Body: <p>I ran the &quot;funcotator&quot; step from the GATK somatic short variant discovery (snvs + indels) pipeline and used the output of <code>filtermutectcalls</code> as input, but I obtain this error:</p>
  <pre><code>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://gsapubftp-anonymous@ftp.broadinstitute.org/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 -&gt; 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 -&gt; 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 -&gt; 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 -&gt; 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 -&gt; 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 -&gt; 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 -&gt; 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 -&gt; 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 -&gt; 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 -&gt; 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 -&gt; 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 -&gt; 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 -&gt; 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 -&gt; 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 -&gt; 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 -&gt; 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 -&gt; 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 -&gt; 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 -&gt; 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 -&gt; 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 -&gt; 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 -&gt; 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 -&gt; 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 -&gt; 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 -&gt; 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 -&gt; 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 -&gt; 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 -&gt; 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 -&gt; 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 -&gt; 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 -&gt; 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 -&gt; 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 -&gt; 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 -&gt; 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 -&gt; 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 -&gt; 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* -&gt; 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* -&gt; 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* -&gt; 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* -&gt; 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* -&gt; 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* -&gt; 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* -&gt; 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<span class="math-container">$traverse$</span>0(VariantWalker.java:104)
          at java.util.stream.ForEachOps<span class="math-container">$ForEachOp$</span>OfRef.accept(ForEachOps.java:183)
          at java.util.stream.ReferencePipeline<span class="math-container">$3$</span>1.accept(ReferencePipeline.java:193)
          at java.util.stream.ReferencePipeline<span class="math-container">$2$</span>1.accept(ReferencePipeline.java:175)
          at java.util.stream.ReferencePipeline<span class="math-container">$3$</span>1.accept(ReferencePipeline.java:193)
          at java.util.Iterator.forEachRemaining(Iterator.java:116)
          at java.util.Spliterators<span class="math-container">$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
          at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
          at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
          at java.util.stream.ForEachOps$</span>ForEachOp.evaluateSequential(ForEachOps.java:150)
          at java.util.stream.ForEachOps<span class="math-container">$ForEachOp$</span>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
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-11-24T18:18:56.413Z
Comments.Text: Are you sure there's a problem? The error appears after the `Funcotator done. Elapsed time: 18.43 minutes.` message, which suggests it had actually finished. Then, the error itself (`Unable to query the database for gene...` and `Caused by: [...]  I/O error in the advisory file locking logic (disk I/O error)`) suggests a problem with reading some DB that may well be transient. Did you try running it again?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-11-24T19:20:46.673Z
Comments.Text: Yes i did runned again but i got the same error and i only obtain a vcf file and not a maf file as output of Funcotator
Comments.UserDisplayName: Rita Soares
Tags: <variant-calling><gatk><somatic>
Title: ERROR IN FUNCOTATOR: [SQLITE_IOERR_LOCK] I/O error in the advisory file locking logic (disk I/O error)
ThreadText: # ERROR IN FUNCOTATOR: [SQLITE_IOERR_LOCK] I/O error in the advisory file locking logic (disk I/O error)
  
  (Asked by: username_0 on 2023-11-24)
  
  I ran the "funcotator" step from the GATK somatic short variant discovery (snvs + indels) pipeline and used the output of `filtermutectcalls` as input, 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 username_0.username_0@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://gsapubftp-anonymous@ftp.broadinstitute.org/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/username_0.username_0/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/username_0.username_0/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/username_0.username_0/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/username_0.username_0/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/username_0.username_0/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/username_0.username_0/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/username_0.username_0/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/username_0.username_0/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/username_0.username_0/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/username_0.username_0/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/username_0.username_0/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/username_0.username_0/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/username_0.username_0/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/username_0.username_0/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/username_0.username_0/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/username_0.username_0/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/username_0.username_0/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/username_0.username_0/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/username_0.username_0/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/username_0.username_0/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/username_0.username_0/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/username_0.username_0/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/username_0.username_0/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/username_0.username_0/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/username_0.username_0/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/username_0.username_0/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/username_0.username_0/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/username_0.username_0/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/username_0.username_0/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/username_0.username_0/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/username_0.username_0/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/username_0.username_0/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/username_0.username_0/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/username_0.username_0/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/username_0.username_0/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/username_0.username_0/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
  
  ```
  
  **Tags:** variant-calling, gatk, somatic
  
  > **Comments:**
  > **username_1**: Are you sure there's a problem? The error appears after the `Funcotator done. Elapsed time: 18.43 minutes.` message, which suggests it had actually finished. Then, the error itself (`Unable to query the database for gene...` and `Caused by: [...]  I/O error in the advisory file locking logic (disk I/O error)`) suggests a problem with reading some DB that may well be transient. Did you try running it again?  
  > **username_0**: Yes i did runned again but i got the same error and i only obtain a vcf file and not a maf file as output of Funcotator  
  
  ---
  
  ## 0 answers
  
  