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Exit code 3 for HaplotypeCaller?

I am getting an exit code 3 for HaplotypeCaller version 4.1.2.0. I checked the command line output and the only thing I can see is this:

WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples

and

htsjdk.samtools.util.RuntimeIOException: Unable to close index for file:///path/to/Sample_DS-bkm-085-N.txt.b37.bam.g.vcf.gz
at htsjdk.variant.variantcontext.writer.IndexingVariantContextWriter.close(IndexingVariantContextWriter.java:183)
at htsjdk.variant.variantcontext.writer.VCFWriter.close(VCFWriter.java:231)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller.closeTool(HaplotypeCaller.java:246)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1043)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
at org.broadinstitute.hellbender.Main.main(Main.java:291)
Caused by: java.io.IOException: Terminator block not found after closing BGZF file /path/to/Sample_DS-bkm-085-N.txt.b37.bam.g.vcf.gz
at htsjdk.samtools.util.BlockCompressedOutputStream.close(BlockCompressedOutputStream.java:329)
at htsjdk.variant.variantcontext.writer.IndexingVariantContextWriter.close(IndexingVariantContextWriter.java:172)



Does anyone know what is going on?
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