GATK GenomicAnnotator Error

[Michael Jones]

I am getting the following Exception when I run GATK GenomicAnnotator. Anyone seen this?

java.lang.RuntimeException: org.broad.tribble.TribbleException$UnableToCreateCorrectIndexType: Unknown index type value1748778604
at org.broad.tribble.index.IndexFactory.loadIndex(IndexFactory.java:100)
at org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder.loadFromDisk(RMDTrackBuilder.java:301)
at org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder.attemptIndexFromDisk(RMDTrackBuilder.java:286)
at org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder.loadIndex(RMDTrackBuilder.java:255)
at org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder.getFeatureSource(RMDTrackBuilder.java:216)
at org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder.createFeatureReader(RMDTrackBuilder.java:167)
at org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder.createInstanceOfTrack(RMDTrackBuilder.java:140)
at org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder.createRequestedTrackObjects(RMDTrackBuilder.java:446)
at org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder.getReferenceMetaDataSources(RMDTrackBuilder.java:398)
at org.broadinstitute.sting.gatk.AbstractGenomeAnalysisEngine.initializeDataSources(AbstractGenomeAnalysisEngine.java:331)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:90)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:97)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:244)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:87)
Caused by: org.broad.tribble.TribbleException$UnableToCreateCorrectIndexType: Unknown index type value1748778604
at org.broad.tribble.index.IndexFactory$IndexType.getIndexType(IndexFactory.java:53)
at org.broad.tribble.index.IndexFactory.loadIndex(IndexFactory.java:89)
... 13 more

Here is the command

java -Xmx1g -jar ~/sequence-tools/gatk/GenomeAnalysisTK-1.0.4705/GenomeAnalysisTK.jar \
-T GenomicAnnotator \
-l info \
-R ../bwa/hg18/Homo_sapiens_assembly18.fasta \
-B:variant,vcf ./snps.jeko.bwa.raw.vcf \
-B:dbsnp,AnnotatorInputTable ~/sequence-tools/db/snp130-hg18-only-the-SNPs.txt \
-B:refseq,AnnotatorInputTable ~/sequence-tools/db/refGene-big-table-hg18.txt \
-m \
-o output.vcf \
-BTI variant \
-s dbsnp.name,dbsnp.refUCSC,dbsnp.strand,dbsnp.observed,dbsnp.avHet

and a reference

http://www.broadinstitute.org/gsa/wiki/index.php/GenomicAnnotator

[Michael Jones]

In case anyone is interested in how this was fixed. Look here. http://getsatisfaction.com/gsa/topic...ibbleexception