Funcotator Error. WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant.
I aligned my reads to Ensembl's GRCh38 genome. I realize that there are differences in the contigs names. Funcotator uses contig names with "chr" prefix followed by the chromosome number and Ensembl's just uses the chromosome number. I edited the fasta file to have the chr prefix and then created a .fa.fai and .dict file. I also modified the contig names in the vcf using awk.
This is the gatk HaplotypeCaller run before calling Funcotator.
gatk \
--java-options "-Xmx8g" HaplotypeCaller \
--max-reads-per-alignment-start 10000 \
-G StandardAnnotation -G AS_StandardAnnotation -G StandardHCAnnotation \
-L !{params.chip_wb} \
--reference !{params.db} \
--sample-name !{meta.id} \
--input !{reads} --output !{meta.id}.g.vcf.gz \
-ERC GVCF
# Append chr to contig names
zcat !{meta.id}.g.vcf.gz | awk '!/^#/ {$0="chr"$0} {print}' | awk '/^##contig=<ID=/ {gsub(/##contig=<ID=/,"&chr"); print} !/^##contig=<ID=/' | bgzip > !{meta.id}.tmp && mv !{meta.id}.tmp !{meta.id}.g.vcf.gz
Do I just need to redo the alignment using hg38 with the chr prefix?
Is that the easiest solution or can I modify the vcf files somehow to work with funcotator?
NOTE: I deleted some of the log since it was redundant for the WARN lines.
a) GATK version used: 4.3
b) Exact command used:
gatk IndexFeatureFile -I CUH00023.g.vcf.gz
gatk Funcotator --variant CUH00023.g.vcf.gz --reference Homo_sapiens.GRCh38.dna_sm.primary_assembly.edit.fa --ref-version hg38 --data-sources-path /mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s --output CUH00023.funcotated.maf --output-file-format MAF
c) Entire program log:
Using GATK jar /opt/gatk-4.3.0.0/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 /opt/gatk-4.3.0.0/gatk-package-4.3.0.0-local.jar IndexFeatureFile -I CUH00023.g.vcf.gz
11:55:10.718 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/gatk-4.3.0.0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
11:55:10.889 INFO IndexFeatureFile - ------------------------------------------------------------
11:55:10.890 INFO IndexFeatureFile - The Genome Analysis Toolkit (GATK) v4.3.0.0
11:55:10.890 INFO IndexFeatureFile - For support and documentation go to https://software.broadinstitute.org/gatk/
11:55:10.890 INFO IndexFeatureFile - Executing as apompetti@cbix2 on Linux v3.10.0-1160.102.1.el7.x86_64 amd64
11:55:10.890 INFO IndexFeatureFile - Java runtime: OpenJDK 64-Bit Server VM v11.0.1+13-LTS
11:55:10.891 INFO IndexFeatureFile - Start Date/Time: January 23, 2024 at 11:55:10 AM EST
11:55:10.891 INFO IndexFeatureFile - ------------------------------------------------------------
11:55:10.891 INFO IndexFeatureFile - ------------------------------------------------------------
11:55:10.891 INFO IndexFeatureFile - HTSJDK Version: 3.0.1
11:55:10.892 INFO IndexFeatureFile - Picard Version: 2.27.5
11:55:10.892 INFO IndexFeatureFile - Built for Spark Version: 2.4.5
11:55:10.892 INFO IndexFeatureFile - HTSJDK Defaults.COMPRESSION_LEVEL : 2
11:55:10.892 INFO IndexFeatureFile - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
11:55:10.892 INFO IndexFeatureFile - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
11:55:10.892 INFO IndexFeatureFile - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
11:55:10.892 INFO IndexFeatureFile - Deflater: IntelDeflater
11:55:10.892 INFO IndexFeatureFile - Inflater: IntelInflater
11:55:10.892 INFO IndexFeatureFile - GCS max retries/reopens: 20
11:55:10.893 INFO IndexFeatureFile - Requester pays: disabled
11:55:10.893 INFO IndexFeatureFile - Initializing engine
11:55:10.893 INFO IndexFeatureFile - Done initializing engine
11:55:11.073 INFO FeatureManager - Using codec VCFCodec to read file file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/CUH00023.g.vcf.gz
11:55:11.098 INFO ProgressMeter - Starting traversal
11:55:11.098 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
11:55:11.241 WARN IntelInflater - Zero Bytes Written : 0
11:55:11.244 INFO ProgressMeter - chr9:5072438 0.0 4184 1755524.5
11:55:11.244 INFO ProgressMeter - Traversal complete. Processed 4184 total records in 0.0 minutes.
11:55:11.264 INFO IndexFeatureFile - Successfully wrote index to /mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/CUH00023.g.vcf.gz.tbi
11:55:11.264 INFO IndexFeatureFile - Shutting down engine
[January 23, 2024 at 11:55:11 AM EST] org.broadinstitute.hellbender.tools.IndexFeatureFile done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2147483648
Tool returned:
/mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/CUH00023.g.vcf.gz.tbi
Using GATK jar /opt/gatk-4.3.0.0/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 /opt/gatk-4.3.0.0/gatk-package-4.3.0.0-local.jar Funcotator --variant CUH00023.g.vcf.gz --reference Homo_sapiens.GRCh38.dna_sm.primary_assembly.edit.fa --ref-version hg38 --data-sources-path /mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s --output CUH00023.funcotated.maf --output-file-format MAF
11:55:14.335 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/gatk-4.3.0.0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
11:55:14.508 INFO Funcotator - ------------------------------------------------------------
11:55:14.508 INFO Funcotator - The Genome Analysis Toolkit (GATK) v4.3.0.0
11:55:14.508 INFO Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
11:55:14.509 INFO Funcotator - Executing as apompetti@cbix2 on Linux v3.10.0-1160.102.1.el7.x86_64 amd64
11:55:14.509 INFO Funcotator - Java runtime: OpenJDK 64-Bit Server VM v11.0.1+13-LTS
11:55:14.509 INFO Funcotator - Start Date/Time: January 23, 2024 at 11:55:14 AM EST
11:55:14.509 INFO Funcotator - ------------------------------------------------------------
11:55:14.509 INFO Funcotator - ------------------------------------------------------------
11:55:14.510 INFO Funcotator - HTSJDK Version: 3.0.1
11:55:14.510 INFO Funcotator - Picard Version: 2.27.5
11:55:14.510 INFO Funcotator - Built for Spark Version: 2.4.5
11:55:14.511 INFO Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
11:55:14.511 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
11:55:14.511 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
11:55:14.511 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
11:55:14.511 INFO Funcotator - Deflater: IntelDeflater
11:55:14.511 INFO Funcotator - Inflater: IntelInflater
11:55:14.511 INFO Funcotator - GCS max retries/reopens: 20
11:55:14.512 INFO Funcotator - Requester pays: disabled
11:55:14.512 INFO Funcotator - Initializing engine
11:55:14.791 INFO FeatureManager - Using codec VCFCodec to read file file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/CUH00023.g.vcf.gz
11:55:14.810 WARN IntelInflater - Zero Bytes Written : 0
11:55:14.834 WARN IntelInflater - Zero Bytes Written : 0
11:55:14.849 INFO Funcotator - Done initializing engine
11:55:14.849 INFO Funcotator - Validating sequence dictionaries...
11:55:14.851 INFO Funcotator - Processing user transcripts/defaults/overrides...
11:55:14.852 INFO Funcotator - Initializing data sources...
11:55:14.855 INFO DataSourceUtils - Initializing data sources from directory: /mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s
11:55:14.856 INFO DataSourceUtils - Data sources version: 1.7.2020429s
11:55:14.856 INFO DataSourceUtils - Data sources source: ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/funcotator/funcotator_dataSources.v1.7.20200429s.tar.gz
11:55:14.856 INFO DataSourceUtils - Data sources alternate source: gs://broad-public-datasets/funcotator/funcotator_dataSources.v1.7.20200429s.tar.gz
11:55:15.600 INFO DataSourceUtils - Resolved data source file path: file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/Cosmic.db -> file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/cosmic/hg38/Cosmic.db
11:55:15.601 INFO DataSourceUtils - Resolved data source file path: file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/cancer_gene_census/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
11:55:15.603 INFO DataSourceUtils - Resolved data source file path: file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/cosmic_tissue.tsv -> file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/cosmic_tissue/hg38/cosmic_tissue.tsv
11:55:15.786 INFO DataSourceUtils - Resolved data source file path: file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/Familial_Cancer_Genes.no_dupes.tsv -> file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/familial/hg38/Familial_Cancer_Genes.no_dupes.tsv
11:55:15.789 INFO DataSourceUtils - Resolved data source file path: file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/gencode.v34.annotation.REORDERED.gtf -> file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/gencode/hg38/gencode.v34.annotation.REORDERED.gtf
11:55:15.790 INFO DataSourceUtils - Resolved data source file path: file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/gencode.v34.pc_transcripts.fa -> file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/gencode/hg38/gencode.v34.pc_transcripts.fa
11:55:15.792 INFO DataSourceUtils - Resolved data source file path: file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/oreganno.tsv -> file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/oreganno/hg38/oreganno.tsv
11:55:15.794 INFO DataSourceUtils - Resolved data source file path: file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/hg38_All_20180418.vcf.gz -> file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/dbsnp/hg38/hg38_All_20180418.vcf.gz
11:55:15.796 INFO DataSourceUtils - Resolved data source file path: file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/dnaRepairGenes.20180524T145835.csv -> file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/dna_repair_genes/hg38/dnaRepairGenes.20180524T145835.csv
11:55:15.798 INFO DataSourceUtils - Resolved data source file path: file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/gencode_xrefseq_v90_38.tsv -> file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/gencode_xrefseq/hg38/gencode_xrefseq_v90_38.tsv
11:55:15.799 INFO DataSourceUtils - Resolved data source file path: file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/cosmic_fusion.tsv -> file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/cosmic_fusion/hg38/cosmic_fusion.tsv
11:55:15.801 INFO DataSourceUtils - Resolved data source file path: file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/clinvar_20180429_hg38.vcf -> file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/clinvar/hg38/clinvar_20180429_hg38.vcf
11:55:15.802 INFO DataSourceUtils - Resolved data source file path: file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/simple_uniprot_Dec012014.tsv -> file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/simple_uniprot/hg38/simple_uniprot_Dec012014.tsv
11:55:15.804 INFO DataSourceUtils - Resolved data source file path: file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/hgnc_download_Nov302017.tsv -> file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/hgnc/hg38/hgnc_download_Nov302017.tsv
11:55:15.805 INFO DataSourceUtils - Resolved data source file path: file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/gencode_xhgnc_v90_38.hg38.tsv -> file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/gencode_xhgnc/hg38/gencode_xhgnc_v90_38.hg38.tsv
11:55:15.806 INFO DataSourceUtils - Resolved data source file path: file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/achilles_lineage_results.import.txt -> file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/achilles/hg38/achilles_lineage_results.import.txt
11:55:15.807 INFO Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
11:55:15.808 INFO DataSourceUtils - Setting lookahead cache for data source: gnomAD_genome : 100000
11:55:18.593 INFO FeatureManager - Using codec VCFCodec to read file gs://broad-public-datasets/funcotator/gnomAD_2.1_VCF_INFO_AF_Only/hg38/gnomad.genomes.r2.1.sites.liftoverToHg38.INFO_ANNOTATIONS_FIXED.vcf.gz
11:55:27.260 INFO FeatureManager - Using codec VCFCodec to read file gs://broad-public-datasets/funcotator/gnomAD_2.1_VCF_INFO_AF_Only/hg38/gnomad.genomes.r2.1.sites.liftoverToHg38.INFO_ANNOTATIONS_FIXED.vcf.gz
11:55:28.234 INFO DataSourceUtils - Resolved data source file path: file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/Cosmic.db -> file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/cosmic/hg38/Cosmic.db
11:55:28.348 INFO DataSourceUtils - Resolved data source file path: file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/cancer_gene_census/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
11:55:28.358 INFO DataSourceUtils - Resolved data source file path: file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/cosmic_tissue.tsv -> file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/cosmic_tissue/hg38/cosmic_tissue.tsv
11:55:28.419 INFO DataSourceUtils - Setting lookahead cache for data source: gnomAD_exome : 100000
11:55:31.096 INFO FeatureManager - Using codec VCFCodec to read file gs://broad-public-datasets/funcotator/gnomAD_2.1_VCF_INFO_AF_Only/hg38/gnomad.exomes.r2.1.sites.liftoverToHg38.INFO_ANNOTATIONS_FIXED.vcf.gz
11:55:38.469 INFO FeatureManager - Using codec VCFCodec to read file gs://broad-public-datasets/funcotator/gnomAD_2.1_VCF_INFO_AF_Only/hg38/gnomad.exomes.r2.1.sites.liftoverToHg38.INFO_ANNOTATIONS_FIXED.vcf.gz
11:55:39.383 INFO DataSourceUtils - Resolved data source file path: file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/Familial_Cancer_Genes.no_dupes.tsv -> file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/familial/hg38/Familial_Cancer_Genes.no_dupes.tsv
11:55:39.385 INFO DataSourceUtils - Resolved data source file path: file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/gencode.v34.annotation.REORDERED.gtf -> file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/gencode/hg38/gencode.v34.annotation.REORDERED.gtf
11:55:39.385 INFO DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
11:55:39.391 INFO FeatureManager - Using codec GencodeGtfCodec to read file file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/gencode/hg38/gencode.v34.annotation.REORDERED.gtf
11:55:39.430 INFO DataSourceUtils - Resolved data source file path: file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/gencode.v34.pc_transcripts.fa -> file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/gencode/hg38/gencode.v34.pc_transcripts.fa
11:55:44.921 INFO DataSourceUtils - Setting lookahead cache for data source: Oreganno : 100000
11:55:44.933 INFO DataSourceUtils - Resolved data source file path: file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/oreganno.tsv -> file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/oreganno/hg38/oreganno.tsv
11:55:44.934 INFO FeatureManager - Using codec XsvLocatableTableCodec to read file file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/oreganno/hg38/oreganno.config
11:55:44.967 INFO DataSourceUtils - Resolved data source file path: file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/oreganno.tsv -> file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/oreganno/hg38/oreganno.tsv
11:55:44.967 INFO DataSourceUtils - Resolved data source file path: file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/oreganno.tsv -> file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/oreganno/hg38/oreganno.tsv
WARNING 2024-01-23 11:55:44 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
11:55:45.040 INFO DataSourceUtils - Resolved data source file path: file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/hg38_All_20180418.vcf.gz -> file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/dbsnp/hg38/hg38_All_20180418.vcf.gz
11:55:45.040 INFO DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
11:55:45.046 INFO FeatureManager - Using codec VCFCodec to read file file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/dbsnp/hg38/hg38_All_20180418.vcf.gz
11:55:45.142 INFO DataSourceUtils - Resolved data source file path: file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/hg38_All_20180418.vcf.gz -> file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/dbsnp/hg38/hg38_All_20180418.vcf.gz
11:55:45.191 INFO FeatureManager - Using codec VCFCodec to read file file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/dbsnp/hg38/hg38_All_20180418.vcf.gz
11:55:45.237 INFO DataSourceUtils - Resolved data source file path: file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/dnaRepairGenes.20180524T145835.csv -> file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/dna_repair_genes/hg38/dnaRepairGenes.20180524T145835.csv
11:55:45.238 INFO DataSourceUtils - Resolved data source file path: file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/gencode_xrefseq_v90_38.tsv -> file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/gencode_xrefseq/hg38/gencode_xrefseq_v90_38.tsv
11:55:45.587 INFO DataSourceUtils - Resolved data source file path: file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/cosmic_fusion.tsv -> file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/cosmic_fusion/hg38/cosmic_fusion.tsv
11:55:45.590 INFO DataSourceUtils - Resolved data source file path: file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/clinvar_20180429_hg38.vcf -> file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/clinvar/hg38/clinvar_20180429_hg38.vcf
11:55:45.590 INFO DataSourceUtils - Setting lookahead cache for data source: ClinVar_VCF : 100000
11:55:45.594 INFO FeatureManager - Using codec VCFCodec to read file file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/clinvar/hg38/clinvar_20180429_hg38.vcf
11:55:45.651 INFO DataSourceUtils - Resolved data source file path: file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/clinvar_20180429_hg38.vcf -> file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/clinvar/hg38/clinvar_20180429_hg38.vcf
11:55:45.709 INFO FeatureManager - Using codec VCFCodec to read file file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/clinvar/hg38/clinvar_20180429_hg38.vcf
11:55:45.764 INFO DataSourceUtils - Resolved data source file path: file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/simple_uniprot_Dec012014.tsv -> file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/simple_uniprot/hg38/simple_uniprot_Dec012014.tsv
11:55:45.891 INFO DataSourceUtils - Resolved data source file path: file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/hgnc_download_Nov302017.tsv -> file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/hgnc/hg38/hgnc_download_Nov302017.tsv
11:55:46.004 INFO DataSourceUtils - Resolved data source file path: file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/gencode_xhgnc_v90_38.hg38.tsv -> file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/gencode_xhgnc/hg38/gencode_xhgnc_v90_38.hg38.tsv
11:55:47.352 INFO DataSourceUtils - Resolved data source file path: file:///mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/achilles_lineage_results.import.txt -> file:///mnt/data/gdata/human/gatk/funcotator_dataSources.v1.7.20200521s/achilles/hg38/achilles_lineage_results.import.txt
11:55:47.354 INFO Funcotator - Initializing Funcotator Engine...
11:55:47.357 INFO FuncotatorEngine - Using given VCF and Reference. No conversion required.
11:55:47.357 INFO Funcotator - Creating a MAF file for output: file:/mnt/data/data_ap/23Aug2023_CHIP_ExomeSeq/work/b7/5289e0a3ef0b65ecb539c8cf6d3194/CUH00023.funcotated.maf
11:55:47.376 INFO ProgressMeter - Starting traversal
11:55:47.377 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
11:55:47.381 WARN IntelInflater - Zero Bytes Written : 0
11:55:47.633 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1785287-1787260 due to alternate allele: <NON_REF>
11:55:47.668 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1785287-1787260 due to alternate allele: <NON_REF>
11:55:47.669 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1785287-1787260 due to alternate allele: <NON_REF>
11:55:53.100 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1787261-1787262 due to alternate allele: <NON_REF>
11:55:53.102 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1787261-1787262 due to alternate allele: <NON_REF>
11:55:53.102 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1787261-1787262 due to alternate allele: <NON_REF>
11:55:53.109 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1787263-1787267 due to alternate allele: <NON_REF>
11:55:53.110 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1787263-1787267 due to alternate allele: <NON_REF>
11:55:53.110 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1787263-1787267 due to alternate allele: <NON_REF>
11:55:53.116 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1787268-1787268 due to alternate allele: <NON_REF>
11:55:53.116 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1787268-1787268 due to alternate allele: <NON_REF>
11:55:53.117 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1787268-1787268 due to alternate allele: <NON_REF>
11:55:53.121 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1787269-1787272 due to alternate allele: <NON_REF>
11:55:53.122 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1787269-1787272 due to alternate allele: <NON_REF>
11:55:53.122 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1787269-1787272 due to alternate allele: <NON_REF>
11:55:53.127 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1787273-1787275 due to alternate allele: <NON_REF>
11:55:53.127 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1787273-1787275 due to alternate allele: <NON_REF>
11:55:53.127 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1787273-1787275 due to alternate allele: <NON_REF>
11:56:01.496 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285619-119285640 due to alternate allele: <NON_REF>
11:56:01.496 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285619-119285640 due to alternate allele: <NON_REF>
11:56:01.502 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285641-119285641 due to alternate allele: <NON_REF>
11:56:01.502 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285641-119285641 due to alternate allele: <NON_REF>
11:56:01.502 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285641-119285641 due to alternate allele: <NON_REF>
11:56:01.509 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285642-119285646 due to alternate allele: <NON_REF>
11:56:01.509 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285642-119285646 due to alternate allele: <NON_REF>
11:56:01.509 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285642-119285646 due to alternate allele: <NON_REF>
11:56:01.515 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285647-119285647 due to alternate allele: <NON_REF>
11:56:01.515 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285647-119285647 due to alternate allele: <NON_REF>
11:56:01.515 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285647-119285647 due to alternate allele: <NON_REF>
11:56:01.522 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285648-119285650 due to alternate allele: <NON_REF>
11:56:01.522 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285648-119285650 due to alternate allele: <NON_REF>
11:56:01.522 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285648-119285650 due to alternate allele: <NON_REF>
11:56:01.528 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285651-119285651 due to alternate allele: <NON_REF>
11:56:01.528 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285651-119285651 due to alternate allele: <NON_REF>
11:56:01.528 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285651-119285651 due to alternate allele: <NON_REF>
11:56:01.535 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285652-119285656 due to alternate allele: <NON_REF>
11:56:01.535 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285652-119285656 due to alternate allele: <NON_REF>
11:56:01.535 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285652-119285656 due to alternate allele: <NON_REF>
11:56:01.542 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285657-119285658 due to alternate allele: <NON_REF>
11:56:01.542 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285657-119285658 due to alternate allele: <NON_REF>
11:56:01.542 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285657-119285658 due to alternate allele: <NON_REF>
11:56:01.548 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285659-119285660 due to alternate allele: <NON_REF>
11:56:01.548 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285659-119285660 due to alternate allele: <NON_REF>
11:56:01.548 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285659-119285660 due to alternate allele: <NON_REF>
11:56:01.556 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285661-119285661 due to alternate allele: <NON_REF>
11:56:01.556 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285661-119285661 due to alternate allele: <NON_REF>
11:56:01.556 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285661-119285661 due to alternate allele: <NON_REF>
11:56:01.562 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285662-119285665 due to alternate allele: <NON_REF>
11:56:01.562 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285662-119285665 due to alternate allele: <NON_REF>
11:56:01.562 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285662-119285665 due to alternate allele: <NON_REF>
11:56:01.570 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285666-119285673 due to alternate allele: <NON_REF>
11:56:01.570 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285666-119285673 due to alternate allele: <NON_REF>
11:56:01.570 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285666-119285673 due to alternate allele: <NON_REF>
11:56:01.589 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285674-119285677 due to alternate allele: <NON_REF>
11:56:01.589 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285674-119285677 due to alternate allele: <NON_REF>
11:56:01.589 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285674-119285677 due to alternate allele: <NON_REF>
11:56:01.603 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285678-119285680 due to alternate allele: <NON_REF>
11:56:01.603 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285678-119285680 due to alternate allele: <NON_REF>
11:56:01.603 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285678-119285680 due to alternate allele: <NON_REF>
11:56:01.613 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285681-119285681 due to alternate allele: <NON_REF>
11:56:01.614 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285681-119285681 due to alternate allele: <NON_REF>
11:56:01.614 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285681-119285681 due to alternate allele: <NON_REF>
11:56:01.624 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285682-119285682 due to alternate allele: <NON_REF>
11:56:01.624 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285682-119285682 due to alternate allele: <NON_REF>
11:56:01.624 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285682-119285682 due to alternate allele: <NON_REF>
11:56:01.633 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285683-119285683 due to alternate allele: <NON_REF>
11:56:01.633 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285683-119285683 due to alternate allele: <NON_REF>
11:56:01.633 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285683-119285683 due to alternate allele: <NON_REF>
11:56:01.642 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285684-119285685 due to alternate allele: <NON_REF>
11:56:01.642 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285684-119285685 due to alternate allele: <NON_REF>
11:56:01.642 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285684-119285685 due to alternate allele: <NON_REF>
11:56:01.650 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285686-119285698 due to alternate allele: <NON_REF>
11:56:01.650 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285686-119285698 due to alternate allele: <NON_REF>
11:56:01.650 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285686-119285698 due to alternate allele: <NON_REF>
11:56:01.657 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285699-119285699 due to alternate allele: <NON_REF>
11:56:01.657 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285699-119285699 due to alternate allele: <NON_REF>
11:56:01.657 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285699-119285699 due to alternate allele: <NON_REF>
11:56:01.664 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285700-119285723 due to alternate allele: <NON_REF>
11:56:01.664 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285700-119285723 due to alternate allele: <NON_REF>
11:56:01.664 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285700-119285723 due to alternate allele: <NON_REF>
11:56:01.670 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285724-119285724 due to alternate allele: <NON_REF>
11:56:01.670 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285724-119285724 due to alternate allele: <NON_REF>
11:56:01.670 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285724-119285724 due to alternate allele: <NON_REF>
11:56:01.677 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285725-119285729 due to alternate allele: <NON_REF>
11:56:01.677 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285725-119285729 due to alternate allele: <NON_REF>
11:56:01.678 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285725-119285729 due to alternate allele: <NON_REF>
11:56:01.684 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285730-119285799 due to alternate allele: <NON_REF>
11:56:01.684 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285730-119285799 due to alternate allele: <NON_REF>
11:56:01.684 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285730-119285799 due to alternate allele: <NON_REF>
11:56:01.691 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285800-119287756 due to alternate allele: <NON_REF>
11:56:01.691 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285800-119287756 due to alternate allele: <NON_REF>
11:56:01.691 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119285800-119287756 due to alternate allele: <NON_REF>
11:56:01.699 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119287757-119287757 due to alternate allele: <NON_REF>
11:56:01.699 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119287757-119287757 due to alternate allele: <NON_REF>
11:56:01.699 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119287757-119287757 due to alternate allele: <NON_REF>
11:56:01.706 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119287758-119287799 due to alternate allele: <NON_REF>
11:56:01.706 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119287758-119287799 due to alternate allele: <NON_REF>
11:56:01.706 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119287758-119287799 due to alternate allele: <NON_REF>
11:56:01.721 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119287800-119287800 due to alternate allele: <NON_REF>
11:56:01.721 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119287800-119287800 due to alternate allele: <NON_REF>
11:56:01.721 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119287800-119287800 due to alternate allele: <NON_REF>
11:56:01.735 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119287801-119287962 due to alternate allele: <NON_REF>
11:56:01.735 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119287801-119287962 due to alternate allele: <NON_REF>
11:56:01.735 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119287801-119287962 due to alternate allele: <NON_REF>
11:56:01.742 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119287963-119287977 due to alternate allele: <NON_REF>
11:56:01.742 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119287963-119287977 due to alternate allele: <NON_REF>
11:56:01.742 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119287963-119287977 due to alternate allele: <NON_REF>
11:56:01.750 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119287978-119287988 due to alternate allele: <NON_REF>
11:56:01.750 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119287978-119287988 due to alternate allele: <NON_REF>
11:56:01.750 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119287978-119287988 due to alternate allele: <NON_REF>
11:56:01.758 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119287989-119287989 due to alternate allele: <NON_REF>
11:56:01.758 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119287989-119287989 due to alternate allele: <NON_REF>
11:56:01.758 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119287989-119287989 due to alternate allele: <NON_REF>
11:56:01.766 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119287990-119291768 due to alternate allele: <NON_REF>
11:56:01.766 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119287990-119291768 due to alternate allele: <NON_REF>
11:56:01.766 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:119287990-119291768 due to alternate allele: <NON_REF>
11:56:01.768 ERROR GencodeFuncotationFactory - Problem creating a GencodeFuncotation on transcript ENST00000410317.1 for variant: chr11:119287990-119291768(T* -> <NON_REF>): Variant overlaps transcript but is not completely contained within it. Funcotator cannot currently handle this case. Transcript: ENST00000410317.1 Variant: [VC Unknown @ chr11:119287990-119291768 Q. of type=SYMBOLIC alleles=[T*, <NON_REF>] attr={END=119291768} GT=GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0 filters=
11:56:01.768 WARN GencodeFuncotationFactory - Creating default GencodeFuncotation on transcript ENST00000410317.1 for problem variant: chr11:119287990-119291768(T* -> <NON_REF>)
11:56:01.790 INFO VcfFuncotationFactory - ClinVar_VCF 20180429_hg38 cache hits/total: 0/17
11:56:01.790 INFO VcfFuncotationFactory - dbSNP 9606_b151 cache hits/total: 0/434
11:56:01.790 INFO VcfFuncotationFactory - gnomAD_exome 2.1 cache hits/total: 0/62
11:56:01.790 INFO VcfFuncotationFactory - gnomAD_genome 2.1 cache hits/total: 0/321
11:56:01.790 INFO Funcotator - Shutting down engine
[January 23, 2024 at 11:56:01 AM EST] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.79 minutes.
Runtime.totalMemory()=3670016000
java.lang.ArrayIndexOutOfBoundsException: Index 0 out of bounds for length 0
at org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils.getNonOverlappingAltAlleleBaseString(FuncotatorUtils.java:302)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.getGenomeChangeString(GencodeFuncotationFactory.java:2355)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createGencodeFuncotationBuilderWithTrivialFieldsPopulated(GencodeFuncotationFactory.java:2223)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createDefaultFuncotationsOnProblemVariant(GencodeFuncotationFactory.java:923)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createDefaultFuncotationsOnProblemVariant(GencodeFuncotationFactory.java:891)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createFuncotationsHelper(GencodeFuncotationFactory.java:861)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createFuncotationsHelper(GencodeFuncotationFactory.java:831)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.lambda$createGencodeFuncotationsByAllTranscripts$0(GencodeFuncotationFactory.java:508)
at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:195)
at java.base/java.util.ArrayList$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$ReduceOp.evaluateSequential(ReduceOps.java:913)
at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.base/java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:578)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createGencodeFuncotationsByAllTranscripts(GencodeFuncotationFactory.java:509)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createFuncotationsOnVariant(GencodeFuncotationFactory.java:564)
at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.determineFuncotations(DataSourceFuncotationFactory.java:243)
at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.createFuncotations(DataSourceFuncotationFactory.java:211)
at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.createFuncotations(DataSourceFuncotationFactory.java:182)
at org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine.lambda$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)
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Looks like you are trying to run Funcotator on GVCF files. Can you try running GenotypeGVCFs on your files and then running Funcotator on them?
Also If you need to rename your contigs using the below tool would be safer.
bcftools annotate --rename-chrs
I hope this helps.
Regards.
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Hi Anthony Pompetti,
To what SkyWarrior said above, I'd add that you can use the GATK tool "CompareReferences" to determine whether it's safe to simply rename your contigs, rather than performing a formal liftover or realignment. See my reply to your other post here:
https://gatk.broadinstitute.org/hc/en-us/community/posts/22012042551707/comments/22605051068699
Regards,David
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