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What does the error message ##### ERROR MESSAGE: For input string: "DP" mean?

This is the command

java -jar ~/app/GATK/GenomeAnalysisTK.jar \
-T VariantAnnotator \
-R ~/repository/annotation/GATK/b37/human_g1k_v37.fasta \
-A SnpEff \
--variant ~/temp/130212_allelestrip_snpeff.vcf \
--snpEffFile ~/temp/130212_allelestrip_snpeff.vcf \
-o ~/temp/130212_allelestrip_snpeff_GATK.vcf

and this is a sample line of the vcf file

1 874816 . C CT 68.5 PASS AC=28;AF=0.737;AN=38;set=Intersection;EFF=DOWNSTREAM(MODIFIER||||NOC2L|processed_transcript|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER||||NOC2L|processed_transcript|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER||||NOC2L|processed_transcript|CODING|ENST00000483767|),DOWNSTREAM(MODIFIER||||SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||SAMD11|protein_coding|CODING|ENST00000437963|),FRAME_SHIFT(HIGH||||SAMD11|protein_coding|CODING|ENST00000342066|exon_1_874655_874840),UPSTREAM(MODIFIER||||SAMD11|protein_coding|CODING|ENST00000464948|),UPSTREAM(MODIFIER||||SAMD11|protein_coding|CODING|ENST00000466827|),UPSTREAM(MODIFIER||||SAMD11|protein_coding|CODING|ENST00000474461|),UPSTREAM(MODIFIER||||SAMD11|protein_coding|CODING|ENST00000478729|) GT:DP:GQ:PL:SP 0/0 0/0 0/0 0/0 0/0 0/0

Thanks! Alexander

Best Answer

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Can you please tell me what version you're using and post the full error/ stack trace?

  • navarininavarini Member

    @node026:~/temp > java -jar ~/app/GATK/GenomeAnalysisTK.jar \ -T VariantAnnotator \ -R ~/repository/annotation/GATK/b37/human_g1k_v37.fasta \ -A SnpEff \ --variant ~/temp/130212_allelestrip_snpeff_allGT_singletabs.vcf \ --snpEffFile ~/temp/130212_allelestrip_snpeff_allGT_singletabs.vcf \ -o ~/temp/130212_allelestrip_snpeff_GATK.vcf
    INFO 08:09:32,603 HelpFormatter - --------------------------------------------------------------------------------
    INFO 08:09:32,605 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-9-ge5ebf34, Compiled 2013/01/11 22:43:14
    INFO 08:09:32,605 HelpFormatter - Copyright (c) 2010 The Broad Institute
    INFO 08:09:32,605 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
    INFO 08:09:32,609 HelpFormatter - Program Args: -T VariantAnnotator -R /home/navarinia/repository/annotation/GATK/b37/human_g1k_v37.fasta -A SnpEff --variant /home/navarinia/temp/130212_allelestrip_snpeff_allGT_singletabs.vcf --snpEffFile /home/navarinia/temp/130212_allelestrip_snpeff_allGT_singletabs.vcf -o /home/navarinia/temp/130212_allelestrip_snpeff_GATK.vcf
    INFO 08:09:32,610 HelpFormatter - Date/Time: 2013/02/13 08:09:32
    INFO 08:09:32,610 HelpFormatter - --------------------------------------------------------------------------------
    INFO 08:09:32,610 HelpFormatter - --------------------------------------------------------------------------------
    INFO 08:09:32,618 ArgumentTypeDescriptor - Dynamically determined type of /home/navarinia/temp/130212_allelestrip_snpeff_allGT_singletabs.vcf to be VCF
    INFO 08:09:32,623 ArgumentTypeDescriptor - Dynamically determined type of /home/navarinia/temp/130212_allelestrip_snpeff_allGT_singletabs.vcf to be VCF
    INFO 08:09:32,634 GenomeAnalysisEngine - Strictness is SILENT
    INFO 08:09:32,776 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000, Using the new downsampling implementation
    INFO 08:09:32,793 RMDTrackBuilder - Loading Tribble index from disk for file /home/navarinia/temp/130212_allelestrip_snpeff_allGT_singletabs.vcf
    INFO 08:09:42,124 RMDTrackBuilder - Loading Tribble index from disk for file /home/navarinia/temp/130212_allelestrip_snpeff_allGT_singletabs.vcf
    INFO 08:09:57,333 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
    INFO 08:09:57,333 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining
    INFO 08:09:59,990 GATKRunReport - Uploaded run statistics report to AWS S3

    ERROR ------------------------------------------------------------------------------------------
    ERROR stack trace

    java.lang.NumberFormatException: For input string: "DP"
    at java.lang.NumberFormatException.forInputString(NumberFormatException.java:48)
    at java.lang.Integer.parseInt(Integer.java:449)
    at java.lang.Integer.valueOf(Integer.java:554)
    at org.broadinstitute.sting.utils.codecs.vcf.AbstractVCFCodec.createGenotypeMap(AbstractVCFCodec.java:645)
    at org.broadinstitute.sting.utils.codecs.vcf.AbstractVCFCodec$LazyVCFGenotypesParser.parse(AbstractVCFCodec.java:92)
    at org.broadinstitute.sting.utils.variantcontext.LazyGenotypesContext.decode(LazyGenotypesContext.java:130)
    at org.broadinstitute.sting.utils.variantcontext.LazyGenotypesContext.getGenotypes(LazyGenotypesContext.java:120)
    at org.broadinstitute.sting.utils.variantcontext.GenotypesContext.iterator(GenotypesContext.java:461)
    at org.broadinstitute.sting.utils.variantcontext.VariantContext.validateGenotypes(VariantContext.java:1193)
    at org.broadinstitute.sting.utils.variantcontext.VariantContext.validate(VariantContext.java:1137)
    at org.broadinstitute.sting.utils.variantcontext.VariantContext.(VariantContext.java:311)
    at org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder.make(VariantContextBuilder.java:495)
    at org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine.annotateContext(VariantAnnotatorEngine.java:212)
    at org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine.annotateContext(VariantAnnotatorEngine.java:185)
    at org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotator.map(VariantAnnotator.java:309)
    at org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotator.map(VariantAnnotator.java:80)
    at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:243)
    at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:231)
    at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:248)
    at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:219)
    at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:120)
    at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:67)
    at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:23)
    at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:74)
    at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:281)
    at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
    at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:237)
    at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:147)
    at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 2.3-9-ge5ebf34):
    ERROR
    ERROR Please visit the wiki to see if this is a known problem
    ERROR If not, please post the error, with stack trace, to the GATK forum
    ERROR Visit our website and forum for extensive documentation and answers to
    ERROR commonly asked questions http://www.broadinstitute.org/gatk
    ERROR
    ERROR MESSAGE: For input string: "DP"
    ERROR ------------------------------------------------------------------------------------------

    Thanks! Alexander

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