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Official code repository for GATK versions 4 and up
https://software.broadinstitute.org/gatk
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gatk Funcotator error #8913

Open l-magnificence opened 1 month ago

l-magnificence commented 1 month ago

Hi, when I run gatk Funcotator, A USER ERROR has occurred

Using GATK jar /export/.conda/envs/wes/share/gatk4-4.0.5.1-0/gatk-package-4.0.5.1-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 /export/bioinfo-team/home/liuhw/.conda/envs/wes/share/gatk4-4.0.5.1-0/gatk-package-4.0.5.1-local.jar Funcotator --data-sources-path /export2/liuhw/software/gatk_Funcotator/funcotator_dataSources.v1.8.hg38.20230908s/ -V /export2/liuhw/wes_test//Mutect2_filter/K001137N_somatic_filtered.vcf.gz -R /Shared_Software/ref_genome/GATK_GRCh38/Homo_sapiens_assembly38.fasta --ref-version hg38 -O /export2/liuhw/wes_test//annotate/K001137N.funcotator.maf --output-file-format MAF
02:55:31.904 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/export/bioinfo-team/home/liuhw/.conda/envs/wes/share/gatk4-4.0.5.1-0/gatk-package-4.0.5.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
02:55:32.062 INFO  Funcotator - ------------------------------------------------------------
02:55:32.062 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.0.5.1-0.0.3
02:55:32.062 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
02:55:32.062 INFO  Funcotator - Executing as liuhw@RichardLi-Lab01 on Linux v5.4.0-74-generic amd64
02:55:32.062 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_412-b08
02:55:32.063 INFO  Funcotator - Start Date/Time: July 12, 2024 2:55:31 AM EDT
02:55:32.063 INFO  Funcotator - ------------------------------------------------------------
02:55:32.063 INFO  Funcotator - ------------------------------------------------------------
02:55:32.063 INFO  Funcotator - HTSJDK Version: 2.15.1
02:55:32.063 INFO  Funcotator - Picard Version: 2.18.2
02:55:32.063 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
02:55:32.063 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
02:55:32.063 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
02:55:32.063 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
02:55:32.063 INFO  Funcotator - Deflater: IntelDeflater
02:55:32.063 INFO  Funcotator - Inflater: IntelInflater
02:55:32.063 INFO  Funcotator - GCS max retries/reopens: 20
02:55:32.063 INFO  Funcotator - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes
02:55:32.063 WARN  Funcotator - 

[1m[31m   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

   Warning: Funcotator is a BETA tool and is not yet ready for use in production

   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!![0m

02:55:32.063 INFO  Funcotator - Initializing engine
02:55:32.318 INFO  FeatureManager - Using codec VCFCodec to read file file:///export2/liuhw/wes_test/Mutect2_filter/K001137N_somatic_filtered.vcf.gz
02:55:32.459 INFO  Funcotator - Done initializing engine
log4j:WARN No appenders could be found for logger (org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
02:55:32.466 INFO  Funcotator - Shutting down engine
[July 12, 2024 2:55:32 AM EDT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2148532224
***********************************************************************

A USER ERROR has occurred: Bad input: ERROR in config file: file:///./software/gatk_Funcotator/funcotator_dataSources.v1.8.hg38.20230908s/gnomAD_exome/hg38/gnomAD_exome.config - src_file does not exist: /./software/gatk_Funcotator/funcotator_dataSources.v1.8.hg38.20230908s/gnomAD_exome/hg38/gs:/broad-public-datasets/funcotator/gnomAD_2.1_VCF_INFO_AF_Only/hg38/gnomad.exomes.r2.1.sites.liftoverToHg38.INFO_ANNOTATIONS_FIXED.vcf.gz

***********************************************************************

How to solved it?

gokalpcelik commented 1 month ago

Use the latest GATK 4.6.0.0 and the latest Funcotator resource.