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broadinstitute / gatk

Official code repository for GATK versions 4 and up
https://software.broadinstitute.org/gatk
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Funcotator keep running without error but no results #7135

Open qindan2008 opened 3 years ago

qindan2008 commented 3 years ago

Hi, I tried to use Funcotator to annotate a vcf file. The vcf file had just 10 records. The program kept running without errors but no results got.

The command I used:

/technology/software_tools/gatk-4.2.0.0/gatk Funcotator \ --variant P01.mutect2.somatic.filterMutectCalls.indels.vcf.gz \ --reference /technology/dependent_resource/genome/hsa/ensembl/GRCh37.p13_GATK/genome.fa \ --ref-version hg19 \ --data-sources-path /technology/dependent_resource/variation/hg19/funcotator_dataSources.v1.7.20200521s \ --output P01.mutect2.somatic.filterMutectCalls.indels.funcotator.vcf \ --output-file-format VCF

Screen output:

Using GATK jar /technology/software_tools/gatk-4.2.0.0/gatk-package-4.2.0.0-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 /technology/software_tools/gatk-4.2.0.0/gatk-package-4.2.0.0-local.jar Funcotator --variant P01.mutect2.somatic.filterMutectCalls.indels.vcf.gz --reference /technology/dependent_resource/genome/hsa/ensembl/GRCh37.p13_GATK/genome.fa --ref-version hg19 --data-sources-path /technology/dependent_resource/variation/hg19/funcotator_dataSources.v1.7.20200521s --output P01.mutect2.somatic.filterMutectCalls.indels.funcotator.vcf --output-file-format VCF 10:25:49.484 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/technology/software_tools/gatk-4.2.0.0/gatk-package-4.2.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so Mar 09, 2021 10:25:49 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 10:25:49.665 INFO Funcotator - ------------------------------------------------------------ 10:25:49.665 INFO Funcotator - The Genome Analysis Toolkit (GATK) v4.2.0.0 10:25:49.665 INFO Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/ 10:25:49.665 INFO Funcotator - Executing as qin_dan@server on Linux v5.4.0-65-generic amd64 10:25:49.665 INFO Funcotator - Java runtime: OpenJDK 64-Bit Server VM v11.0.10+9-Ubuntu-0ubuntu1.20.04 10:25:49.666 INFO Funcotator - Start Date/Time: March 9, 2021 at 10:25:49 AM UTC 10:25:49.666 INFO Funcotator - ------------------------------------------------------------ 10:25:49.666 INFO Funcotator - ------------------------------------------------------------ 10:25:49.666 INFO Funcotator - HTSJDK Version: 2.24.0 10:25:49.666 INFO Funcotator - Picard Version: 2.25.0 10:25:49.666 INFO Funcotator - Built for Spark Version: 2.4.5 10:25:49.666 INFO Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2 10:25:49.667 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 10:25:49.667 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 10:25:49.667 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 10:25:49.667 INFO Funcotator - Deflater: IntelDeflater 10:25:49.667 INFO Funcotator - Inflater: IntelInflater 10:25:49.667 INFO Funcotator - GCS max retries/reopens: 20 10:25:49.667 INFO Funcotator - Requester pays: disabled 10:25:49.667 INFO Funcotator - Initializing engine 10:25:49.761 INFO FeatureManager - Using codec VCFCodec to read file file:///technology/research_development/WES/vcf/P01.mutect2.somatic.filterMutectCalls.indels.vcf.gz 10:25:49.781 INFO Funcotator - Done initializing engine 10:25:49.781 INFO Funcotator - Validating sequence dictionaries... 10:25:49.782 INFO Funcotator - Processing user transcripts/defaults/overrides... 10:25:49.783 INFO Funcotator - Initializing data sources... 10:25:49.784 INFO DataSourceUtils - Initializing data sources from directory: /technology/dependent_resource/variation/hg19/funcotator_dataSources.v1.7.20200521s 10:25:49.785 INFO DataSourceUtils - Data sources version: 1.7.2020429s 10:25:49.785 INFO DataSourceUtils - Data sources source: ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/funcotator/funcotator_dataSources.v1.7.20200429s.tar.gz 10:25:49.785 INFO DataSourceUtils - Data sources alternate source: gs://broad-public-datasets/funcotator/funcotator_dataSources.v1.7.20200429s.tar.gz 10:25:49.788 INFO DataSourceUtils - Resolved data source file path: file:///technology/research_development/WES/vcf/gencode_xrefseq_v75_37.tsv -> file:///technology/dependent_resource/variation/hg19/funcotator_dataSources.v1.7.20200521s/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv 10:25:49.789 INFO DataSourceUtils - Resolved data source file path: file:///technology/research_development/WES/vcf/achilles_lineage_results.import.txt -> file:///technology/dependent_resource/variation/hg19/funcotator_dataSources.v1.7.20200521s/achilles/hg19/achilles_lineage_results.import.txt 10:25:49.789 INFO DataSourceUtils - Resolved data source file path: file:///technology/research_development/WES/vcf/clinvar_20180401.vcf -> file:///technology/dependent_resource/variation/hg19/funcotator_dataSources.v1.7.20200521s/clinvar/hg19/clinvar_20180401.vcf 10:25:49.790 INFO DataSourceUtils - Resolved data source file path: file:///technology/research_development/WES/vcf/simple_uniprot_Dec012014.tsv -> file:///technology/dependent_resource/variation/hg19/funcotator_dataSources.v1.7.20200521s/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv 10:25:49.791 INFO DataSourceUtils - Resolved data source file path: file:///technology/research_development/WES/vcf/clinvar_hgmd.tsv -> file:///technology/dependent_resource/variation/hg19/funcotator_dataSources.v1.7.20200521s/clinvar_hgmd/hg19/clinvar_hgmd.tsv

The input vcf file was from gatk FilterMutectCalls and just keep indel record

what's the problem with the program? It have run a long time but without any results and errors.

Thank you.

jonn-smith commented 3 years ago

Hi @qindan2008 - is this the full log file that is produced, or is there more to it? If there is more to the log file can you post it? Would you mind posting one or two of your variants as well? They can be simplified - I only the need position and alleles.

Also, did you happen to make any modifications to the data sources? If you enabled gnomAD, Funcotator will try to read the gnomAD data sources via the Google Cloud API, which may be slow or fail depending on your internet connection and settings. You could experience similar issues if you added another web-facing data source.