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We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
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=)