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Error with HaplotypeCaller
yasin
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
-
d0ct0r
Aarhus ✭
Please check if you have any empty spaces after backslash '\' in your commands. If you have copied the commands straight from GATK page and replaced just the values with your own, it is very likely that you have empty spaces after the backslash "\", which might have caused this error.
Answers
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)
Please check if you have any empty spaces after backslash '\' in your commands. If you have copied the commands straight from GATK page and replaced just the values with your own, it is very likely that you have empty spaces after the backslash "\", which might have caused this error.