Funcotator - Unexpected value: Ensembl_canonical
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)
-
The resource bundle 1.8 is updated and designed to be used with GATK 4.5.0.0 which will be released soon. If you wish to use this bundle we recommend using the nightly docker builds or building GATK from the github master branch. Beware that this version is still being tested and although it is tested rigorously there may still be some uncaught edge cases. If you still observe issues please let us know.
-
Allright. The bundle 1.7 works fine.
Thank you for clarifying
Please sign in to leave a comment.
2 comments