Hi GATK Team

I'm having trouble using Funcotator to annotate somatic vcf files.

I ran GATK (v4.1.9.0) Funcotator using the command below.

gatk Funcotator \

--variant Somatic.vcf.gz \

--reference genome.fa \

--ref-version hg19 \

--data-sources-path funcotator_dataSources.v1.6.20190124s \

--output Somatic.merge.funcotated.maf \

--output-file-format MAF

However, this error message popped up.

Error Message:

Using GATK jar /mnt/ruby/Users/uugi0620/phenomata/Anaconda3/envs/gatk4/share/gatk4-4.1.9.0-0/gatk-package-4.1.9.0-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 /mnt/ruby/Users/uugi0620/phenomata/Anaconda3/envs/gatk4/share/gatk4-4.1.9.0-0/gatk-package-4.1.9.0-local.jar Funcotator --variant 20004_T.somatic.merge.vcf.gz --reference /clinix1/Analysis/mongol/phenomata/Reference/PCAWG_reference/bwa-mem/genome.fa --ref-version hg19 --data-sources-path /clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s --output 20004_T.somatic.merge.funcotated.maf --output-file-format MAF
21:57:56.549 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/mnt/ruby/Users/uugi0620/phenomata/Anaconda3/envs/gatk4/share/gatk4-4.1.9.0-0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Nov 25, 2020 9:58:03 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
21:58:03.732 INFO Funcotator - ------------------------------------------------------------
21:58:03.733 INFO Funcotator - The Genome Analysis Toolkit (GATK) v4.1.9.0
21:58:03.733 INFO Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
21:58:03.733 INFO Funcotator - Executing as phenomata@cm156 on Linux v3.10.0-862.14.4.el7.x86_64 amd64
21:58:03.733 INFO Funcotator - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_265-b11
21:58:03.734 INFO Funcotator - Start Date/Time: November 25, 2020 9:57:56 PM KST
21:58:03.734 INFO Funcotator - ------------------------------------------------------------
21:58:03.734 INFO Funcotator - ------------------------------------------------------------
21:58:03.735 INFO Funcotator - HTSJDK Version: 2.23.0
21:58:03.735 INFO Funcotator - Picard Version: 2.23.3
21:58:03.735 INFO Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:58:03.735 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:58:03.735 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:58:03.735 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:58:03.736 INFO Funcotator - Deflater: IntelDeflater
21:58:03.736 INFO Funcotator - Inflater: IntelInflater
21:58:03.736 INFO Funcotator - GCS max retries/reopens: 20
21:58:03.736 INFO Funcotator - Requester pays: disabled
21:58:03.736 INFO Funcotator - Initializing engine
21:58:04.094 INFO FeatureManager - Using codec VCFCodec to read file file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/20004_T.somatic.merge.vcf.gz
21:58:04.160 INFO Funcotator - Done initializing engine
21:58:04.160 INFO Funcotator - Validating sequence dictionaries...
21:58:04.161 INFO Funcotator - Processing user transcripts/defaults/overrides...
21:58:04.161 INFO Funcotator - Initializing data sources...
21:58:04.163 INFO DataSourceUtils - Initializing data sources from directory: /clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s
21:58:04.165 INFO DataSourceUtils - Data sources version: 1.6.2019124s
21:58:04.165 INFO DataSourceUtils - Data sources source: ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/funcotator/funcotator_dataSources.v1.6.20190124s.tar.gz
21:58:04.165 INFO DataSourceUtils - Data sources alternate source: gs://broad-public-datasets/funcotator/funcotator_dataSources.v1.6.20190124s.tar.gz
21:58:04.206 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/gencode_xhgnc_v75_37.hg19.tsv -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
21:58:04.209 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/Familial_Cancer_Genes.no_dupes.tsv -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
21:58:04.212 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/dnaRepairGenes.20180524T145835.csv -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/dna_repair_genes/hg19/dnaRepairGenes.20180524T145835.csv
21:58:04.214 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/hg19_All_20170710.vcf.gz -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/dbsnp/hg19/hg19_All_20170710.vcf.gz
21:58:04.216 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/Cosmic.db -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/cosmic/hg19/Cosmic.db
21:58:04.218 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/clinvar_hgmd.tsv -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/clinvar/hg19/clinvar_hgmd.tsv
21:58:04.220 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/simple_uniprot_Dec012014.tsv -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
21:58:04.222 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/cosmic_tissue.tsv -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/cosmic_tissue/hg19/cosmic_tissue.tsv
21:58:04.225 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/chr1_a_bed.tsv -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/chr1_a_bed/hg19/chr1_a_bed.tsv
21:58:04.227 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/achilles_lineage_results.import.txt -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/achilles/hg19/achilles_lineage_results.import.txt
21:58:04.229 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/cosmic_fusion.tsv -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/cosmic_fusion/hg19/cosmic_fusion.tsv
21:58:04.231 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/hgnc_download_Nov302017.tsv -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/hgnc/hg19/hgnc_download_Nov302017.tsv
21:58:04.233 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/gencode_xrefseq_v75_37.tsv -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
21:58:04.235 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
21:58:04.237 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/oreganno.tsv -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/oreganno/hg19/oreganno.tsv
21:58:04.239 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/gencode.v19.annotation.REORDERED.gtf -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/gencode/hg19/gencode.v19.annotation.REORDERED.gtf
21:58:04.240 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/gencode.v19.pc_transcripts.fa -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/gencode/hg19/gencode.v19.pc_transcripts.fa
21:58:04.242 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/chr1_b_bed.tsv -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/chr1_b_bed/hg19/chr1_b_bed.tsv
21:58:04.242 INFO Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
21:58:04.243 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/gencode_xhgnc_v75_37.hg19.tsv -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
21:58:04.969 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/Familial_Cancer_Genes.no_dupes.tsv -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
21:58:04.971 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/dnaRepairGenes.20180524T145835.csv -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/dna_repair_genes/hg19/dnaRepairGenes.20180524T145835.csv
21:58:04.972 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/hg19_All_20170710.vcf.gz -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/dbsnp/hg19/hg19_All_20170710.vcf.gz
21:58:04.972 INFO DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
21:58:04.993 INFO FeatureManager - Using codec VCFCodec to read file file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/dbsnp/hg19/hg19_All_20170710.vcf.gz
21:58:05.071 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/hg19_All_20170710.vcf.gz -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/dbsnp/hg19/hg19_All_20170710.vcf.gz
21:58:05.119 INFO FeatureManager - Using codec VCFCodec to read file file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/dbsnp/hg19/hg19_All_20170710.vcf.gz
21:58:05.179 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/Cosmic.db -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/cosmic/hg19/Cosmic.db
21:58:05.325 INFO DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
21:58:05.331 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/clinvar_hgmd.tsv -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/clinvar/hg19/clinvar_hgmd.tsv
21:58:05.332 INFO FeatureManager - Using codec XsvLocatableTableCodec to read file file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/clinvar/hg19/clinvar_hgmd.config
21:58:05.423 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/clinvar_hgmd.tsv -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/clinvar/hg19/clinvar_hgmd.tsv
21:58:05.423 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/clinvar_hgmd.tsv -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/clinvar/hg19/clinvar_hgmd.tsv
WARNING 2020-11-25 21:58:05 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
21:58:05.428 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/simple_uniprot_Dec012014.tsv -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
21:58:05.474 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/cosmic_tissue.tsv -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/cosmic_tissue/hg19/cosmic_tissue.tsv
21:58:05.490 INFO DataSourceUtils - Setting lookahead cache for data source: chr1_a_bed : 100000
21:58:05.494 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/chr1_a_bed.tsv -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/chr1_a_bed/hg19/chr1_a_bed.tsv
21:58:05.495 INFO FeatureManager - Using codec XsvLocatableTableCodec to read file file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/chr1_a_bed/hg19/chr1_a_bed.config
21:58:05.498 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/chr1_a_bed.tsv -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/chr1_a_bed/hg19/chr1_a_bed.tsv
21:58:05.498 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/chr1_a_bed.tsv -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/chr1_a_bed/hg19/chr1_a_bed.tsv
WARNING 2020-11-25 21:58:05 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
21:58:05.500 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/achilles_lineage_results.import.txt -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/achilles/hg19/achilles_lineage_results.import.txt
21:58:05.503 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/cosmic_fusion.tsv -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/cosmic_fusion/hg19/cosmic_fusion.tsv
21:58:05.508 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/hgnc_download_Nov302017.tsv -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/hgnc/hg19/hgnc_download_Nov302017.tsv
21:58:05.720 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/gencode_xrefseq_v75_37.tsv -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
21:58:05.771 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
21:58:05.772 INFO DataSourceUtils - Setting lookahead cache for data source: Oreganno : 100000
21:58:05.776 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/oreganno.tsv -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/oreganno/hg19/oreganno.tsv
21:58:05.777 INFO FeatureManager - Using codec XsvLocatableTableCodec to read file file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/oreganno/hg19/oreganno.config
21:58:05.795 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/oreganno.tsv -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/oreganno/hg19/oreganno.tsv
21:58:05.796 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/oreganno.tsv -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/oreganno/hg19/oreganno.tsv
WARNING 2020-11-25 21:58:05 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
21:58:05.798 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/gencode.v19.annotation.REORDERED.gtf -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/gencode/hg19/gencode.v19.annotation.REORDERED.gtf
21:58:05.798 INFO DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
21:58:05.801 INFO FeatureManager - Using codec GencodeGtfCodec to read file file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/gencode/hg19/gencode.v19.annotation.REORDERED.gtf
21:58:05.808 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/gencode.v19.pc_transcripts.fa -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/gencode/hg19/gencode.v19.pc_transcripts.fa
21:58:10.064 INFO DataSourceUtils - Setting lookahead cache for data source: chr1_b_bed : 100000
21:58:10.068 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/chr1_b_bed.tsv -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/chr1_b_bed/hg19/chr1_b_bed.tsv
21:58:10.069 INFO FeatureManager - Using codec XsvLocatableTableCodec to read file file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/chr1_b_bed/hg19/chr1_b_bed.config
21:58:10.071 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/chr1_b_bed.tsv -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/chr1_b_bed/hg19/chr1_b_bed.tsv
21:58:10.072 INFO DataSourceUtils - Resolved data source file path: file:///mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/chr1_b_bed.tsv -> file:///clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/funcotator_dataSources.v1.6.20190124s/chr1_b_bed/hg19/chr1_b_bed.tsv
WARNING 2020-11-25 21:58:10 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
21:58:10.073 INFO Funcotator - Initializing Funcotator Engine...
21:58:10.094 INFO FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode. Performing conversion.
21:58:10.094 WARN FuncotatorEngine - WARNING: You are using B37 as a reference. Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases. There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
21:58:10.094 INFO Funcotator - Creating a MAF file for output: file:/mnt/clinix1/Analysis/mongol/phenomata/04.GC_CC/Whole_new_2020/01.WGS/02.SNV_INDELS/Strelka/SomaticVariants/MERGED/VCF2MAF/Funcotator/20004_T.somatic.merge.funcotated.maf
21:58:10.105 WARN MafOutputRenderer - No tumor/normal pairs were seen, cannot populate the some of the MAF fields (e.g. t_alt_count). Please add '##tumor_sample=<tumor_sample_name>' and (if applicable) '##normal_sample=<normal_sample_name>' to the input VCF header
21:58:10.149 INFO ProgressMeter - Starting traversal
21:58:10.149 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
21:58:10.337 INFO VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
21:58:10.346 INFO Funcotator - Shutting down engine
[November 25, 2020 9:58:10 PM KST] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.23 minutes.
Runtime.totalMemory()=3271557120
org.broadinstitute.hellbender.exceptions.GATKException: Unable to query the database for geneName: RP11-206L10.8
at org.broadinstitute.hellbender.tools.funcotator.dataSources.cosmic.CosmicFuncotationFactory.createFuncotationsOnVariant(CosmicFuncotationFactory.java:320)
at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.determineFuncotations(DataSourceFuncotationFactory.java:245)
at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.createFuncotations(DataSourceFuncotationFactory.java:211)
at org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine.createFuncotationMapForVariant(FuncotatorEngine.java:173)
at org.broadinstitute.hellbender.tools.funcotator.Funcotator.enqueueAndHandleVariant(Funcotator.java:907)
at org.broadinstitute.hellbender.tools.funcotator.Funcotator.apply(Funcotator.java:861)
at org.broadinstitute.hellbender.engine.VariantWalker.lambda$traverse$0(VariantWalker.java:104)
at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:485)
at org.broadinstitute.hellbender.engine.VariantWalker.traverse(VariantWalker.java:102)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1049)
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)
Caused by: org.sqlite.SQLiteException: [SQLITE_IOERR_LOCK] I/O error in the advisory file locking logic (disk I/O error)
at org.sqlite.core.DB.newSQLException(DB.java:909)
at org.sqlite.core.DB.newSQLException(DB.java:921)
at org.sqlite.core.DB.throwex(DB.java:886)
at org.sqlite.core.NativeDB.prepare_utf8(Native Method)
at org.sqlite.core.NativeDB.prepare(NativeDB.java:127)
at org.sqlite.core.DB.prepare(DB.java:227)
at org.sqlite.jdbc3.JDBC3Statement.executeQuery(JDBC3Statement.java:81)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.cosmic.CosmicFuncotationFactory.createFuncotationsOnVariant(CosmicFuncotationFactory.java:288)
... 26 more

Note:

• Reference fasta i'm using is b37 reference with hs37d5 decoy sequence.
• Somatic variant calling was done by Strelka2 
• Using funcotator_dataSources.v1.7.20200521s as a data source, similar error has occurred except for the gene funcotator having trouble with:
  org.broadinstitute.hellbender.exceptions.GATKException: Unable to query the database for geneName: LINC01409

Oddly, I've checked whether RP11-206L10.8 is in the gencode hg19 database and it turned out this gene is in the gencode.v19.annotation.REORDERED.gtf file but not in gencode.v19.pc_transcripts.fa

grep 'RP11-206L10.8' gencode.v19.pc_transcripts.fa # No output

grep 'RP11-206L10.8' gencode.v19.annotation.REORDERED.gtf

chr1	HAVANA	gene	736259	745541	.	-	.	gene_id "ENSG00000230092.3"; transcript_id "ENSG00000230092.3"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "RP11-206L10.8"; transcript_type "pseudogene"; transcript_status "KNOWN"; transcript_name "RP11-206L10.8"; level 2; havana_gene "OTTHUMG00000002403.2";
chr1	HAVANA	transcript	736259	745541	.	-	.	gene_id "ENSG00000230092.3"; transcript_id "ENST00000590817.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "RP11-206L10.8"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "RP11-206L10.8-001"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; havana_gene "OTTHUMG00000002403.2"; havana_transcript "OTTHUMT00000006886.1";
chr1	HAVANA	exon	745447	745541	.	-	.	gene_id "ENSG00000230092.3"; transcript_id "ENST00000590817.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "RP11-206L10.8"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "RP11-206L10.8-001"; exon_number 1; exon_id "ENSE00001651951.1"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; havana_gene "OTTHUMG00000002403.2"; havana_transcript "OTTHUMT00000006886.1";
chr1	HAVANA	exon	743954	744003	.	-	.	gene_id "ENSG00000230092.3"; transcript_id "ENST00000590817.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "RP11-206L10.8"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "RP11-206L10.8-001"; exon_number 2; exon_id "ENSE00001782999.1"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; havana_gene "OTTHUMG00000002403.2"; havana_transcript "OTTHUMT00000006886.1";
chr1	HAVANA	exon	741179	741271	.	-	.	gene_id "ENSG00000230092.3"; transcript_id "ENST00000590817.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "RP11-206L10.8"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "RP11-206L10.8-001"; exon_number 3; exon_id "ENSE00001640641.1"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; havana_gene "OTTHUMG00000002403.2"; havana_transcript "OTTHUMT00000006886.1";
chr1	HAVANA	exon	736259	736543	.	-	.	gene_id "ENSG00000230092.3"; transcript_id "ENST00000590817.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "RP11-206L10.8"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "RP11-206L10.8-001"; exon_number 4; exon_id "ENSE00001716345.1"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; havana_gene "OTTHUMG00000002403.2"; havana_transcript "OTTHUMT00000006886.1";
chr1	HAVANA	transcript	736259	745541	.	-	.	gene_id "ENSG00000230092.3"; transcript_id "ENST00000447500.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "RP11-206L10.8"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "RP11-206L10.8-002"; level 2; tag "basic"; havana_gene "OTTHUMG00000002403.2"; havana_transcript "OTTHUMT00000448550.1";
chr1	HAVANA	exon	745447	745541	.	-	.	gene_id "ENSG00000230092.3"; transcript_id "ENST00000447500.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "RP11-206L10.8"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "RP11-206L10.8-002"; exon_number 1; exon_id "ENSE00001651951.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000002403.2"; havana_transcript "OTTHUMT00000448550.1";
chr1	HAVANA	exon	743954	744003	.	-	.	gene_id "ENSG00000230092.3"; transcript_id "ENST00000447500.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "RP11-206L10.8"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "RP11-206L10.8-002"; exon_number 2; exon_id "ENSE00001782999.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000002403.2"; havana_transcript "OTTHUMT00000448550.1";
chr1	HAVANA	exon	741179	741271	.	-	.	gene_id "ENSG00000230092.3"; transcript_id "ENST00000447500.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "RP11-206L10.8"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "RP11-206L10.8-002"; exon_number 3; exon_id "ENSE00001640641.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000002403.2"; havana_transcript "OTTHUMT00000448550.1";
chr1	HAVANA	exon	736259	736543	.	-	.	gene_id "ENSG00000230092.3"; transcript_id "ENST00000447500.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "RP11-206L10.8"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "RP11-206L10.8-002"; exon_number 4; exon_id "ENSE00001716345.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000002403.2"; havana_transcript "OTTHUMT00000448550.1";

Is there anything I can do to fix this issue? 

Best regards,

Ryan