genotypeGVCFs InvocationTargetException

bruce01bruce01 Member
edited June 2014 in Ask the GATK team

Hi, first off I like the idea of the new Joint Genotyping method of 3.1, thanks for the hard work!

My issue: I have been running HaplotypeCaller in -ERC GVCF mode as is best practice. From the output GVCFs I have tried a few things but am now Joint Genotyping them. I did this for 16 exomes I have to test. There are 2 treatments, so 8 and 8 per treatment. On the final header line (#CHROM POS etc...) the sampleID only had 'treat1' or 'treat2', and so the resultant joint GVCF has two cols, instead of 16 which I want (and I presume I should expect?).

I am running:

java -Xmx4g -jarGenomeAnalysisTK.jar -R my.ref.fa -T GenotypeGVCFs -V gvcf.all.list -o genotyped.all.gvcf

which had worked for the list I gave it but only gave two treatment cols. I then sed'd out the 'treat1', or 'treat2' and put in sample IDs. This gives the error:

##### ERROR stack trace
java.lang.RuntimeException: java.lang.reflect.InvocationTargetException
        at org.broad.tribble.index.IndexFactory.loadIndex(IndexFactory.java:171)
        at org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.loadFromDisk(RMDTrackBuilder.java:324)
        at org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.attemptToLockAndLoadIndexFromDisk(RMDTrackBuilder.java:308)
        at org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.loadIndex(RMDTrackBuilder.java:267)
        at org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.getFeatureSource(RMDTrackBuilder.java:213)
        at org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.createInstanceOfTrack(RMDTrackBuilder.java:140)
        at org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedQueryDataPool.<init>(ReferenceOrderedDataSource.java:208)
        at org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource.<init>(ReferenceOrderedDataSource.java:88)
        at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.getReferenceOrderedDataSources(GenomeAnalysisEngine.java:973)
        at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.initializeDataSources(GenomeAnalysisEngine.java:767)
        at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:284)
        at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:121)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
        at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:107)
Caused by: java.lang.reflect.InvocationTargetException
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
        at org.broad.tribble.index.IndexFactory.loadIndex(IndexFactory.java:167)
        ... 14 more
Caused by: java.io.EOFException
        at org.broad.tribble.util.LittleEndianInputStream.readInt(LittleEndianInputStream.java:62)
        at org.broad.tribble.index.interval.IntervalTreeIndex$ChrIndex.read(IntervalTreeIndex.java:201)
        at org.broad.tribble.index.AbstractIndex.read(AbstractIndex.java:359)
        at org.broad.tribble.index.interval.IntervalTreeIndex.<init>(IntervalTreeIndex.java:51)
        ... 19 more
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.1-1-g07a4bf8):
##### 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.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: java.lang.reflect.InvocationTargetException

I appreciate any help you can give me=)

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