GATK Unknown index type value808519985

[quoclinh]

Hi,

I am using GATK for 'table recalibration & variant call'. However, I have an error messages:

$genome# GenomeAnalysisTK.jar -l INFO -R hg19.GATK.fasta --DBSNP hg19.dbSNP130.rod --default_platform illumina -I NAME-EXOME.RG.bam -T CountCovariates -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate --default_read_group 1

INFO 14:21:23,592 HelpFormatter - ---------------------------------------------------------------------------
INFO 14:21:23,593 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.0.4905, Compiled 2010/12/23 10:17:26
INFO 14:21:23,594 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 14:21:23,594 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki
INFO 14:21:23,594 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa
INFO 14:21:23,594 HelpFormatter - Program Args: -l INFO -R /stf/home/cluster/nguyenqxx/pipeline/resources/hg19.GATK.fasta --DBSNP /stf/home/cluster/nguyenqxx/pipeline/resources/hg19.dbSNP130.rod --default_platform illumina -I /stf/home/cluster/stroms/bin/pipelines/results/201103/exome/l1/NAME-EXOME.RG.bam -T CountCovariates -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate --default_read_group 1
INFO 14:21:23,594 HelpFormatter - Date/Time: 2011/04/12 14:21:23
INFO 14:21:23,595 HelpFormatter - ---------------------------------------------------------------------------
INFO 14:21:23,595 HelpFormatter - ---------------------------------------------------------------------------
INFO 14:21:23,607 GenomeAnalysisEngine - Strictness is SILENT
INFO 14:21:23,772 RMDTrackBuilder - Loading Tribble index from disk for file /stf/home/cluster/nguyenqxx/pipeline/resources/hg19.dbSNP130.rod
INFO 14:21:23,790 GATKRunReport - Aggregating data for run report
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
java.lang.RuntimeException: org.broad.tribble.TribbleException$UnableToCreateCorrectIndexType: Unknown index type value808519985
at org.broad.tribble.index.IndexFactory.loadIndex(IndexFactory.java:100)
at org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder.loadFromDisk(RMDTrackBuilder.java:320)
at org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder.attemptIndexFromDisk(RMDTrackBuilder.java:305)
at org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder.loadIndex(RMDTrackBuilder.java:274)
at org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder.getFeatureSource(RMDTrackBuilder.java:235)
at org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder.createFeatureReader(RMDTrackBuilder.java:186)
at org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder.createInstanceOfTrack(RMDTrackBuilder.java:159)
at org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder.getReferenceMetaDataSources(RMDTrackBuilder.java:423)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.initializeDataSources(GenomeAnalysisEngine.java:665)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:194)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:109)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:239)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:87)
Caused by: org.broad.tribble.TribbleException$UnableToCreateCorrectIndexType: Unknown index type value808519985
at org.broad.tribble.index.IndexFactory$IndexType.getIndexType(IndexFactory.java:53)
at org.broad.tribble.index.IndexFactory.loadIndex(IndexFactory.java:89)
... 12 more
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0.4905):
##### ERROR
##### ERROR Please visit to wiki to see if this is a known problem
##### ERROR If not, please post the error, with stack trace, to the GATK forum
##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: org.broad.tribble.TribbleException$UnableToCreateCorrectIndexType: Unknown index type value808519985
##### ERROR ------------------------------------------------------------------------------------------

Does anyone have any idea?

Thanks,
Q

[quoclinh]

The problem resolved! I just need to remove the *.idx files on the hg19 reference, and upgrade the GATK newest version.