Problem with RealignerTargetCreator

Hi guys,

I'm trying to run GATK on one chromosome (chr1) from a sample (NA12877) distributed via Illumina Platinum Genomes. To do so, I downloaded their BAM file, subsetted to chr1, sorted and indexed. Hoping to simplify the procedure, I also have a fasta file for chr1.

When attempting to run:

${GATK} -T RealignerTargetCreator -R ${REFERENCE} -I ${INPUTBAM} -o ${INTERVALS} -L chr1:1-249250621

I get the error below, which I don't know how to solve. Any suggestion?

INFO  11:17:36,626 ProgressMeter -  chr1:246007661   2.4600576E8    35.0 m       8.0 s       98.7%    35.5 m      27.0 s
INFO  11:18:01,168 GATKRunReport - Uploaded run statistics report to AWS S3
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
java.lang.IllegalArgumentException
        at java.nio.ByteBuffer.allocate(ByteBuffer.java:330)
        at htsjdk.samtools.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:195)
        at org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.ja
va:329)
        at org.broadinstitute.gatk.engine.datasources.providers.LocusReferenceView.initializeReferenceSequence(LocusReferenceView.
java:150)
        at org.broadinstitute.gatk.engine.datasources.providers.LocusReferenceView.<init>(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

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