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java.lang.ArrayIndexOutOfBoundsException

Below is my error after running GatK, I got the vcf file but its idx file is empty. Is there a solution for that?

INFO 17:02:46,750 HelpFormatter - ---------------------------------------------------------------------------------
INFO 17:02:46,753 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
INFO 17:02:46,753 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 17:02:46,754 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 17:02:46,758 HelpFormatter - Program Args: -R /Users/junbai/NSCcourse/nscCourseDir/refData/gatkBundle/2.8/b37/human_g1k_v37_decoy.fasta -T UnifiedGenotyper -I WGS_control_4105105_merged_rmdup_sorted.bam_markDup.fixedMate.baseQreCali.bam -glm INDEL -stand_call_conf 40 -stand_emit_conf 20 -dcov 200 -A Coverage --dbsnp /Users/junbai/NSCcourse/nscCourseDir/refData/gatkBundle/2.8/b37/dbsnp_138.b37.vcf -o indel.raw_WGS_control_4105105_merged_rmdup_sorted.bam_markDup.fixedMate.baseQreCali.vcf -L /Users/junbai/EGA_download/genome_lib/gencode/gencode.v19.annotation.gtf_proteinGene_bed_geneU_10000_geneD_1000.bed
INFO 17:02:46,764 HelpFormatter - Executing as [email protected] on Mac OS X 10.7.5 x86_64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_79-b15.
INFO 17:02:46,764 HelpFormatter - Date/Time: 2015/10/27 17:02:46
INFO 17:02:46,764 HelpFormatter - ---------------------------------------------------------------------------------
INFO 17:02:46,764 HelpFormatter - ---------------------------------------------------------------------------------
INFO 17:02:47,337 GenomeAnalysisEngine - Strictness is SILENT
INFO 17:02:47,444 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 200
INFO 17:02:47,454 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 17:02:47,499 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
INFO 17:02:48,344 IntervalUtils - Processing 203227294 bp from intervals
INFO 17:02:48,466 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
INFO 17:02:48,734 GenomeAnalysisEngine - Done preparing for traversal
INFO 17:02:48,735 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 17:02:48,735 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 17:02:48,736 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 17:02:48,782 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
INFO 17:02:48,782 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
INFO 17:03:18,742 ProgressMeter - 1:16683313 2464615.0 30.0 s 12.0 s 1.1% 44.2 m 43.7 m

INFO 17:39:19,060 ProgressMeter - X:37855836 2.04193903E8 36.5 m 10.0 s 96.2% 37.9 m 85.0 s
INFO 17:39:49,063 ProgressMeter - X:99988011 2.07380221E8 37.0 m 10.0 s 97.8% 37.9 m 51.0 s
INFO 17:40:19,067 ProgressMeter - X:152765817 2.10577369E8 37.5 m 10.0 s 99.3% 37.8 m 16.0 s
INFO 17:40:31,182 GATKRunReport - Uploaded run statistics report to AWS S3

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

java.lang.ArrayIndexOutOfBoundsException: 200
at org.broadinstitute.gatk.utils.contexts.ReferenceContext.getBase(ReferenceContext.java:179)
at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.getFilteredAndStratifiedContexts(UnifiedGenotypingEngine.java:434)
at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateLikelihoodsAndGenotypes(UnifiedGenotypingEngine.java:196)
at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:376)
at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:148)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:315)
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)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.4-46-gbc02625):
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: 200
ERROR ------------------------------------------------------------------------------------------

(END)

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