_TO/hg19_ucsc_filtered.fa -V PATH_TO/sample.vcf -O test.vcf --output-file-format VCF --ref-version hg19 --data-sources-path ./funcotator_dataSources.v1.8.hg19.20230908g/
c) Entire program log: 
Using GATK jar /scratch/miniconda3/envs/germinal_pipeline/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-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 /scratch/miniconda3/envs/germinal_pipeline/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar Funcotator -R /scratch/pipeline_data/ref/hg19_ucsc_filtered.fa -V /scratch/pipeline_data/results/231004_ccp17/231004/MGM22-1207_S2/MGM22-1207_S2.filter.vcf -O test.vcf --output-file-format VCF --ref-version hg19 --data-sources-path funcotator_dataSources.v1.8.hg19.20230908g/
17:10:46.467 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/scratch/miniconda3/envs/germinal_pipeline/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
17:10:46.714 INFO  Funcotator - ------------------------------------------------------------
17:10:46.715 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.3.0.0
17:10:46.715 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:10:46.715 INFO  Funcotator - Executing as t.mazza@hpc001.css-mendel.it on Linux v4.18.0-425.3.1.el8.x86_64 amd64
17:10:46.715 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v11.0.1+13-LTS
17:10:46.716 INFO  Funcotator - Start Date/Time: October 11, 2023 at 5:10:46 PM CEST
17:10:46.716 INFO  Funcotator - ------------------------------------------------------------
17:10:46.716 INFO  Funcotator - ------------------------------------------------------------
17:10:46.718 INFO  Funcotator - HTSJDK Version: 3.0.1
17:10:46.718 INFO  Funcotator - Picard Version: 2.27.5
17:10:46.718 INFO  Funcotator - Built for Spark Version: 2.4.5
17:10:46.718 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:10:46.718 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:10:46.719 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:10:46.719 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:10:46.719 INFO  Funcotator - Deflater: IntelDeflater
17:10:46.719 INFO  Funcotator - Inflater: IntelInflater
17:10:46.720 INFO  Funcotator - GCS max retries/reopens: 20
17:10:46.720 INFO  Funcotator - Requester pays: disabled
17:10:46.720 INFO  Funcotator - Initializing engine
17:10:47.018 INFO  FeatureManager - Using codec VCFCodec to read file file:///scratch/pipeline_data/results/231004_ccp17/231004/MGM22-1207_S2/MGM22-1207_S2.filter.vcf
17:10:47.065 INFO  Funcotator - Done initializing engine
17:10:47.066 INFO  Funcotator - Validating sequence dictionaries...
17:10:47.068 INFO  Funcotator - Processing user transcripts/defaults/overrides...
17:10:47.069 INFO  Funcotator - Initializing data sources...
17:10:47.072 INFO  DataSourceUtils - Initializing data sources from directory: funcotator_dataSources.v1.8.hg19.20230908g/
17:10:47.074 WARN  DataSourceUtils - README file has improperly formatted version string: Version:          v1.8.hg19.20230908g
17:10:47.075 WARN  DataSourceUtils - Unable to read version information from data sources info/readme file: file:///scratch/tom/funcotator_dataSources.v1.8.hg19.20230908g/MANIFEST.txt
17:10:47.075 INFO  DataSourceUtils - Data sources source: ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/funcotator/funcotator_dataSources.v1.8.hg19.20230908g.tar.gz
17:10:47.075 INFO  DataSourceUtils - Data sources alternate source: gs://broad-public-datasets/funcotator/funcotator_dataSources.v1.8.hg19.20230908g.tar.gz
17:10:47.087 INFO  DataSourceUtils - Resolved data source file path: file:///scratch/tom/clinvar_20230717.vcf -> file:///scratch/tom/funcotator_dataSources.v1.8.hg19.20230908g/clinvar/hg19/clinvar_20230717.vcf
17:10:47.091 INFO  DataSourceUtils - Resolved data source file path: file:///scratch/tom/acmg59_test_cleaned.txt -> file:///scratch/tom/funcotator_dataSources.v1.8.hg19.20230908g/acmg_rec/hg19/acmg59_test_cleaned.txt
17:10:47.094 INFO  DataSourceUtils - Resolved data source file path: file:///scratch/tom/LMM_Path_LP_VUS5-variants-6-12-18.sorted.vcf -> file:///scratch/tom/funcotator_dataSources.v1.8.hg19.20230908g/lmm_known/hg19/LMM_Path_LP_VUS5-variants-6-12-18.sorted.vcf
17:10:47.097 INFO  DataSourceUtils - Resolved data source file path: file:///scratch/tom/gencode.v43lift37.annotation.REORDERED.gtf -> file:///scratch/tom/funcotator_dataSources.v1.8.hg19.20230908g/gencode/hg19/gencode.v43lift37.annotation.REORDERED.gtf
17:10:47.098 INFO  DataSourceUtils - Resolved data source file path: file:///scratch/tom/gencode.v43lift37.pc_transcripts.fa -> file:///scratch/tom/funcotator_dataSources.v1.8.hg19.20230908g/gencode/hg19/gencode.v43lift37.pc_transcripts.fa
17:10:47.100 INFO  DataSourceUtils - Resolved data source file path: file:///scratch/tom/acmg_lof.tsv -> file:///scratch/tom/funcotator_dataSources.v1.8.hg19.20230908g/acmg_lof/hg19/acmg_lof.tsv
17:10:47.101 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:10:47.101 INFO  DataSourceUtils - Resolved data source file path: file:///scratch/tom/clinvar_20230717.vcf -> file:///scratch/tom/funcotator_dataSources.v1.8.hg19.20230908g/clinvar/hg19/clinvar_20230717.vcf
17:10:47.102 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar_VCF : 100000
17:10:47.108 INFO  FeatureManager - Using codec VCFCodec to read file file:///scratch/tom/funcotator_dataSources.v1.8.hg19.20230908g/clinvar/hg19/clinvar_20230717.vcf
17:10:47.260 INFO  DataSourceUtils - Resolved data source file path: file:///scratch/tom/clinvar_20230717.vcf -> file:///scratch/tom/funcotator_dataSources.v1.8.hg19.20230908g/clinvar/hg19/clinvar_20230717.vcf
17:10:47.413 INFO  FeatureManager - Using codec VCFCodec to read file file:///scratch/tom/funcotator_dataSources.v1.8.hg19.20230908g/clinvar/hg19/clinvar_20230717.vcf
17:10:47.523 INFO  DataSourceUtils - Resolved data source file path: file:///scratch/tom/acmg59_test_cleaned.txt -> file:///scratch/tom/funcotator_dataSources.v1.8.hg19.20230908g/acmg_rec/hg19/acmg59_test_cleaned.txt
17:10:47.527 INFO  DataSourceUtils - Resolved data source file path: file:///scratch/tom/LMM_Path_LP_VUS5-variants-6-12-18.sorted.vcf -> file:///scratch/tom/funcotator_dataSources.v1.8.hg19.20230908g/lmm_known/hg19/LMM_Path_LP_VUS5-variants-6-12-18.sorted.vcf
17:10:47.527 INFO  DataSourceUtils - Setting lookahead cache for data source: LMMKnown : 100000
17:10:47.532 INFO  FeatureManager - Using codec VCFCodec to read file file:///scratch/tom/funcotator_dataSources.v1.8.hg19.20230908g/lmm_known/hg19/LMM_Path_LP_VUS5-variants-6-12-18.sorted.vcf
17:10:47.540 INFO  DataSourceUtils - Resolved data source file path: file:///scratch/tom/LMM_Path_LP_VUS5-variants-6-12-18.sorted.vcf -> file:///scratch/tom/funcotator_dataSources.v1.8.hg19.20230908g/lmm_known/hg19/LMM_Path_LP_VUS5-variants-6-12-18.sorted.vcf
17:10:47.552 INFO  FeatureManager - Using codec VCFCodec to read file file:///scratch/tom/funcotator_dataSources.v1.8.hg19.20230908g/lmm_known/hg19/LMM_Path_LP_VUS5-variants-6-12-18.sorted.vcf
17:10:47.560 INFO  DataSourceUtils - Resolved data source file path: file:///scratch/tom/gencode.v43lift37.annotation.REORDERED.gtf -> file:///scratch/tom/funcotator_dataSources.v1.8.hg19.20230908g/gencode/hg19/gencode.v43lift37.annotation.REORDERED.gtf
17:10:47.560 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:10:47.565 WARN  GencodeGtfCodec - GENCODE GTF Header line 1 has a version number that is above maximum tested version (v 34) (given: 43): ##description: evidence-based annotation of the human genome (GRCh38), version 43 (Ensembl 109), mapped to GRCh37 with gencode-backmap   Continuing, but errors may occur.
17:10:47.566 WARN  GencodeGtfCodec - GENCODE GTF Header line 1 has a version number that is above maximum tested version (v 34) (given: 43): ##description: evidence-based annotation of the human genome (GRCh38), version 43 (Ensembl 109), mapped to GRCh37 with gencode-backmap   Continuing, but errors may occur.
17:10:47.567 INFO  FeatureManager - Using codec EnsemblGtfCodec to read file file:///scratch/tom/funcotator_dataSources.v1.8.hg19.20230908g/gencode/hg19/gencode.v43lift37.annotation.REORDERED.gtf
17:10:47.590 INFO  DataSourceUtils - Resolved data source file path: file:///scratch/tom/gencode.v43lift37.pc_transcripts.fa -> file:///scratch/tom/funcotator_dataSources.v1.8.hg19.20230908g/gencode/hg19/gencode.v43lift37.pc_transcripts.fa
17:10:54.974 INFO  DataSourceUtils - Resolved data source file path: file:///scratch/tom/acmg_lof.tsv -> file:///scratch/tom/funcotator_dataSources.v1.8.hg19.20230908g/acmg_lof/hg19/acmg_lof.tsv
17:10:54.977 INFO  Funcotator - Initializing Funcotator Engine...
17:10:54.990 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
17:10:54.990 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
17:10:54.991 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
17:10:54.991 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
17:10:54.991 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
17:10:54.991 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
17:10:54.991 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
17:10:54.991 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
17:10:54.992 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
17:10:54.992 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
17:10:54.992 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
17:10:54.992 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
17:10:54.992 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
17:10:54.992 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
17:10:54.992 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
17:10:54.993 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
17:10:54.993 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
17:10:54.993 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
17:10:54.993 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
17:10:54.993 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
17:10:54.993 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
17:10:54.993 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
17:10:54.994 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
17:10:54.994 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
17:10:54.994 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
17:10:54.994 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
17:10:54.994 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
17:10:54.994 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
17:10:54.995 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
17:10:54.995 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
17:10:54.995 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
17:10:54.995 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
17:10:54.995 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
17:10:54.995 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
17:10:54.995 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
17:10:54.996 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
17:10:54.996 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
17:10:54.996 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
17:10:54.996 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
17:10:54.996 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
17:10:54.996 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
17:10:54.996 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
17:10:54.997 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
17:10:54.997 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
17:10:54.997 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
17:10:54.997 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
17:10:54.997 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
17:10:54.997 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
17:10:54.998 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
17:10:54.998 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
17:10:54.998 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
17:10:54.998 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
17:10:54.998 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
17:10:54.998 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
17:10:54.998 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
17:10:54.999 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
17:10:54.999 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
17:10:54.999 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
17:10:54.999 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
17:10:54.999 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
17:10:54.999 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
17:10:54.999 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
17:10:55.000 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
17:10:55.000 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
17:10:55.000 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
17:10:55.000 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
17:10:55.000 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
17:10:55.000 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
17:10:55.000 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
17:10:55.001 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
17:10:55.001 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
17:10:55.001 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
17:10:55.001 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
17:10:55.002 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
17:10:55.002 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
17:10:55.002 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
17:10:55.002 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
17:10:55.002 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
17:10:55.002 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
17:10:55.002 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
17:10:55.003 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
17:10:55.003 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
17:10:55.003 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
17:10:55.003 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
17:10:55.003 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
17:10:55.003 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
17:10:55.003 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
17:10:55.003 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
17:10:55.004 INFO  Funcotator - Creating a VCF file for output: file:/scratch/tom/test.vcf
17:10:55.054 INFO  ProgressMeter - Starting traversal
17:10:55.054 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
17:10:55.086 INFO  VcfFuncotationFactory - ClinVar_VCF 20230717 cache hits/total: 0/0
17:10:55.086 INFO  VcfFuncotationFactory - LMMKnown 20180612 cache hits/total: 0/0
17:10:55.096 INFO  Funcotator - Shutting down engine
[October 11, 2023 at 5:10:55 PM CEST] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=5469372416
java.lang.IllegalArgumentException: Unexpected value: Ensembl_canonical
        at org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature$FeatureTag.getEnum(GencodeGtfFeature.java:1394)
        at org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.<init>(GencodeGtfFeature.java:197)
        at org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfTranscriptFeature.<init>(GencodeGtfTranscriptFeature.java:19)
        at org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfTranscriptFeature.create(GencodeGtfTranscriptFeature.java:23)
        at org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature$FeatureType$2.create(GencodeGtfFeature.java:768)
        at org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.create(GencodeGtfFeature.java:327)
        at org.broadinstitute.hellbender.utils.codecs.gtf.AbstractGtfCodec.decode(AbstractGtfCodec.java:138)
        at org.broadinstitute.hellbender.utils.codecs.gtf.AbstractGtfCodec.decode(AbstractGtfCodec.java:23)
        at htsjdk.tribble.TribbleIndexedFeatureReader$QueryIterator.readNextRecord(TribbleIndexedFeatureReader.java:502)
        at htsjdk.tribble.TribbleIndexedFeatureReader$QueryIterator.<init>(TribbleIndexedFeatureReader.java:442)
        at htsjdk.tribble.TribbleIndexedFeatureReader.query(TribbleIndexedFeatureReader.java:298)
        at org.broadinstitute.hellbender.engine.FeatureDataSource.refillQueryCache(FeatureDataSource.java:622)
        at org.broadinstitute.hellbender.engine.FeatureDataSource.queryAndPrefetch(FeatureDataSource.java:591)
        at org.broadinstitute.hellbender.engine.FeatureManager.getFeatures(FeatureManager.java:363)
        at org.broadinstitute.hellbender.engine.FeatureContext.getValues(FeatureContext.java:173)
        at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.queryFeaturesFromFeatureContext(DataSourceFuncotationFactory.java:314)
        at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.getFeaturesFromFeatureContext(DataSourceFuncotationFactory.java:229)
        at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.createFuncotations(DataSourceFuncotationFactory.java:207)
        at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.createFuncotations(DataSourceFuncotationFactory.java:182)
        at org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine.lambda$createFuncotationMapForVariant$0(FuncotatorEngine.java:152)
        at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:195)
        at java.base/java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:177)
        at java.base/java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1654)
        at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484)
        at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474)
        at java.base/java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:913)
        at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
        at java.base/java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:578)
        at org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine.createFuncotationMapForVariant(FuncotatorEngine.java:162)
        at org.broadinstitute.hellbender.tools.funcotator.Funcotator.enqueueAndHandleVariant(Funcotator.java:924)
        at org.broadinstitute.hellbender.tools.funcotator.Funcotator.apply(Funcotator.java:878)
        at org.broadinstitute.hellbender.engine.VariantWalker.lambda$traverse$0(VariantWalker.java:104)
        at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
        at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:195)
        at java.base/java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:177)
        at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:195)
        at java.base/java.util.Iterator.forEachRemaining(Iterator.java:133)
        at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
        at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484)
        at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474)
        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:497)
        at org.broadinstitute.hellbender.engine.VariantWalker.traverse(VariantWalker.java:102)
        at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1095)
        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)