I have been following GATK variant calling. Everything works fine from mapping to  Funcotator using data sources with version number 1.7 and reference seq hg38. However, when I download the new data source "funcotator_dataSources.v1.8.hg38.20230908g" it returns zero match. I also redid the whole process (from mapping to funcotation) using hg19 and still got the same result.
No hits:

14:50:58.064 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
14:50:58.066 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)

...

13:46:25.203 INFO  VcfFuncotationFactory - ClinVar_VCF 20230717 cache hits/total: 0/0
13:46:25.204 INFO  VcfFuncotationFactory - LMMKnown 20180612 cache hits/total: 0/0
13:46:25.205 INFO  Funcotator - Shutting down engine

...

I tried lifting to b37tohg19 for the second run and did not change anything. Interestingly lifting or Not lifting didn't change anything. It still cannot find the contigs.

I even matched a clinvar variant in the files. This is an example of a variant I found in my dataset;

chr11    6637739    .    ATT    A,AT    458.02    PASS    AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-0.495;DP=57;ExcessHet=0.0000;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=60.00;MQRankSum=0.000;QD=13.47;ReadPosRankSum=-0.113;SOR=0.836    GT:AD:DP:GQ:PL    1/2:6,13,15:34:99:475,146,271,132,0,158

and this is its corresponding variant in funcotator datasource:

Before liftover:

11    6637739    305512    AT    A    .    .    ALLELEID=321432;CLNDISDB=MONDO:MONDO:0008769,MedGen:C1876161,OMIM:204500,Orphanet:168491,Orphanet:228349,Orphanet:79264|MedGen:CN517202|MedGen:CN239323|MedGen:CN169374;CLNDN=Neuronal_ceroid_lipofuscinosis_2|not_provided|Neuronal_Ceroid-Lipofuscinosis,_Recessive|not_specified;CLNHGVS=NC_000011.9:g.6637759del;CLNREVSTAT=criteria_provided,_conflicting_interpretations;CLNSIG=Conflicting_interpretations_of_pathogenicity;CLNSIGCONF=Uncertain_significance(2)|Benign(1);CLNVC=Deletion;CLNVCSO=SO:0000159;CLNVI=ClinGen:CA5858813;GENEINFO=TPP1:1200;MC=SO:0001627|intron_variant;ORIGIN=1;RS=35039601

after liftover:

chr11    6637739    305512    AT    A    .    PASS    ALLELEID=321432;CLNDISDB=MONDO:MONDO:0008769,MedGen:C1876161,OMIM:204500,Orphanet:168491,Orphanet:228349,Orphanet:79264|MedGen:CN517202|MedGen:CN239323|MedGen:CN169374;CLNDN=Neuronal_ceroid_lipofuscinosis_2|not_provided|Neuronal_Ceroid-Lipofuscinosis,_Recessive|not_specified;CLNHGVS=NC_000011.9:g.6637759del;CLNREVSTAT=criteria_provided,_conflicting_interpretations;CLNSIG=Conflicting_interpretations_of_pathogenicity;CLNSIGCONF=Uncertain_significance(2)|Benign(1);CLNVC=Deletion;CLNVCSO=SO:0000159;CLNVI=ClinGen:CA5858813;GENEINFO=TPP1:1200;MC=SO:0001627|intron_variant;ORIGIN=1;RS=35039601

 

Thank you,

a) GATK version used: 4.4.0.0
b) Exact command used:

gatk Funcotator \
     --variant ${results}/${sampleID}_analysis-ready-snps.vcf \
     --reference ${ref} \
     --ref-version hg19 \
     --data-sources-path ${data_sources_path} \
     --output ${results}/${sampleID}_variants_snps.funcotated.vcf \
     --output-file-format VCF 

c) Entire program log:

 

$ bash variantCalling.sh
Using GATK jar /home/osman/Desktop/GATK_pipeline/gatk-4.4.0.0/gatk-package-4.4.0.0-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 /home/osman/Desktop/GATK_pipeline/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar Funcotator --variant /home/osman/Desktop/GATK_pipeline/results/11207400009_analysis-ready-snps.vcf --reference /home/osman/Desktop/GATK_pipeline/supporting/hg19/hg19.fa --ref-version hg19 --data-sources-path /home/osman/Desktop/GATK_pipeline/supporting/data_sources/funcotator_dataSources.v1.8.hg19.20230908g --output /home/osman/Desktop/GATK_pipeline/results/11207400009_variants_snps.funcotated.vcf --output-file-format VCF
13:46:17.144 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/osman/Desktop/GATK_pipeline/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
13:46:17.176 INFO  Funcotator - ------------------------------------------------------------
13:46:17.179 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.4.0.0
13:46:17.179 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:46:17.179 INFO  Funcotator - Executing as osman@BEETHOVEN on Linux v5.4.0-144-generic amd64
13:46:17.179 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.7+7-Ubuntu-0ubuntu118.04
13:46:17.179 INFO  Funcotator - Start Date/Time: October 19, 2023 at 1:46:17 PM TRT
13:46:17.179 INFO  Funcotator - ------------------------------------------------------------
13:46:17.179 INFO  Funcotator - ------------------------------------------------------------
13:46:17.180 INFO  Funcotator - HTSJDK Version: 3.0.5
13:46:17.180 INFO  Funcotator - Picard Version: 3.0.0
13:46:17.181 INFO  Funcotator - Built for Spark Version: 3.3.1
13:46:17.181 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:46:17.181 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:46:17.181 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:46:17.181 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:46:17.181 INFO  Funcotator - Deflater: IntelDeflater
13:46:17.181 INFO  Funcotator - Inflater: IntelInflater
13:46:17.182 INFO  Funcotator - GCS max retries/reopens: 20
13:46:17.182 INFO  Funcotator - Requester pays: disabled
13:46:17.182 INFO  Funcotator - Initializing engine
13:46:17.288 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/osman/Desktop/GATK_pipeline/results/11207400009_analysis-ready-snps.vcf
13:46:17.336 INFO  Funcotator - Done initializing engine
13:46:17.337 INFO  Funcotator - Validating sequence dictionaries...
13:46:17.338 INFO  Funcotator - Processing user transcripts/defaults/overrides...
13:46:17.339 INFO  Funcotator - Initializing data sources...
13:46:17.340 INFO  DataSourceUtils - Initializing data sources from directory: /home/osman/Desktop/GATK_pipeline/supporting/data_sources/funcotator_dataSources.v1.8.hg19.20230908g
13:46:17.340 WARN  DataSourceUtils - README file has improperly formatted version string: Version:          v1.8.hg19.20230908g
13:46:17.341 WARN  DataSourceUtils - Unable to read version information from data sources info/readme file: file:///home/osman/Desktop/GATK_pipeline/supporting/data_sources/funcotator_dataSources.v1.8.hg19.20230908g/MANIFEST.txt
13:46:17.341 INFO  DataSourceUtils - Data sources source: ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/funcotator/funcotator_dataSources.v1.8.hg19.20230908g.tar.gz
13:46:17.341 INFO  DataSourceUtils - Data sources alternate source: gs://broad-public-datasets/funcotator/funcotator_dataSources.v1.8.hg19.20230908g.tar.gz
13:46:17.344 INFO  DataSourceUtils - Resolved data source file path: file:///home/osman/Desktop/GATK_pipeline/clinvar_20230717.vcf -> file:///home/osman/Desktop/GATK_pipeline/supporting/data_sources/funcotator_dataSources.v1.8.hg19.20230908g/clinvar/hg19/clinvar_20230717.vcf
13:46:17.345 INFO  DataSourceUtils - Resolved data source file path: file:///home/osman/Desktop/GATK_pipeline/acmg59_test_cleaned.txt -> file:///home/osman/Desktop/GATK_pipeline/supporting/data_sources/funcotator_dataSources.v1.8.hg19.20230908g/acmg_rec/hg19/acmg59_test_cleaned.txt
13:46:17.345 INFO  DataSourceUtils - Resolved data source file path: file:///home/osman/Desktop/GATK_pipeline/gencode.v43lift37.annotation.REORDERED.gtf -> file:///home/osman/Desktop/GATK_pipeline/supporting/data_sources/funcotator_dataSources.v1.8.hg19.20230908g/gencode/hg19/gencode.v43lift37.annotation.REORDERED.gtf
13:46:17.346 INFO  DataSourceUtils - Resolved data source file path: file:///home/osman/Desktop/GATK_pipeline/gencode.v43lift37.pc_transcripts.fa -> file:///home/osman/Desktop/GATK_pipeline/supporting/data_sources/funcotator_dataSources.v1.8.hg19.20230908g/gencode/hg19/gencode.v43lift37.pc_transcripts.fa
13:46:17.346 INFO  DataSourceUtils - Resolved data source file path: file:///home/osman/Desktop/GATK_pipeline/LMM_Path_LP_VUS5-variants-6-12-18.sorted.vcf -> file:///home/osman/Desktop/GATK_pipeline/supporting/data_sources/funcotator_dataSources.v1.8.hg19.20230908g/lmm_known/hg19/LMM_Path_LP_VUS5-variants-6-12-18.sorted.vcf
13:46:17.347 INFO  DataSourceUtils - Resolved data source file path: file:///home/osman/Desktop/GATK_pipeline/acmg_lof.tsv -> file:///home/osman/Desktop/GATK_pipeline/supporting/data_sources/funcotator_dataSources.v1.8.hg19.20230908g/acmg_lof/hg19/acmg_lof.tsv
13:46:17.347 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
13:46:17.347 INFO  DataSourceUtils - Resolved data source file path: file:///home/osman/Desktop/GATK_pipeline/clinvar_20230717.vcf -> file:///home/osman/Desktop/GATK_pipeline/supporting/data_sources/funcotator_dataSources.v1.8.hg19.20230908g/clinvar/hg19/clinvar_20230717.vcf
13:46:17.349 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar_VCF : 100000
13:46:17.351 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/osman/Desktop/GATK_pipeline/supporting/data_sources/funcotator_dataSources.v1.8.hg19.20230908g/clinvar/hg19/clinvar_20230717.vcf
13:46:17.411 INFO  DataSourceUtils - Resolved data source file path: file:///home/osman/Desktop/GATK_pipeline/clinvar_20230717.vcf -> file:///home/osman/Desktop/GATK_pipeline/supporting/data_sources/funcotator_dataSources.v1.8.hg19.20230908g/clinvar/hg19/clinvar_20230717.vcf
13:46:17.457 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/osman/Desktop/GATK_pipeline/supporting/data_sources/funcotator_dataSources.v1.8.hg19.20230908g/clinvar/hg19/clinvar_20230717.vcf
13:46:17.529 INFO  DataSourceUtils - Resolved data source file path: file:///home/osman/Desktop/GATK_pipeline/acmg59_test_cleaned.txt -> file:///home/osman/Desktop/GATK_pipeline/supporting/data_sources/funcotator_dataSources.v1.8.hg19.20230908g/acmg_rec/hg19/acmg59_test_cleaned.txt
13:46:17.531 INFO  DataSourceUtils - Resolved data source file path: file:///home/osman/Desktop/GATK_pipeline/gencode.v43lift37.annotation.REORDERED.gtf -> file:///home/osman/Desktop/GATK_pipeline/supporting/data_sources/funcotator_dataSources.v1.8.hg19.20230908g/gencode/hg19/gencode.v43lift37.annotation.REORDERED.gtf
13:46:17.531 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
13:46:17.534 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.
13:46:17.534 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.
13:46:17.535 INFO  FeatureManager - Using codec EnsemblGtfCodec to read file file:///home/osman/Desktop/GATK_pipeline/supporting/data_sources/funcotator_dataSources.v1.8.hg19.20230908g/gencode/hg19/gencode.v43lift37.annotation.REORDERED.gtf
13:46:17.543 INFO  DataSourceUtils - Resolved data source file path: file:///home/osman/Desktop/GATK_pipeline/gencode.v43lift37.pc_transcripts.fa -> file:///home/osman/Desktop/GATK_pipeline/supporting/data_sources/funcotator_dataSources.v1.8.hg19.20230908g/gencode/hg19/gencode.v43lift37.pc_transcripts.fa
13:46:20.260 INFO  DataSourceUtils - Resolved data source file path: file:///home/osman/Desktop/GATK_pipeline/LMM_Path_LP_VUS5-variants-6-12-18.sorted.vcf -> file:///home/osman/Desktop/GATK_pipeline/supporting/data_sources/funcotator_dataSources.v1.8.hg19.20230908g/lmm_known/hg19/LMM_Path_LP_VUS5-variants-6-12-18.sorted.vcf
13:46:20.260 INFO  DataSourceUtils - Setting lookahead cache for data source: LMMKnown : 100000
13:46:20.262 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/osman/Desktop/GATK_pipeline/supporting/data_sources/funcotator_dataSources.v1.8.hg19.20230908g/lmm_known/hg19/LMM_Path_LP_VUS5-variants-6-12-18.sorted.vcf
13:46:20.265 INFO  DataSourceUtils - Resolved data source file path: file:///home/osman/Desktop/GATK_pipeline/LMM_Path_LP_VUS5-variants-6-12-18.sorted.vcf -> file:///home/osman/Desktop/GATK_pipeline/supporting/data_sources/funcotator_dataSources.v1.8.hg19.20230908g/lmm_known/hg19/LMM_Path_LP_VUS5-variants-6-12-18.sorted.vcf
13:46:20.269 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/osman/Desktop/GATK_pipeline/supporting/data_sources/funcotator_dataSources.v1.8.hg19.20230908g/lmm_known/hg19/LMM_Path_LP_VUS5-variants-6-12-18.sorted.vcf
13:46:20.272 INFO  DataSourceUtils - Resolved data source file path: file:///home/osman/Desktop/GATK_pipeline/acmg_lof.tsv -> file:///home/osman/Desktop/GATK_pipeline/supporting/data_sources/funcotator_dataSources.v1.8.hg19.20230908g/acmg_lof/hg19/acmg_lof.tsv
13:46:20.273 INFO  Funcotator - Initializing Funcotator Engine...
13:46:20.280 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:
13:46:20.280 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:
13:46:20.282 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)
13:46:20.283 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)
13:46:20.283 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)
13:46:20.283 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)
13:46:20.283 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)
13:46:20.283 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)
13:46:20.283 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)
13:46:20.283 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)
13:46:20.283 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)
13:46:20.283 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)
13:46:20.283 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)
13:46:20.283 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)
13:46:20.283 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)
13:46:20.283 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)
13:46:20.283 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)
13:46:20.283 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)
13:46:20.283 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)
13:46:20.283 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)
13:46:20.284 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)
13:46:20.284 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)
13:46:20.284 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)
13:46:20.284 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)
13:46:20.284 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)
13:46:20.284 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)
13:46:20.284 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)
13:46:20.284 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)
13:46:20.284 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)
13:46:20.284 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)
13:46:20.284 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)
13:46:20.284 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)
13:46:20.284 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)
13:46:20.284 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)
13:46:20.284 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)
13:46:20.284 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)
13:46:20.284 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)
13:46:20.285 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)
13:46:20.285 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)
13:46:20.285 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)
13:46:20.285 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)
13:46:20.285 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)
13:46:20.285 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)
13:46:20.285 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)
13:46:20.285 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)
13:46:20.285 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)
13:46:20.285 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)
13:46:20.285 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)
13:46:20.285 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)
13:46:20.285 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)
13:46:20.285 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)
13:46:20.285 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)
13:46:20.285 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)
13:46:20.285 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)
13:46:20.285 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)
13:46:20.285 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)
13:46:20.286 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)
13:46:20.286 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)
13:46:20.286 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)
13:46:20.286 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)
13:46:20.286 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)
13:46:20.286 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)
13:46:20.286 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)
13:46:20.286 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)
13:46:20.286 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)
13:46:20.286 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)
13:46:20.286 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)
13:46:20.286 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)
13:46:20.286 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)
13:46:20.286 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)
13:46:20.286 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)
13:46:20.287 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)
13:46:20.287 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)
13:46:20.287 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)
13:46:20.287 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)
13:46:20.287 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)
13:46:20.287 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)
13:46:20.287 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)
13:46:20.287 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)
13:46:20.287 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)
13:46:20.287 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)
13:46:20.287 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)
13:46:20.287 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)
13:46:20.287 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)
13:46:20.287 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)
13:46:20.287 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)
13:46:20.287 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)
13:46:20.288 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
13:46:20.288 INFO  Funcotator - Creating a VCF file for output: file:/home/osman/Desktop/GATK_pipeline/results/11207400009_variants_snps.funcotated.vcf
13:46:20.308 INFO  ProgressMeter - Starting traversal
13:46:20.309 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:46:20.323 INFO  VcfFuncotationFactory - ClinVar_VCF 20230717 cache hits/total: 0/0
13:46:20.323 INFO  VcfFuncotationFactory - LMMKnown 20180612 cache hits/total: 0/0
13:46:20.325 INFO  Funcotator - Shutting down engine
[October 19, 2023 at 1:46:20 PM TRT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=1677721600
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:197)
    at java.base/java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:179)
    at java.base/java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1625)
    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$ReduceOp.evaluateSequential(ReduceOps.java:921)
    at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
    at java.base/java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:682)
    at org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine.createFuncotationMapForVariant(FuncotatorEngine.java:162)
    at org.broadinstitute.hellbender.tools.funcotator.Funcotator.enqueueAndHandleVariant(Funcotator.java:924)
    at org.broadinstitute.hellbender.tools.funcotator.Funcotator.apply(Funcotator.java:878)
    at org.broadinstitute.hellbender.engine.VariantWalker.lambda$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: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.forEach(ReferencePipeline.java:596)
    at org.broadinstitute.hellbender.engine.VariantWalker.traverse(VariantWalker.java:102)
    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)
    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
    at org.broadinstitute.hellbender.Main.main(Main.java:289)