I DID FUNCOTATOR STEP FROM THE GATK Somatic short variant discovery (SNVs + Indels) PIPELINE AND USE AS INPUT, THE OUTPUT OF FILTERMUTECTCALLS, BUT I OBTAIN THIS ERROR:

17:00:18.816 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 17:00:19.105 INFO Funcotator - ------------------------------------------------------------ 17:00:19.106 INFO Funcotator - The Genome Analysis Toolkit (GATK) v4.3.0.0 17:00:19.106 INFO Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/ 17:00:19.106 INFO Funcotator - Executing as rita.soares@compute-19 on Linux v5.4.0-148-generic amd64 17:00:19.106 INFO Funcotator - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_242-8u242-b08-0ubuntu3~18.04-b08 17:00:19.106 INFO Funcotator - Start Date/Time: November 24, 2023 5:00:18 PM GMT 17:00:19.106 INFO Funcotator - ------------------------------------------------------------ 17:00:19.106 INFO Funcotator - ------------------------------------------------------------ 17:00:19.107 INFO Funcotator - HTSJDK Version: 3.0.1 17:00:19.107 INFO Funcotator - Picard Version: 2.27.5 17:00:19.107 INFO Funcotator - Built for Spark Version: 2.4.5 17:00:19.107 INFO Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2 17:00:19.107 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 17:00:19.107 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 17:00:19.108 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 17:00:19.108 INFO Funcotator - Deflater: IntelDeflater 17:00:19.108 INFO Funcotator - Inflater: IntelInflater 17:00:19.108 INFO Funcotator - GCS max retries/reopens: 20 17:00:19.108 INFO Funcotator - Requester pays: disabled 17:00:19.108 INFO Funcotator - Initializing engine 17:00:19.577 INFO FeatureManager - Using codec VCFCodec to read file file:///mnt/nfs/lobo/IMM-NFS/cfranco/MCPP-Lung/DNA/Variant_Calling/FilterMutectCalls/10LC_tumor_S2.filtered.vcf.gz 17:00:19.880 INFO Funcotator - Done initializing engine 17:00:19.880 INFO Funcotator - Skipping sequence dictionary validation. 17:00:19.880 INFO Funcotator - Processing user transcripts/defaults/overrides... 17:00:19.881 INFO Funcotator - Initializing data sources... 17:00:19.883 INFO DataSourceUtils - Initializing data sources from directory: /mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s 17:00:19.953 INFO DataSourceUtils - Data sources version: 1.7.2020429s 17:00:19.953 INFO DataSourceUtils - Data sources source: ftp://[email protected]/bundle/funcotator/funcotator_dataSources.v1.7.20200429s.tar.gz 17:00:19.953 INFO DataSourceUtils - Data sources alternate source: gs://broad-public-datasets/funcotator/funcotator_dataSources.v1.7.20200429s.tar.gz 17:00:20.435 INFO DataSourceUtils - Resolved data source file path: file:///home/rita.soares/gencode.v34.annotation.REORDERED.gtf -> file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/gencode/hg38/gencode.v34.annotation.REORDERED.gtf 17:00:20.437 INFO DataSourceUtils - Resolved data source file path: file:///home/rita.soares/gencode.v34.pc_transcripts.fa -> file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/gencode/hg38/gencode.v34.pc_transcripts.fa 17:00:20.513 INFO DataSourceUtils - Resolved data source file path: file:///home/rita.soares/hg38_All_20180418.vcf.gz -> file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/dbsnp/hg38/hg38_All_20180418.vcf.gz 17:00:20.584 INFO DataSourceUtils - Resolved data source file path: file:///home/rita.soares/Familial_Cancer_Genes.no_dupes.tsv -> file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/familial/hg38/Familial_Cancer_Genes.no_dupes.tsv 17:00:20.711 INFO DataSourceUtils - Resolved data source file path: file:///home/rita.soares/dnaRepairGenes.20180524T145835.csv -> file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/dna_repair_genes/hg38/dnaRepairGenes.20180524T145835.csv 17:00:20.779 INFO DataSourceUtils - Resolved data source file path: file:///home/rita.soares/cosmic_fusion.tsv -> file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/cosmic_fusion/hg38/cosmic_fusion.tsv 17:00:20.911 INFO DataSourceUtils - Resolved data source file path: file:///home/rita.soares/hgnc_download_Nov302017.tsv -> file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/hgnc/hg38/hgnc_download_Nov302017.tsv 17:00:20.967 INFO DataSourceUtils - Resolved data source file path: file:///home/rita.soares/simple_uniprot_Dec012014.tsv -> file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/simple_uniprot/hg38/simple_uniprot_Dec012014.tsv 17:00:21.034 INFO DataSourceUtils - Resolved data source file path: file:///home/rita.soares/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/cancer_gene_census/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt 17:00:21.073 INFO DataSourceUtils - Resolved data source file path: file:///home/rita.soares/achilles_lineage_results.import.txt -> file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/achilles/hg38/achilles_lineage_results.import.txt 17:00:21.161 INFO DataSourceUtils - Resolved data source file path: file:///home/rita.soares/clinvar_20180429_hg38.vcf -> file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/clinvar/hg38/clinvar_20180429_hg38.vcf 17:00:21.171 INFO DataSourceUtils - Resolved data source file path: file:///home/rita.soares/gencode_xhgnc_v90_38.hg38.tsv -> file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/gencode_xhgnc/hg38/gencode_xhgnc_v90_38.hg38.tsv 17:00:21.187 INFO DataSourceUtils - Resolved data source file path: file:///home/rita.soares/Cosmic.db -> file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/cosmic/hg38/Cosmic.db 17:00:21.341 INFO DataSourceUtils - Resolved data source file path: file:///home/rita.soares/oreganno.tsv -> file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/oreganno/hg38/oreganno.tsv 17:00:21.357 INFO DataSourceUtils - Resolved data source file path: file:///home/rita.soares/gencode_xrefseq_v90_38.tsv -> file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/gencode_xrefseq/hg38/gencode_xrefseq_v90_38.tsv 17:00:21.378 INFO DataSourceUtils - Resolved data source file path: file:///home/rita.soares/cosmic_tissue.tsv -> file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/cosmic_tissue/hg38/cosmic_tissue.tsv 17:00:21.379 INFO Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)... 17:00:21.379 INFO DataSourceUtils - Resolved data source file path: file:///home/rita.soares/gencode.v34.annotation.REORDERED.gtf -> file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/gencode/hg38/gencode.v34.annotation.REORDERED.gtf 17:00:21.380 INFO DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000 17:00:21.553 INFO FeatureManager - Using codec GencodeGtfCodec to read file file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/gencode/hg38/gencode.v34.annotation.REORDERED.gtf 17:00:21.691 INFO DataSourceUtils - Resolved data source file path: file:///home/rita.soares/gencode.v34.pc_transcripts.fa -> file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/gencode/hg38/gencode.v34.pc_transcripts.fa 17:00:27.190 INFO DataSourceUtils - Resolved data source file path: file:///home/rita.soares/hg38_All_20180418.vcf.gz -> file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/dbsnp/hg38/hg38_All_20180418.vcf.gz 17:00:27.190 INFO DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000 17:00:27.412 INFO FeatureManager - Using codec VCFCodec to read file file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/dbsnp/hg38/hg38_All_20180418.vcf.gz 17:00:27.563 INFO DataSourceUtils - Resolved data source file path: file:///home/rita.soares/hg38_All_20180418.vcf.gz -> file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/dbsnp/hg38/hg38_All_20180418.vcf.gz 17:00:27.666 INFO FeatureManager - Using codec VCFCodec to read file file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/dbsnp/hg38/hg38_All_20180418.vcf.gz 17:00:27.814 INFO DataSourceUtils - Resolved data source file path: file:///home/rita.soares/Familial_Cancer_Genes.no_dupes.tsv -> file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/familial/hg38/Familial_Cancer_Genes.no_dupes.tsv 17:00:27.837 INFO DataSourceUtils - Resolved data source file path: file:///home/rita.soares/dnaRepairGenes.20180524T145835.csv -> file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/dna_repair_genes/hg38/dnaRepairGenes.20180524T145835.csv 17:00:27.853 INFO DataSourceUtils - Resolved data source file path: file:///home/rita.soares/cosmic_fusion.tsv -> file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/cosmic_fusion/hg38/cosmic_fusion.tsv 17:00:27.875 INFO DataSourceUtils - Resolved data source file path: file:///home/rita.soares/hgnc_download_Nov302017.tsv -> file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/hgnc/hg38/hgnc_download_Nov302017.tsv 17:00:28.142 INFO DataSourceUtils - Resolved data source file path: file:///home/rita.soares/simple_uniprot_Dec012014.tsv -> file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/simple_uniprot/hg38/simple_uniprot_Dec012014.tsv 17:00:28.400 INFO DataSourceUtils - Resolved data source file path: file:///home/rita.soares/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/cancer_gene_census/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt 17:00:28.426 INFO DataSourceUtils - Resolved data source file path: file:///home/rita.soares/achilles_lineage_results.import.txt -> file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/achilles/hg38/achilles_lineage_results.import.txt 17:00:28.449 INFO DataSourceUtils - Resolved data source file path: file:///home/rita.soares/clinvar_20180429_hg38.vcf -> file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/clinvar/hg38/clinvar_20180429_hg38.vcf 17:00:28.449 INFO DataSourceUtils - Setting lookahead cache for data source: ClinVar_VCF : 100000 17:00:28.502 INFO FeatureManager - Using codec VCFCodec to read file file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/clinvar/hg38/clinvar_20180429_hg38.vcf 17:00:28.702 INFO DataSourceUtils - Resolved data source file path: file:///home/rita.soares/clinvar_20180429_hg38.vcf -> file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/clinvar/hg38/clinvar_20180429_hg38.vcf 17:00:28.780 INFO FeatureManager - Using codec VCFCodec to read file file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/clinvar/hg38/clinvar_20180429_hg38.vcf 17:00:28.835 INFO DataSourceUtils - Resolved data source file path: file:///home/rita.soares/gencode_xhgnc_v90_38.hg38.tsv -> file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/gencode_xhgnc/hg38/gencode_xhgnc_v90_38.hg38.tsv 17:00:29.651 INFO DataSourceUtils - Resolved data source file path: file:///home/rita.soares/Cosmic.db -> file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/cosmic/hg38/Cosmic.db 17:00:29.807 INFO DataSourceUtils - Setting lookahead cache for data source: Oreganno : 100000 17:00:29.828 INFO DataSourceUtils - Resolved data source file path: file:///home/rita.soares/oreganno.tsv -> file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/oreganno/hg38/oreganno.tsv 17:00:29.871 INFO FeatureManager - Using codec XsvLocatableTableCodec to read file file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/oreganno/hg38/oreganno.config 17:00:30.155 INFO DataSourceUtils - Resolved data source file path: file:///home/rita.soares/oreganno.tsv -> file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/oreganno/hg38/oreganno.tsv 17:00:30.158 INFO DataSourceUtils - Resolved data source file path: file:///home/rita.soares/oreganno.tsv -> file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/oreganno/hg38/oreganno.tsv WARNING 2023-11-24 17:00:30 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream 17:00:30.168 INFO DataSourceUtils - Resolved data source file path: file:///home/rita.soares/gencode_xrefseq_v90_38.tsv -> file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/gencode_xrefseq/hg38/gencode_xrefseq_v90_38.tsv 17:00:30.284 INFO DataSourceUtils - Resolved data source file path: file:///home/rita.soares/cosmic_tissue.tsv -> file:///mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s/cosmic_tissue/hg38/cosmic_tissue.tsv 17:00:30.398 INFO Funcotator - Initializing Funcotator Engine... 17:00:30.400 INFO FuncotatorEngine - Using given VCF and Reference. No conversion required. 17:00:30.402 INFO Funcotator - Creating a MAF file for output: file:/mnt/nfs/lobo/IMM-NFS/cfranco/MCPP-Lung/DNA/Variant_Calling/FUNCOTATOR/10LC_tumor_S2.FiltPASS.maf 17:00:30.420 INFO ProgressMeter - Starting traversal 17:00:30.420 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 17:00:42.145 INFO ProgressMeter - chr1:1129652 0.2 1000 5117.3 17:00:52.621 INFO ProgressMeter - chr1:1544800 0.4 2000 5405.4 17:01:03.582 INFO ProgressMeter - chr1:2088265 0.6 3000 5427.9 17:01:23.573 INFO ProgressMeter - chr1:2868977 0.9 5000 5644.2 17:01:45.697 INFO ProgressMeter - chr1:3708722 1.3 7000 5579.4 17:01:47.516 ERROR GencodeFuncotationFactory - Problem creating a GencodeFuncotation on transcript ENST00000581512.2 for variant: chr1:3783110-3783112(TAA* -> T): Variant overlaps transcript but is not completely contained within it. Funcotator cannot currently handle this case. Transcript: ENST00000581512.2 Variant: [VC Unknown @ chr1:3783110-3783112 Q. of type=INDEL alleles=[TAA*, T] attr={AS_FilterStatus=[weak_evidence, contamination], AS_SB_TABLE=[0, 0|0, 0], DP=1, ECNT=2, GERMQ=1, MBQ=[0, 31], MFRL=[0, 259], MMQ=[60, 60], MPOS=66, POPAF=2.21, ROQ=93, RPA=[15, 13], RU=A, STR=true, STRQ=93, TLOD=4.20} GT=GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0,1:0|1:3783099_C_T:3783099:0,0,1,0 filters=haplotype,germline,contamination,weak_evidence ... (CODE OMITTED BECAUSE OF CHARACTERS LIMINATION OF THE BODY OF THE QUESTION) 17:06:03.884 ERROR GencodeFuncotationFactory - Problem creating a GencodeFuncotation on transcript ENST00000375071.4 for variant: chr1:20589096-20589097(TC* -> T): Variant overlaps transcript but is not completely contained within it. Funcotator cannot currently handle this case. Transcript: ENST00000375071.4 Variant: [VC Unknown @ chr1:20589096-20589097 Q. of type=INDEL alleles=[TC*, T] attr={AS_FilterStatus=SITE, AS_SB_TABLE=[108, 95|79, 72], DP=369, ECNT=2, GERMQ=1, MBQ=[20, 20], MFRL=[119, 123], MMQ=[60, 60], MPOS=26, PON=true, POPAF=0.256, ROQ=93, RPA=[3, 2], RU=C, STR=true, STRQ=93, TLOD=206.22} GT=GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:203,151:0.422:354:57,38:55,42:114,83:108,95,79,72 filters=panel_of_normals,germline 17:06:03.885 WARN GencodeFuncotationFactory - Creating default GencodeFuncotation on transcript ENST00000375071.4 for problem variant: chr1:20589096-20589097(TC* -> T) 17:06:20.587 INFO ProgressMeter - chr1:21789645 5.8 38000 6511.2 17:06:38.318 INFO ProgressMeter - chr1:22910935 6.1 40000 6523.5 17:06:55.667 INFO ProgressMeter - chr1:24196391 6.4 42000 6541.3 17:07:12.288 INFO ProgressMeter - chr1:25333744 6.7 44000 6569.3 17:07:29.628 INFO ProgressMeter - chr1:26561968 7.0 46000 6583.9 17:08:54.624 INFO ProgressMeter - chr1:27258140 8.4 47000 5593.0 17:09:11.523 INFO ProgressMeter - chr1:28509457 8.7 49000 5641.9 17:09:14.750 ERROR GencodeFuncotationFactory - Problem creating a GencodeFuncotation on transcript ENST00000294409.2 for variant: chr1:28714873-28714874(TA* -> T): Variant overlaps transcript but is not completely contained within it. Funcotator cannot currently handle this case. Transcript: ENST00000294409.2 Variant: [VC Unknown @ chr1:28714873-28714874 Q. of type=INDEL alleles=[TA*, T] attr={AS_FilterStatus=SITE, AS_SB_TABLE=[1, 8|0, 5], DP=14, ECNT=1, GERMQ=1, MBQ=[29, 29], MFRL=[277, 190], MMQ=[60, 60], MPOS=19, PON=true, POPAF=1.96, ROQ=93, RPA=[13, 12], RU=A, STR=true, STRQ=1, TLOD=6.90} GT=GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:9,5:0.377:14:1,1:4,1:8,5:1,8,0,5 filters=panel_of_normals,germline,slippage 17:09:14.750 WARN GencodeFuncotationFactory - Creating default GencodeFuncotation on transcript ENST00000294409.2 for problem variant: chr1:28714873-28714874(TA* -> T) 17:09:28.156 INFO ProgressMeter - chr1:29742106 9.0 51000 5690.5 17:09:44.363 INFO ProgressMeter - chr1:31000060 9.2 53000 5740.7 17:10:02.660 INFO ProgressMeter - chr1:32309371 9.5 55000 5766.8 17:10:21.404 INFO ProgressMeter - chr1:33875394 9.8 57000 5787.0 17:10:39.604 INFO ProgressMeter - chr1:35564548 10.2 59000 5811.1 17:11:13.558 INFO ProgressMeter - chr1:36959618 10.7 61000 5690.8 17:11:30.930 INFO ProgressMeter - chr1:38301837 11.0 63000 5722.9 17:11:48.409 INFO ProgressMeter - chr1:39672835 11.3 65000 5752.3 17:12:04.997 INFO ProgressMeter - chr1:40888483 11.6 67000 5787.7 17:12:22.171 INFO ProgressMeter - chr1:42389559 11.9 69000 5816.6 17:13:07.894 INFO ProgressMeter - chr1:43856329 12.6 71000 5624.0 17:13:25.958 INFO ProgressMeter - chr1:45154774 12.9 73000 5647.7 17:13:43.676 INFO ProgressMeter - chr1:46612646 13.2 75000 5672.8 17:14:00.829 INFO ProgressMeter - chr1:48197446 13.5 77000 5700.8 17:14:19.050 INFO ProgressMeter - chr1:50725644 13.8 79000 5720.3 17:14:29.607 ERROR GencodeFuncotationFactory - Problem creating a GencodeFuncotation on transcript ENST00000361556.9 for variant: chr1:51729808-51729817(GGGGGGTGAA* -> G): Variant overlaps transcript but is not completely contained within it. Funcotator cannot currently handle this case. Transcript: ENST00000361556.9 Variant: [VC Unknown @ chr1:51729808-51729817 Q. of type=INDEL alleles=[GGGGGGTGAA*, G] attr={AS_FilterStatus=SITE, AS_SB_TABLE=[44, 1|46, 0], DP=110, ECNT=1, GERMQ=1, MBQ=[37, 37], MFRL=[163, 167], MMQ=[60, 60], MPOS=35, POPAF=1.89, ROQ=93, RPA=[2, 1], RU=GGGGGTGAA, STR=true, STRQ=93, TLOD=175.52} GT=GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:45,46:0.514:91:23,24:12,22:44,46:44,1,46,0 filters=germline 17:14:29.607 WARN GencodeFuncotationFactory - Creating default GencodeFuncotation on transcript ENST00000361556.9 for problem variant: chr1:51729808-51729817(GGGGGGTGAA* -> G) 17:14:29.715 INFO ProgressMeter - chr1:51744810 14.0 80000 5719.1 17:14:47.317 INFO ProgressMeter - chr1:53112621 14.3 82000 5741.6 17:15:03.760 INFO ProgressMeter - chr1:54313159 14.6 84000 5770.9 17:15:20.710 INFO ProgressMeter - chr1:55702719 14.8 86000 5795.9 17:15:38.363 INFO ProgressMeter - chr1:57618601 15.1 88000 5815.3 17:15:55.381 INFO ProgressMeter - chr1:59379903 15.4 90000 5838.1 17:16:13.770 INFO ProgressMeter - chr1:61650616 15.7 92000 5851.5 17:16:29.978 INFO ProgressMeter - chr1:63193764 16.0 94000 5877.7 17:17:46.249 INFO ProgressMeter - chr1:64973681 17.3 96000 5560.8 17:18:29.297 INFO ProgressMeter - chr1:65743799 18.0 97000 5394.5 17:18:44.743 INFO VcfFuncotationFactory - ClinVar_VCF 20180429_hg38 cache hits/total: 0/138 17:18:44.746 INFO VcfFuncotationFactory - dbSNP 9606_b151 cache hits/total: 0/63294 17:18:44.748 INFO Funcotator - Shutting down engine [November 24, 2023 5:18:44 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 18.43 minutes. Runtime.totalMemory()=2054684672 org.broadinstitute.hellbender.exceptions.GATKException: Unable to query the database for geneName: LINC01702 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:178) 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$0(VariantWalker.java:104) at java.util.stream.ForEachOps$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: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) 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:1030) at org.sqlite.core.DB.newSQLException(DB.java:1042) at org.sqlite.core.DB.execute(DB.java:884) at org.sqlite.core.CoreStatement.exec(CoreStatement.java:80) at org.sqlite.jdbc3.JDBC3Statement.executeQuery(JDBC3Statement.java:68) at org.broadinstitute.hellbender.tools.funcotator.dataSources.cosmic.CosmicFuncotationFactory.createFuncotationsOnVariant(CosmicFuncotationFactory.java:288) ... 26 more Using GATK jar /gatk/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 /gatk/gatk-package-4.3.0.0-local.jar Funcotator -R /mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/bwa_prefiles/GRCh38.primary_assembly.genome.fa -V /mnt/nfs/lobo/IMM-NFS/cfranco/MCPP-Lung/DNA/Variant_Calling/FilterMutectCalls/10LC_tumor_S2.filtered.vcf.gz -O /mnt/nfs/lobo/IMM-NFS/cfranco/MCPP-Lung/DNA/Variant_Calling/FUNCOTATOR/10LC_tumor_S2.FiltPASS.maf --output-file-format MAF --ref-version hg38 --data-sources-path /mnt/nfs/lobo/SALMEIDA-NFS/lcosta/MCPP-Lung/gatk_files/funcotator_dataSources.v1.7.20200521s --disable-sequence-dictionary-validation srun: error: compute-19: task 0: Exited with exit code 3 srun: launch/slurm: _step_signal: Terminating StepId=2949215.0