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Error with HaplotypeCaller

yasinyasin PhiladelphiaMember

I have a bam file with duplicates removed. And I added the read groups using picard as:
java -jar gatk/picard-tools-2.5.0/picard.jar AddOrReplaceReadGroups \
I=input.bam \
O=input.group.bam \
RGID=4 \
RGLB=lib1 \
RGPL=illumina \
RGPU=unit1 \
RGSM=20

Then I run the HaplotypeCaller
java -jar gatk/GenomeAnalysisTK.jar -T HaplotypeCaller \
-R /hg19/ucsc.hg19.fasta \
-I input.group.bam \
--dbsnp snps.vcf \
-o input.raw.vcf

But I get the following error:
java.lang.NumberFormatException: empty String
at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:1842)
at sun.misc.FloatingDecimal.parseDouble(FloatingDecimal.java:110)
at java.lang.Double.parseDouble(Double.java:538)
at java.lang.Double.valueOf(Double.java:502)
at htsjdk.variant.vcf.AbstractVCFCodec.parseQual(AbstractVCFCodec.java:511)
at htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:317)
at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:279)
at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:257)
at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:60)
at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:74)
at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:36)
at htsjdk.tribble.AbstractFeatureCodec.decodeLoc(AbstractFeatureCodec.java:43)
at htsjdk.tribble.index.IndexFactory$FeatureIterator.readNextFeature(IndexFactory.java:493)
at htsjdk.tribble.index.IndexFactory$FeatureIterator.(IndexFactory.java:394)
at htsjdk.tribble.index.IndexFactory.createDynamicIndex(IndexFactory.java:303)
at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.createIndexInMemory(RMDTrackBuilder.java:441)
at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.loadIndex(RMDTrackBuilder.java:327)
at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.getFeatureSource(RMDTrackBuilder.java:264)
at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.createInstanceOfTrack(RMDTrackBuilder.java:153)
at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.(ReferenceOrderedDataSource.java:208)
at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource.(ReferenceOrderedDataSource.java:88)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.getReferenceOrderedDataSources(GenomeAnalysisEngine.java:1047)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.initializeDataSources(GenomeAnalysisEngine.java:824)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:282)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:255)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:157)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.6-0-g89b7209):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.

Can you help about this problem? Thanks.

Best Answer

Answers

  • yasinyasin PhiladelphiaMember

    Let me give the other details:

    INFO 11:47:28,551 HelpFormatter - Executing as...
    INFO 11:47:28,552 HelpFormatter - Date/Time: 2016/07/28
    INFO 11:47:28,552 HelpFormatter - --------------------------------------------------------------------------------
    INFO 11:47:28,553 HelpFormatter - --------------------------------------------------------------------------------
    INFO 11:47:28,580 GenomeAnalysisEngine - Strictness is SILENT
    INFO 11:47:28,673 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
    INFO 11:47:28,679 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
    INFO 11:47:28,706 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
    INFO 11:47:28,716 HCMappingQualityFilter - Filtering out reads with MAPQ < 20

    ERROR --
    ERROR stack trace

    java.lang.NumberFormatException: empty String
    at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:1842)
    at sun.misc.FloatingDecimal.parseDouble(FloatingDecimal.java:110)
    at java.lang.Double.parseDouble(Double.java:538)
    at java.lang.Double.valueOf(Double.java:502)
    at htsjdk.variant.vcf.AbstractVCFCodec.parseQual(AbstractVCFCodec.java:511)
    at htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:317)
    at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:279)
    at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:257)
    at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:60)
    at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:74)
    at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:36)
    at htsjdk.tribble.AbstractFeatureCodec.decodeLoc(AbstractFeatureCodec.java:43)
    at htsjdk.tribble.index.IndexFactory$FeatureIterator.readNextFeature(IndexFactory.java:493)
    at htsjdk.tribble.index.IndexFactory$FeatureIterator.(IndexFactory.java:394)
    at htsjdk.tribble.index.IndexFactory.createDynamicIndex(IndexFactory.java:303)
    at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.createIndexInMemory(RMDTrackBuilder.java:441)
    at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.loadIndex(RMDTrackBuilder.java:327)
    at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.getFeatureSource(RMDTrackBuilder.java:264)
    at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.createInstanceOfTrack(RMDTrackBuilder.java:153)
    at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.(ReferenceOrderedDataSource.java:208)
    at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource.(ReferenceOrderedDataSource.java:88)
    at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.getReferenceOrderedDataSources(GenomeAnalysisEngine.java:1047)
    at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.initializeDataSources(GenomeAnalysisEngine.java:824)
    at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:282)
    at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:113)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:255)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:157)
    at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)

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