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java.lang.NullPointerException at picard.vcf.processor.VcfFileSegmentGenerator$ByWholeContig.readSequences(VcfFileSegmentGenerator.java:112) at picard.vcf.processor.VcfFileSegmentGenerator$ByWholeContig.forVcf(VcfFileSegmentGenerator.java:98) at picard.vcf.processor.VcfFileSegmentGenerator$WidthLimitingDecorator.forVcf(VcfFileSegmentGenerator.java:194) at picard.vcf.processor.VcfFileSegmentGenerator$1.forVcf(VcfFileSegmentGenerator.java:64) at picard.vcf.processor.VariantIteratorProducer$Threadsafe.<init>(VariantIteratorProducer.java:140) at picard.vcf.processor.VariantIteratorProducer.byHundredMegabaseChunksWithOnTheFlyFilteringByInterval(VariantIteratorProducer.java:72) at picard.vcf.processor.VariantProcessor$Builder.composeVcfIteratorProducerFromBuilderArguments(VariantProcessor.java:166) at picard.vcf.processor.VariantProcessor$Builder.build(VariantProcessor.java:149) at picard.vcf.CollectVariantCallingMetrics.doWork(CollectVariantCallingMetrics.java:128) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:206) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)