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Funcotator IllegalArgumentException
This request was created from a contribution made by Jay Singh on May 09, 2020 12:47 UTC.
Link: https://gatk.broadinstitute.org/hc/en-us/community/posts/360062649991-java-lang-IllegalArgumentException-Invalid-interval-Contig-chr1-start-9-end-10464
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Can you please provide
a) GATK version used - gatk-4.1.7.0
b) Exact GATK commands used
./gatk Funcotator --variant /home/deepak/software_library/gatk-4.1.7.0/SAMPLE3_Haplo.g.vcf.gz --reference /media/deepak/EXTRA/Genomedir/hg38/hg38.fasta --ref-version hg38 --data-sources-path /media/deepak/EXTRA/FUNCOTATOR_DATA/DATA_SOURCES --output SAMPLE_3_variants.funcotated.vcf --output-file-format VCF
Using GATK jar /home/deepak/software_library/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar
I am using Funcotator and have used the above commands but I am not getting the correct annotated output file. Also I am getting the following error " java.lang.IllegalArgumentException: Invalid interval. Contig:chr1 start:-9 end:10464 "
I have also attached the screenshot of the output result.
Thanks.
(created from Zendesk ticket #5579)
gz#5579
Here is the command line.
./gatk Funcotator --variant /home/deepak/software_library/gatk-4.1.7.0/SAMPL3_VARIANTFIL.vcf --reference /media/deepak/EXTRA/Genomedir/hg38/hg38.fasta --ref-version hg38 --data-sources-path /media/deepak/EXTRA/FUNCOTATOR_DATA/DATA_SOURCES --output variants.funcotated.vcf --output-file-format VCF
Using GATK jar /home/deepak/software_library/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar
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 /home/deepak/software_library/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar Funcotator --variant /home/deepak/software_library/gatk-4.1.7.0/SAMPL3_VARIANTFIL.vcf --reference /media/deepak/EXTRA/Genomedir/hg38/hg38.fasta --ref-version hg38 --data-sources-path /media/deepak/EXTRA/FUNCOTATOR_DATA/DATA_SOURCES --output variants.funcotated.vcf --output-file-format VCF
16:01:36.165 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/deepak/software_library/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
May 12, 2020 4:01:36 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
16:01:36.870 INFO Funcotator - ------------------------------------------------------------
16:01:36.871 INFO Funcotator - The Genome Analysis Toolkit (GATK) v4.1.7.0
16:01:36.871 INFO Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
16:01:36.871 INFO Funcotator - Executing as deepak@ngs on Linux v5.3.0-26-generic amd64
16:01:36.871 INFO Funcotator - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_241-b07
16:01:36.871 INFO Funcotator - Start Date/Time: 12 May, 2020 4:01:35 PM IST
16:01:36.871 INFO Funcotator - ------------------------------------------------------------
16:01:36.871 INFO Funcotator - ------------------------------------------------------------
16:01:36.872 INFO Funcotator - HTSJDK Version: 2.21.2
16:01:36.872 INFO Funcotator - Picard Version: 2.21.9
16:01:36.872 INFO Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:01:36.872 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:01:36.872 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:01:36.872 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:01:36.872 INFO Funcotator - Deflater: IntelDeflater
16:01:36.872 INFO Funcotator - Inflater: IntelInflater
16:01:36.872 INFO Funcotator - GCS max retries/reopens: 20
16:01:36.872 INFO Funcotator - Requester pays: disabled
16:01:36.872 INFO Funcotator - Initializing engine
16:01:37.316 INFO FeatureManager - Using codec VCFCodec to read file file:///home/deepak/software_library/gatk-4.1.7.0/SAMPL3_VARIANTFIL.vcf
16:01:37.360 INFO Funcotator - Done initializing engine
16:01:37.360 INFO Funcotator - Validating Sequence Dictionaries...
16:01:37.366 INFO Funcotator - Processing user transcripts/defaults/overrides...
16:01:37.366 INFO Funcotator - Initializing data sources...
16:01:37.368 INFO DataSourceUtils - Initializing data sources from directory: /media/deepak/EXTRA/FUNCOTATOR_DATA/DATA_SOURCES
16:01:37.369 WARN DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.
16:01:37.375 INFO DataSourceUtils - Resolved data source file path: file:///home/deepak/software_library/gatk-4.1.7.0/simple_uniprot_Dec012014.tsv -> file:///media/deepak/EXTRA/FUNCOTATOR_DATA/DATA_SOURCES/data_source_14/hg38/simple_uniprot_Dec012014.tsv
16:01:37.391 INFO DataSourceUtils - Resolved data source file path: file:///home/deepak/software_library/gatk-4.1.7.0/hgnc_download_Nov302017.tsv -> file:///media/deepak/EXTRA/FUNCOTATOR_DATA/DATA_SOURCES/data_source_13/hg38/hgnc_download_Nov302017.tsv
16:01:37.393 INFO DataSourceUtils - Resolved data source file path: file:///home/deepak/software_library/gatk-4.1.7.0/oreganno.tsv -> file:///media/deepak/EXTRA/FUNCOTATOR_DATA/DATA_SOURCES/data_source_12/hg38/oreganno.tsv
16:01:37.398 INFO DataSourceUtils - Resolved data source file path: file:///home/deepak/software_library/gatk-4.1.7.0/gencode.v28.annotation.REORDERED.gtf -> file:///media/deepak/EXTRA/FUNCOTATOR_DATA/DATA_SOURCES/data_source_11/hg38/gencode.v28.annotation.REORDERED.gtf
16:01:37.399 INFO DataSourceUtils - Resolved data source file path: file:///home/deepak/software_library/gatk-4.1.7.0/gencode.v28.pc_transcripts.fa -> file:///media/deepak/EXTRA/FUNCOTATOR_DATA/DATA_SOURCES/data_source_11/hg38/gencode.v28.pc_transcripts.fa
16:01:37.400 INFO DataSourceUtils - Resolved data source file path: file:///home/deepak/software_library/gatk-4.1.7.0/achilles_lineage_results.import.txt -> file:///media/deepak/EXTRA/FUNCOTATOR_DATA/DATA_SOURCES/data_source_1/hg38/achilles_lineage_results.import.txt
16:01:37.409 INFO DataSourceUtils - Resolved data source file path: file:///home/deepak/software_library/gatk-4.1.7.0/Cosmic.db -> file:///media/deepak/EXTRA/FUNCOTATOR_DATA/DATA_SOURCES/data_source_3/hg38/Cosmic.db
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16:01:43.969 INFO DataSourceUtils - Resolved data source file path: file:///home/deepak/software_library/gatk-4.1.7.0/dnaRepairGenes.20180524T145835.csv -> file:///media/deepak/EXTRA/FUNCOTATOR_DATA/DATA_SOURCES/data_source_8/hg38/dnaRepairGenes.20180524T145835.csv
16:01:43.979 INFO Funcotator - Initializing Funcotator Engine...
16:01:43.983 INFO Funcotator - Creating a VCF file for output: file:/home/deepak/software_library/gatk-4.1.7.0/variants.funcotated.vcf
16:01:44.020 INFO ProgressMeter - Starting traversal
16:01:44.020 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
16:01:44.068 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1-10454 due to alternate allele: <NON_REF>
16:01:44.116 INFO VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
16:01:44.121 INFO Funcotator - Shutting down engine
[12 May, 2020 4:01:44 PM IST] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.14 minutes.
Runtime.totalMemory()=2889875456
java.lang.IllegalArgumentException: Invalid interval. Contig:chr1 start:-9 end:10464
at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:733)
at org.broadinstitute.hellbender.utils.SimpleInterval.validatePositions(SimpleInterval.java:59)
at org.broadinstitute.hellbender.utils.SimpleInterval.<init>(SimpleInterval.java:35)
at org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils.createReferenceSnippet(FuncotatorUtils.java:1439)
at org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils.getBasesInWindowAroundReferenceAllele(FuncotatorUtils.java:1468)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createFuncotationForSymbolicAltAllele(GencodeFuncotationFactory.java:2560)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createFlankFuncotation(GencodeFuncotationFactory.java:2465)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createGencodeFuncotationOnSingleTranscript(GencodeFuncotationFactory.java:953)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createFuncotationsHelper(GencodeFuncotationFactory.java:812)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createFuncotationsHelper(GencodeFuncotationFactory.java:796)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.lambda$createGencodeFuncotationsByAllTranscripts$0(GencodeFuncotationFactory.java:473)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1382)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createGencodeFuncotationsByAllTranscripts(GencodeFuncotationFactory.java:474)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createFuncotationsOnVariant(GencodeFuncotationFactory.java:529)
at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.determineFuncotations(DataSourceFuncotationFactory.java:233)
at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.createFuncotations(DataSourceFuncotationFactory.java:201)
at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.createFuncotations(DataSourceFuncotationFactory.java:172)
at org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine.lambda$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:1382)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499)
at org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine.createFuncotationMapForVariant(FuncotatorEngine.java:157)
at org.broadinstitute.hellbender.tools.funcotator.Funcotator.enqueueAndHandleVariant(Funcotator.java:903)
at org.broadinstitute.hellbender.tools.funcotator.Funcotator.apply(Funcotator.java:857)
at org.broadinstitute.hellbender.engine.VariantWalker.lambda$traverse$0(VariantWalker.java:104)
at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
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$ForEachOp.evaluateSequential(ForEachOps.java:151)
at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
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:163)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:206)
at org.broadinstitute.hellbender.Main.main(Main.java:292)
I'm getting a similar error. any solutions?
17:14:13.170 INFO FuncotateSegments - The following datasources support funcotation on segments:
17:14:13.171 INFO FuncotateSegments - Gencode 34 CANONICAL
17:14:13.209 INFO FuncotatorEngine - VCF sequence dictionary detected as B37 in HG19 annotation mode. Performing conversion.
17:14:13.209 WARN FuncotatorEngine - WARNING: You are using B37 as a reference. Funcotator will convert your variants to GRCh37, and this will be fine in the vast majority of cases. There MAY be some errors (e.g. in the Y chromosome, but possibly in other places as well) due to changes between the two references.
17:14:13.411 INFO ProgressMeter - Starting traversal
17:14:13.412 INFO ProgressMeter - Current Locus Elapsed Minutes Features Processed Features/Minute
17:14:15.391 INFO FuncotateSegments - Shutting down engine
[September 11, 2022 5:14:15 PM GMT] org.broadinstitute.hellbender.tools.funcotator.FuncotateSegments done. Elapsed time: 0.30 minutes.
Runtime.totalMemory()=1752170496
java.lang.IllegalArgumentException: Invalid interval. Contig:chr1 start:917445 end:911649
at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:804)
at org.broadinstitute.hellbender.utils.SimpleInterval.validatePositions(SimpleInterval.java:59)
at org.broadinstitute.hellbender.utils.SimpleInterval.<init>(SimpleInterval.java:35)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.segment.SegmentExonUtils.findInclusiveExonIndex(SegmentExonUtils.java:95)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.segment.SegmentExonUtils.determineSegmentExonPosition(SegmentExonUtils.java:63)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createSegmentFuncotations(GencodeFuncotationFactory.java:2939)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createSegmentFuncotations(GencodeFuncotationFactory.java:2914)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createFuncotationsOnSegment(GencodeFuncotationFactory.java:2866)
at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.determineFuncotations(DataSourceFuncotationFactory.java:239)
at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.createFuncotations(DataSourceFuncotationFactory.java:211)
at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.createFuncotations(DataSourceFuncotationFactory.java:182)
at org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine.lambda$createFuncotationMapForSegment$2(FuncotatorEngine.java:223)
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:1382)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:566)
at org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine.createFuncotationMapForSegment(FuncotatorEngine.java:226)
at org.broadinstitute.hellbender.tools.funcotator.FuncotateSegments.apply(FuncotateSegments.java:191)
at org.broadinstitute.hellbender.tools.funcotator.FuncotateSegments.apply(FuncotateSegments.java:59)
at org.broadinstitute.hellbender.engine.FeatureWalker.lambda$traverse$0(FeatureWalker.java:99)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.ReferencePipeline$Head.forEach(ReferencePipeline.java:647)
at org.broadinstitute.hellbender.engine.FeatureWalker.traverse(FeatureWalker.java:97)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1085)
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)
Using GATK jar /gatk/gatk-package-4.2.6.1-local.jar
@asalimih it looks like you're using a different tool than the original post in this thread. Could you post on the GATK forum to get help from the GATK support team? https://gatk.broadinstitute.org/hc/en-us/community/topics
