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problem of Base quality score recalibration by using GATK

xdzperfectxdzperfect Beijing Institute of genomicsMember

Dear GATK teams:
when I use the following script to Base quality score recalibration ,
java -Xmx1g -jar $Gbin/GenomeAnalysisTK.jar \
-R $GATK_ref/ucsc.hg19.fasta \
-T BaseRecalibrator \
-I chr2.merged.uniqPairs.sort.dupMarked.addGR.order.realn.bam \
-o chr2.merged.uniqPairs.sort.dupMarked.addGR.order.realn.recal1.grp \
-knownSites $GATK_ref/dbsnp_138.hg19.vcf \
-knownSites $GATK_ref/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf \
-knownSites $GATK_ref/1000G_phase1.indels.hg19.sites.vcf
I come across the err report,as following:
INFO 11:27:24,759 HelpFormatter - Date/Time: 2015/09/18 11:27:24
INFO 11:27:24,760 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:27:24,760 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:27:25,521 GenomeAnalysisEngine - Strictness is SILENT
INFO 11:27:25,954 GenomeAnalysisEngine - Downsampling Settings: No downsampling
INFO 11:27:25,962 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 11:27:27,877 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 1.90

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.RuntimeException: java.lang.reflect.InvocationTargetException
at htsjdk.tribble.index.IndexFactory.loadIndex(IndexFactory.java:189)
at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.loadFromDisk(RMDTrackBuilder.java:335)
at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.attemptToLockAndLoadIndexFromDisk(RMDTrackBuilder.java:19)
at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.loadIndex(RMDTrackBuilder.java:278)
at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.getFeatureSource(RMDTrackBuilder.java:224)
at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.createInstanceOfTrack(RMDTrackBuilder.java:147)
at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.(ReferenceOrderedDataSource.java:08)
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:828)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:286)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:106)
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
at htsjdk.tribble.index.IndexFactory.loadIndex(IndexFactory.java:185)
... 14 more
Caused by: java.io.EOFException
at htsjdk.tribble.util.LittleEndianInputStream.readFully(LittleEndianInputStream.java:138)
at htsjdk.tribble.util.LittleEndianInputStream.readLong(LittleEndianInputStream.java:80)
at htsjdk.tribble.index.linear.LinearIndex$ChrIndex.read(LinearIndex.java:271)
at htsjdk.tribble.index.AbstractIndex.read(AbstractIndex.java:363)
at htsjdk.tribble.index.linear.LinearIndex.(LinearIndex.java:101)
... 19 more

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.4-0-g7e26428):
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
ERROR -----------------------------------------------

I'm confused , how to conque it?
thanks

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