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Exit code 3 for HaplotypeCaller?

I am getting an exit code 3 for HaplotypeCaller version 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


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(
at htsjdk.variant.variantcontext.writer.VCFWriter.close(
at org.broadinstitute.hellbender.engine.GATKTool.doWork(
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(
at org.broadinstitute.hellbender.Main.runCommandLineProgram(
at org.broadinstitute.hellbender.Main.mainEntry(
at org.broadinstitute.hellbender.Main.main(
Caused by: 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(
at htsjdk.variant.variantcontext.writer.IndexingVariantContextWriter.close(

Does anyone know what is going on?


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