Funcotator throwing error more than one config file

[parth2608]

Hi,

When I try to run Funcotator, using the below command:

gatk Funcotator
--variant /rsrch5/home/tdccct/ppshah/shared/CAS_MOSAIC/mutect/mrn_2507919/WES/KShaw-ROPR0004-DNA-229761-WX01-T_HMCKJDSX2-4-ATTGGCTC/KShaw-ROPR0004-DNA-229761-WX01-T_HMCKJDSX2-4-ATTGGCTC_filtered.vcf.gz
--reference /rsrch5/home/tdccct/ppshah/shared/gencode/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
--ref-version hg38
--data-sources-path /rsrch5/home/tdccct/ppshah/shared/pipelines/mutect/funcotator_dataSources.v1.7.20200521s
--output /rsrch5/home/tdccct/ppshah/shared/CAS_MOSAIC/mutect/mrn_2507919/WES/KShaw-ROPR0004-DNA-229761-WX01-T_HMCKJDSX2-4-ATTGGCTC/KShaw-ROPR0004-DNA-229761-WX01-T_HMCKJDSX2-4-ATTGGCTC_funcotated.vcf
--output-file-format VCF

I get the following error:

Using GATK jar /gatk/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 /gatk/gatk-package-4.4.0.0-local.jar Funcotator --variant /home/ppshah/shared/CAS_MOSAIC/mutect/mrn_2507919/WES/KShaw-ROPR0004-DNA-229761-WX01-T_HMCKJDSX2-4-ATTGGCTC/KShaw-ROPR0004-DNA-229761-WX01-T_HMCKJDSX2-4-ATTGGCTC_filtered.vcf.gz --reference /home/ppshah/shared/gencode/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta --ref-version hg38 --data-sources-path /home/ppshah/shared/pipelines/mutect/funcotator_dataSources.v1.7.20200521s --output /home/ppshah/shared/CAS_MOSAIC/mutect/mrn_2507919/WES/KShaw-ROPR0004-DNA-229761-WX01-T_HMCKJDSX2-4-ATTGGCTC/KShaw-ROPR0004-DNA-229761-WX01-T_HMCKJDSX2-4-ATTGGCTC_funcotated.vcf --output-file-format VCF 16:36:22.352 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 16:36:22.392 INFO Funcotator - ------------------------------------------------------------ 16:36:22.396 INFO Funcotator - The Genome Analysis Toolkit (GATK) v4.4.0.0 16:36:22.396 INFO Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/ 16:36:22.396 INFO Funcotator - Executing as ppshah@ldragon1 on Linux v3.10.0-1160.15.2.el7.x86_64 amd64 16:36:22.396 INFO Funcotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10-Ubuntu-0ubuntu118.04.1 16:36:22.396 INFO Funcotator - Start Date/Time: January 10, 2024 at 4:36:22 PM GMT 16:36:22.396 INFO Funcotator - ------------------------------------------------------------ 16:36:22.396 INFO Funcotator - ------------------------------------------------------------ 16:36:22.397 INFO Funcotator - HTSJDK Version: 3.0.5 16:36:22.397 INFO Funcotator - Picard Version: 3.0.0 16:36:22.397 INFO Funcotator - Built for Spark Version: 3.3.1 16:36:22.397 INFO Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2 16:36:22.397 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 16:36:22.398 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 16:36:22.398 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 16:36:22.398 INFO Funcotator - Deflater: IntelDeflater 16:36:22.398 INFO Funcotator - Inflater: IntelInflater 16:36:22.399 INFO Funcotator - GCS max retries/reopens: 20 16:36:22.399 INFO Funcotator - Requester pays: disabled 16:36:22.399 INFO Funcotator - Initializing engine 16:36:22.624 INFO FeatureManager - Using codec VCFCodec to read file file:///home/ppshah/shared/CAS_MOSAIC/mutect/mrn_2507919/WES/KShaw-ROPR0004-DNA-229761-WX01-T_HMCKJDSX2-4-ATTGGCTC/KShaw-ROPR0004-DNA-229761-WX01-T_HMCKJDSX2-4-ATTGGCTC_filtered.vcf.gz 16:36:22.842 INFO Funcotator - Done initializing engine 16:36:22.842 INFO Funcotator - Validating sequence dictionaries... 16:36:22.856 INFO Funcotator - Processing user transcripts/defaults/overrides... 16:36:22.857 INFO Funcotator - Initializing data sources... 16:36:22.859 INFO DataSourceUtils - Initializing data sources from directory: /home/ppshah/shared/pipelines/mutect/funcotator_dataSources.v1.7.20200521s 16:36:22.871 INFO DataSourceUtils - Data sources version: 1.7.2020429s 16:36:22.871 INFO DataSourceUtils - Data sources source: ftp://[email protected]/bundle/funcotator/funcotator_dataSources.v1.7.20200429s.tar.gz 16:36:22.871 INFO DataSourceUtils - Data sources alternate source: gs://broad-public-datasets/funcotator/funcotator_dataSources.v1.7.20200429s.tar.gz 16:36:22.891 INFO Funcotator - Shutting down engine [January 10, 2024 at 4:36:22 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=285212672

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A USER ERROR has occurred: ERROR: Directory contains more than one config file: file:///home/ppshah/shared/pipelines/mutect/funcotator_dataSources.v1.7.20200521s/gencode_xrefseq/hg38/

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Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.

Any guidance to resolve the issue is appreciated. Thank you!