java.lang.RuntimeException

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  • java.lang.RuntimeException: java.lang.reflect.InvocationTargetException at htsjdk.tribble.index.IndexFactory.loadIndex(IndexFactory.java:189) at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.loadFromDisk(RMDTrackBuilder.java:336) at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.attemptToLockAndLoadIndexFromDisk(RMDTrackBuilder.java:320) at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.loadIndex(RMDTrackBuilder.java:279) at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.getFeatureSource(RMDTrackBuilder.java:225) at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.createInstanceOfTrack(RMDTrackBuilder.java:148) at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.<init>(ReferenceOrderedDataSource.java:208) at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource.<init>(ReferenceOrderedDataSource.java:88) at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.getReferenceOrderedDataSources(GenomeAnalysisEngine.java:997) at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.initializeDataSources(GenomeAnalysisEngine.java:779) at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:290) 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: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 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.<init>(LinearIndex.java:101) ... 19 more
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