INFO 01:05:48,346 HelpFormatter - --------------------------------------------------------------------------------
INFO 01:05:48,349 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5-0-ge91472d, Compiled 2016/03/18 09:18:48
INFO 01:05:48,349 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 01:05:48,349 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 01:05:48,352 HelpFormatter - Program Args: -T RealignerTargetCreator -R ucsc.hg19.fasta -I input.bam -known 1000G_phase1.indels.hg19.sites.vcf -known Mills_and_1000G_gold_standard.indels.hg19.sites.vcf --downsampling_type NONE
-o sample.intervals
INFO 01:05:48,358 HelpFormatter - Executing as root@d73b8eec27a3 on Linux 4.4.0-34-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_72-intern$
l-b15.
INFO 01:05:48,358 HelpFormatter - Date/Time: 2016/11/17 01:05:48
INFO 01:05:48,358 HelpFormatter - --------------------------------------------------------------------------------
INFO 01:05:48,358 HelpFormatter - --------------------------------------------------------------------------------
INFO 01:05:48,460 GenomeAnalysisEngine - Strictness is SILENT
INFO 01:05:49,083 GenomeAnalysisEngine - Downsampling Settings: No downsampling
INFO 01:05:49,089 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 01:05:49,172 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
INFO 01:06:13,929 RMDTrackBuilder - Writing Tribble index to disk for file 1000G_phase1.indels.hg19.sites.vcf.idx
INFO 01:06:29,320 RMDTrackBuilder - Writing Tribble index to disk for file Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.idx
INFO 01:06:31,411 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
INFO 01:06:32,089 GenomeAnalysisEngine - Done preparing for traversal
INFO 01:06:32,089 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 01:06:32,090 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 01:06:32,090 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 01:06:33,501 GATKRunReport - Uploaded run statistics report to AWS S3
ERROR ------------------------------------------------------------------------------------------
ERROR stack trace
java.lang.ArrayIndexOutOfBoundsException: -94
at org.broadinstitute.gatk.utils.BaseUtils.convertIUPACtoN(BaseUtils.java:215)
at org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:347)
at org.broadinstitute.gatk.engine.datasources.providers.LocusReferenceView.initializeReferenceSequence(LocusReferenceView.java:163)
at org.broadinstitute.gatk.engine.datasources.providers.LocusReferenceView.(LocusReferenceView.java:139)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:90)
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)