Unified Genotyper Code exception - java.lang.IllegalArgumentException

nbedelmannbedelman Cambridge, MAMember

I've seen a few java.lang.IllegalArgumentException questions here, but I haven't been able to find any quit like mine! Let me know if this has in fact been answered somewhere else, or if you have any insight into the problem! Here is the output from my UnifiedGenotyper run:

INFO 16:37:28,331 HelpFormatter - ---------------------------------------------------------------------------------
INFO 16:37:28,364 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
INFO 16:37:28,364 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 16:37:28,364 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 16:37:28,366 HelpFormatter - Program Args: -T UnifiedGenotyper -R /n/regal/mallet_lab/edelman/18Genomes/data/reference/Herato2/Herato2.fasta -I bam/h_erato_himera_hybrid_RG.bam -I bam/h_erato_pe_aln_sorted.bam -I bam/h_himera_pe_aln_sorted.bam -o snps.raw.vcf -stand_emit_conf 10 -stand_call_conf 50
INFO 16:37:28,487 HelpFormatter - Executing as nedelman@holyitc07.rc.fas.harvard.edu on Linux 2.6.32-431.17.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_45-b14.
INFO 16:37:28,488 HelpFormatter - Date/Time: 2016/01/06 16:37:28
INFO 16:37:28,488 HelpFormatter - ---------------------------------------------------------------------------------
INFO 16:37:28,488 HelpFormatter - ---------------------------------------------------------------------------------
INFO 16:37:29,264 GenomeAnalysisEngine - Strictness is SILENT
INFO 16:37:29,525 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
INFO 16:37:29,535 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 16:37:29,719 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.18
INFO 16:37:30,310 GenomeAnalysisEngine - Preparing for traversal over 3 BAM files
INFO 16:37:30,360 GenomeAnalysisEngine - Done preparing for traversal
INFO 16:37:30,360 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 16:37:30,361 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 16:37:30,361 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 16:37:30,394 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
INFO 16:37:30,394 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
INFO 16:38:00,381 ProgressMeter - Herato_chr11_8:315097 430691.0 30.0 s 69.0 s 0.1% 7.3 h 7.3 h
INFO 16:38:07,739 GATKRunReport - Uploaded run statistics report to AWS S3

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

java.lang.IllegalArgumentException
at java.nio.ByteBuffer.allocate(ByteBuffer.java:334)
at htsjdk.samtools.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:195)
at org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:329)
at org.broadinstitute.gatk.engine.datasources.providers.LocusReferenceView.initializeReferenceSequence(LocusReferenceView.java:150)
at org.broadinstitute.gatk.engine.datasources.providers.LocusReferenceView.(LocusReferenceView.java:126)
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)

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: Code exception (see stack trace for error itself)
ERROR ------------------------------------------------------------------------------------------

Thanks,
Nate

Answers

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