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Official code repository for GATK versions 4 and up
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Funcotator "Unexpected value: lncRNA" #7090

Open Ning-310 opened 3 years ago

Ning-310 commented 3 years ago

Using GATK jar /usr/local/gatk-4.1.3.0/gatk-package-4.1.3.0-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 /usr/local/gatk-4.1.3.0/gatk-package-4.1.3.0-local.jar Funcotator -R /data/nws/WES/reference/Homo_sapiens_assembly38.fasta -V /data/nws/WES/GenomicsDBImport/200923_A00268_0517_AHKL37DSXY/Set20-5_L2_159A59.somatic.filterMutectCalls.vcf.gz -O /data/nws/WES/GenomicsDBImport/200923_A00268_0517_AHKL37DSXY/Set20-5_L2_159A59.somatic.filterMutectCalls.funcotator.maf --data-sources-path /data/nws/WES/reference/funcotator_dataSources.v1.7.20200521g --output-file-format MAF --ref-version hg38 06:42:10.395 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/gatk-4.1.3.0/gatk-package-4.1.3.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 06:42:25.662 INFO Funcotator - ------------------------------------------------------------ 06:42:25.662 INFO Funcotator - The Genome Analysis Toolkit (GATK) v4.1.3.0 06:42:25.663 INFO Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/ 06:42:40.672 INFO Funcotator - Executing as nws@cuckoolab on Linux v3.10.0-1127.19.1.el7.x86_64 amd64 06:42:40.672 INFO Funcotator - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_262-b10 06:42:40.672 INFO Funcotator - Start Date/Time: 2021年2月21日 上午06时42分10秒 06:42:40.672 INFO Funcotator - ------------------------------------------------------------ 06:42:40.672 INFO Funcotator - ------------------------------------------------------------ 06:42:40.673 INFO Funcotator - HTSJDK Version: 2.20.1 06:42:40.673 INFO Funcotator - Picard Version: 2.20.5 06:42:40.673 INFO Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2 06:42:40.673 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 06:42:40.673 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 06:42:40.673 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 06:42:40.673 INFO Funcotator - Deflater: IntelDeflater 06:42:40.674 INFO Funcotator - Inflater: IntelInflater 06:42:40.674 INFO Funcotator - GCS max retries/reopens: 20 06:42:40.674 INFO Funcotator - Requester pays: disabled 06:42:40.674 INFO Funcotator - Initializing engine 06:42:41.406 INFO FeatureManager - Using codec VCFCodec to read file file:///data/nws/WES/GenomicsDBImport/200923_A00268_0517_AHKL37DSXY/Set20-5_L2_159A59.somatic.filterMutectCalls.vcf.gz 06:42:41.561 INFO Funcotator - Done initializing engine 06:42:41.561 INFO Funcotator - Validating Sequence Dictionaries... 06:42:41.589 INFO Funcotator - Processing user transcripts/defaults/overrides... 06:42:41.590 INFO Funcotator - Initializing data sources... 06:42:41.594 INFO DataSourceUtils - Initializing data sources from directory: /data/nws/WES/reference/funcotator_dataSources.v1.7.20200521g 06:42:41.596 INFO DataSourceUtils - Data sources version: 1.7.2020521g 06:42:41.597 INFO DataSourceUtils - Data sources source: ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/funcotator/funcotator_dataSources.v1.7.20200521g.tar.gz 06:42:41.597 INFO DataSourceUtils - Data sources alternate source: gs://broad-public-datasets/funcotator/funcotator_dataSources.v1.7.20200521.tar.gz 06:42:41.609 INFO DataSourceUtils - Resolved data source file path: file:///data/nws/WES/LMM_Path_LP_VUS5-variants-6-12-18.sorted_liftover_b38.corrected.vcf -> file:///data/nws/WES/reference/funcotator_dataSources.v1.7.20200521g/lmm_known/hg38/LMM_Path_LP_VUS5-variants-6-12-18.sorted_liftover_b38.corrected.vcf 06:42:41.612 INFO DataSourceUtils - Resolved data source file path: file:///data/nws/WES/gencode.v34.annotation.REORDERED.gtf -> file:///data/nws/WES/reference/funcotator_dataSources.v1.7.20200521g/gencode/hg38/gencode.v34.annotation.REORDERED.gtf 06:42:41.612 INFO DataSourceUtils - Resolved data source file path: file:///data/nws/WES/gencode.v34.pc_transcripts.fa -> file:///data/nws/WES/reference/funcotator_dataSources.v1.7.20200521g/gencode/hg38/gencode.v34.pc_transcripts.fa 06:42:41.614 INFO DataSourceUtils - Resolved data source file path: file:///data/nws/WES/clinvar_20180429_hg38.vcf -> file:///data/nws/WES/reference/funcotator_dataSources.v1.7.20200521g/clinvar/hg38/clinvar_20180429_hg38.vcf 06:42:41.615 INFO DataSourceUtils - Resolved data source file path: file:///data/nws/WES/acmg_lof.tsv -> file:///data/nws/WES/reference/funcotator_dataSources.v1.7.20200521g/acmg_lof/hg38/acmg_lof.tsv 06:42:41.617 INFO DataSourceUtils - Resolved data source file path: file:///data/nws/WES/acmg59_test_cleaned.txt -> file:///data/nws/WES/reference/funcotator_dataSources.v1.7.20200521g/acmg_rec/hg38/acmg59_test_cleaned.txt 06:42:41.617 INFO Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)... 06:42:41.618 INFO DataSourceUtils - Resolved data source file path: file:///data/nws/WES/LMM_Path_LP_VUS5-variants-6-12-18.sorted_liftover_b38.corrected.vcf -> file:///data/nws/WES/reference/funcotator_dataSources.v1.7.20200521g/lmm_known/hg38/LMM_Path_LP_VUS5-variants-6-12-18.sorted_liftover_b38.corrected.vcf 06:42:41.618 INFO DataSourceUtils - Setting lookahead cache for data source: LMMKnown : 100000 06:42:41.622 INFO FeatureManager - Using codec VCFCodec to read file file:///data/nws/WES/reference/funcotator_dataSources.v1.7.20200521g/lmm_known/hg38/LMM_Path_LP_VUS5-variants-6-12-18.sorted_liftover_b38.corrected.vcf 06:42:41.641 INFO DataSourceUtils - Resolved data source file path: file:///data/nws/WES/LMM_Path_LP_VUS5-variants-6-12-18.sorted_liftover_b38.corrected.vcf -> file:///data/nws/WES/reference/funcotator_dataSources.v1.7.20200521g/lmm_known/hg38/LMM_Path_LP_VUS5-variants-6-12-18.sorted_liftover_b38.corrected.vcf 06:42:41.652 INFO FeatureManager - Using codec VCFCodec to read file file:///data/nws/WES/reference/funcotator_dataSources.v1.7.20200521g/lmm_known/hg38/LMM_Path_LP_VUS5-variants-6-12-18.sorted_liftover_b38.corrected.vcf 06:42:41.663 INFO DataSourceUtils - Resolved data source file path: file:///data/nws/WES/gencode.v34.annotation.REORDERED.gtf -> file:///data/nws/WES/reference/funcotator_dataSources.v1.7.20200521g/gencode/hg38/gencode.v34.annotation.REORDERED.gtf 06:42:41.663 INFO DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000 06:42:41.665 WARN GencodeGtfCodec - GENCODE GTF Header line 1 has a version number that is above maximum tested version (v 28) (given: 34): ##description: evidence-based annotation of the human genome (GRCh38), version 34 (Ensembl 100) Continuing, but errors may occur. 06:42:41.665 INFO FeatureManager - Using codec GencodeGtfCodec to read file file:///data/nws/WES/reference/funcotator_dataSources.v1.7.20200521g/gencode/hg38/gencode.v34.annotation.REORDERED.gtf 06:42:41.666 WARN GencodeGtfCodec - GENCODE GTF Header line 1 has a version number that is above maximum tested version (v 28) (given: 34): ##description: evidence-based annotation of the human genome (GRCh38), version 34 (Ensembl 100) Continuing, but errors may occur. 06:42:41.691 INFO DataSourceUtils - Resolved data source file path: file:///data/nws/WES/gencode.v34.pc_transcripts.fa -> file:///data/nws/WES/reference/funcotator_dataSources.v1.7.20200521g/gencode/hg38/gencode.v34.pc_transcripts.fa 06:42:46.805 INFO DataSourceUtils - Resolved data source file path: file:///data/nws/WES/clinvar_20180429_hg38.vcf -> file:///data/nws/WES/reference/funcotator_dataSources.v1.7.20200521g/clinvar/hg38/clinvar_20180429_hg38.vcf 06:42:46.805 INFO DataSourceUtils - Setting lookahead cache for data source: ClinVar_VCF : 100000 06:42:46.807 INFO FeatureManager - Using codec VCFCodec to read file file:///data/nws/WES/reference/funcotator_dataSources.v1.7.20200521g/clinvar/hg38/clinvar_20180429_hg38.vcf 06:42:46.951 INFO DataSourceUtils - Resolved data source file path: file:///data/nws/WES/clinvar_20180429_hg38.vcf -> file:///data/nws/WES/reference/funcotator_dataSources.v1.7.20200521g/clinvar/hg38/clinvar_20180429_hg38.vcf 06:42:47.023 INFO FeatureManager - Using codec VCFCodec to read file file:///data/nws/WES/reference/funcotator_dataSources.v1.7.20200521g/clinvar/hg38/clinvar_20180429_hg38.vcf 06:42:47.098 INFO DataSourceUtils - Resolved data source file path: file:///data/nws/WES/acmg_lof.tsv -> file:///data/nws/WES/reference/funcotator_dataSources.v1.7.20200521g/acmg_lof/hg38/acmg_lof.tsv 06:42:47.107 INFO DataSourceUtils - Resolved data source file path: file:///data/nws/WES/acmg59_test_cleaned.txt -> file:///data/nws/WES/reference/funcotator_dataSources.v1.7.20200521g/acmg_rec/hg38/acmg59_test_cleaned.txt 06:42:47.109 INFO Funcotator - Initializing Funcotator Engine... 06:42:47.139 INFO Funcotator - Creating a MAF file for output: file:/data/nws/WES/GenomicsDBImport/200923_A00268_0517_AHKL37DSXY/Set20-5_L2_159A59.somatic.filterMutectCalls.funcotator.maf 06:42:47.186 INFO ProgressMeter - Starting traversal 06:42:47.187 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 06:42:47.233 INFO VcfFuncotationFactory - ClinVar_VCF 20180429_hg38 cache hits/total: 0/0 06:42:47.233 INFO VcfFuncotationFactory - LMMKnown 20180618 cache hits/total: 0/0 06:42:47.287 INFO Funcotator - Shutting down engine [2021年2月21日 上午06时42分47秒] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.62 minutes. Runtime.totalMemory()=1988100096 java.lang.IllegalArgumentException: Unexpected value: lncRNA at org.broadinstitute.hellbender.utils.codecs.gencode.GencodeGtfFeature$GeneTranscriptType.getEnum(GencodeGtfFeature.java:1016) at org.broadinstitute.hellbender.utils.codecs.gencode.GencodeGtfFeature.(GencodeGtfFeature.java:144) at org.broadinstitute.hellbender.utils.codecs.gencode.GencodeGtfGeneFeature.(GencodeGtfGeneFeature.java:19) at org.broadinstitute.hellbender.utils.codecs.gencode.GencodeGtfGeneFeature.create(GencodeGtfGeneFeature.java:23) at org.broadinstitute.hellbender.utils.codecs.gencode.GencodeGtfFeature$FeatureType$1.create(GencodeGtfFeature.java:729) at org.broadinstitute.hellbender.utils.codecs.gencode.GencodeGtfFeature.create(GencodeGtfFeature.java:299) at org.broadinstitute.hellbender.utils.codecs.gencode.GencodeGtfCodec.decode(GencodeGtfCodec.java:193) at org.broadinstitute.hellbender.utils.codecs.gencode.GencodeGtfCodec.decode(GencodeGtfCodec.java:61) at htsjdk.tribble.TribbleIndexedFeatureReader$QueryIterator.readNextRecord(TribbleIndexedFeatureReader.java:486) at htsjdk.tribble.TribbleIndexedFeatureReader$QueryIterator.(TribbleIndexedFeatureReader.java:426) at htsjdk.tribble.TribbleIndexedFeatureReader.query(TribbleIndexedFeatureReader.java:297) at org.broadinstitute.hellbender.engine.FeatureDataSource.refillQueryCache(FeatureDataSource.java:557) at org.broadinstitute.hellbender.engine.FeatureDataSource.queryAndPrefetch(FeatureDataSource.java:526) at org.broadinstitute.hellbender.engine.FeatureManager.getFeatures(FeatureManager.java:351) at org.broadinstitute.hellbender.engine.FeatureContext.getValues(FeatureContext.java:172) at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.queryFeaturesFromFeatureContext(DataSourceFuncotationFactory.java:304) at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.getFeaturesFromFeatureContext(DataSourceFuncotationFactory.java:219) at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.createFuncotations(DataSourceFuncotationFactory.java:197) at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.createFuncotations(DataSourceFuncotationFactory.java:172) at org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine.lambda$createFuncotationMapForVariant$0(FuncotatorEngine.java:147) at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193) at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175) at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1384) at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482) at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472) at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708) at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:566) at org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine.createFuncotationMapForVariant(FuncotatorEngine.java:157) at org.broadinstitute.hellbender.tools.funcotator.Funcotator.enqueueAndHandleVariant(Funcotator.java:903) at org.broadinstitute.hellbender.tools.funcotator.Funcotator.apply(Funcotator.java:857) at org.broadinstitute.hellbender.engine.VariantWalker.lambda$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:1048) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205) at org.broadinstitute.hellbender.Main.main(Main.java:291)

droazen commented 3 years ago

@Ning-310 I believe this was fixed in a later release. Can you please try running Funcotator with the latest GATK release (4.2.0.0), and see if the problem persists?