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java.lang.IllegalArgumentException: Invalid interval. Contig:chr1 start:-9 end:10464

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Jay Singh

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.

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  • Avatar
    Bhanu Gandham
    • Edited

    Hi,

     

    Couple of things:

    1. We don't recommend running funcotator on gvcf. Looks like you are running it on a gvcf file. Funcotator is run after genotypeGVCF step on a vcf file.
    2. Can you please post the entire stack trace to help us troubleshoot.
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    Jay Singh

    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)

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    Bhanu Gandham

    Hi,

     

    We are looking into this. We have created a github issue ticket for this and you can follow its progress here: https://github.com/broadinstitute/gatk/issues/6598

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    Bhanu Gandham

    Jay Singh

     

    If you could also please share your dataset so we can reproduce the error on our end. that woudl be very helpful. Please use these instructions to share your data: https://gatk.zendesk.com/hc/en-us/articles/360035889671
    Once you have uploaded the data can you please update the github ticket with that info.

    Thank you!

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    Jay Singh

    Thanks for the reply.

    I have already prepared the file to share with You. But I couldn't able to open the FTP server to upload the file.

    Can you please check " ftp.broadinstitute.org " working or not.

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    Bhanu Gandham

    That is know to happen sometimes. It is a transient error. Can you please try again.

    Also one you have uploaded the data can you please update the github ticket with that info.

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    Jay Singh

    The link is still not accessible. It is not at all opening.

    Is there any other way to share the files?

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    Bhanu Gandham

    Another option is to put it in a google bucket and share that with us.

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