Dear GATK team member,
When I used the GenomeAnalysisTK.jar, the "ERROR MESSAGE: java.lang.reflect.InvocationTargetException" appeared. Could you please tell me how to fix it? Thanks a lot!
the code is following:
-bash-4.1$ /java -Xmx10g -jar ~/GenomeAnalysisTK.jar -T RealignerTargetCreator -R $ref_dir/ucsc.hg19.fasta -o $other_dir/WGC033081U.realigner.intervals -I $bam_dir/WGC033081U.dedupped.bam -known $ref_dir/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf -known $ref_dir/1000G_phase1.indels.hg19.sites.vcf
The process is following:
INFO 18:05:32,432 HelpFormatter - --------------------------------------------------------------------------------
INFO 18:05:32,476 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
INFO 18:05:32,477 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 18:05:32,477 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 18:05:32,490 HelpFormatter - Program Args: -T RealignerTargetCreator -R /workstation/database/temp/refdir/ucsc.hg19.fasta -o /workstation/database/temp/otherdir/WGC033081U.realigner.intervals -I /workstation/database/temp/bamdir/WGC033081U.dedupped.bam -known /workstation/database/temp/refdir/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf -known /workstation/database/temp/refdir/1000G_phase1.indels.hg19.sites.vcf
INFO 18:05:32,556 HelpFormatter - Executing as huangt@Konglab.server on Linux 2.6.32-504.23.4.el6.centos.plus.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_80-b15.
INFO 18:05:32,557 HelpFormatter - Date/Time: 2015/09/06 18:05:32
INFO 18:05:32,557 HelpFormatter - --------------------------------------------------------------------------------
INFO 18:05:32,558 HelpFormatter - --------------------------------------------------------------------------------
INFO 18:05:37,622 GenomeAnalysisEngine - Strictness is SILENT
INFO 18:05:38,655 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 18:05:38,685 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 18:05:38,823 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
INFO 18:05:42,777 GATKRunReport - Uploaded run statistics report to AWS S3
ERROR ------------------------------------------------------------------------------------------
ERROR stack trace
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.(ReferenceOrderedDataSource.java:208)
at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource.(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.(LinearIndex.java:101)
... 19 more