Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

ERROR MESSAGE: java.lang.reflect.InvocationTargetException

caileicailei ShanghaiMember

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 [email protected] 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

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.3-0-g37228af):
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 ------------------------------------------------------------------------------------------

Best Answer

Answers

Sign In or Register to comment.