Getting java.lang.InternalError while annotation with 1000 Genome Db

[Habush]

I have this small code that I am testing to annotate a sample vcf file using 1000 Genome Db.

 try(VCFFileReader vcfReader = new VCFFileReader(FileUtils.getFile(properties.getProperty("basePath"), "example.vcf"), false)) {
            logger.info("Starting annotation...");
            VCFHeader vcfHeader = vcfReader.getFileHeader();
            Stream<VariantContext> stream = vcfReader.iterator().stream();
            DBAnnotationOptions options = DBAnnotationOptions.createDefaults();
            options.setIdentifierPrefix("1K_");
            DBVariantContextAnnotator thousandGenomeAnno = new DBVariantContextAnnotator(new ThousandGenomesAnnotationDriver(genomeRepo.findById("1k").get(), refRepo.findById("hg38").get(), options), options);
            thousandGenomeAnno.extendHeader(vcfHeader);
            stream = stream.map(thousandGenomeAnno::annotateVariantContext);
            JannovarData data = transcriptRepo.findById("hg38_ensembl").orElse(null);
            assert data != null;
            VariantEffectHeaderExtender effectHeader = new VariantEffectHeaderExtender();
            effectHeader.addHeaders(vcfHeader);
            VariantContextAnnotator annotator = new VariantContextAnnotator(data.getRefDict(), data.getChromosomes());
            stream = stream.map(annotator::annotateVariantContext);

            try(VariantContextWriter writer = buildVariantContextWrite(vcfHeader, PathUtil.join(properties.getProperty("basePath"), "output.vcf"));
                VariantContextProcessor processor = new ConsumerProcessor(vc -> writer.add(vc))
            ){
               stream.forEachOrdered(processor::put);
            }
            logger.info("Wrote annotation result to output.vcf");
            logger.info("Finished Annotation");
        }

I have modified the ThousandGenomesAnnotationDriver constructor to accept a VCFFIleReader and AlleleMatcher objects instead of files

But when I run the above code I get the following exception:

Exception in thread "main" java.lang.InternalError
        at java.util.zip.Inflater.reset(Native Method)
        at java.util.zip.Inflater.reset(Inflater.java:352)
        at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:141)
        at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:96)
        at htsjdk.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:550)
        at htsjdk.samtools.util.BlockCompressedInputStream.processNextBlock(BlockCompressedInputStream.java:532)
        at htsjdk.samtools.util.BlockCompressedInputStream.nextBlock(BlockCompressedInputStream.java:468)
        at htsjdk.samtools.util.BlockCompressedInputStream.seek(BlockCompressedInputStream.java:380)
        at htsjdk.tribble.readers.TabixReader$IteratorImpl.next(TabixReader.java:428)
        at htsjdk.tribble.readers.TabixIteratorLineReader.readLine(TabixIteratorLineReader.java:46)
        at htsjdk.tribble.TabixFeatureReader$FeatureIterator.readNextRecord(TabixFeatureReader.java:170)
        at htsjdk.tribble.TabixFeatureReader$FeatureIterator.<init>(TabixFeatureReader.java:159)
        at htsjdk.tribble.TabixFeatureReader.query(TabixFeatureReader.java:133)
        at htsjdk.variant.vcf.VCFFileReader.query(VCFFileReader.java:322)
        at de.charite.compbio.jannovar.vardbs.base.VCFReaderVariantProvider.query(VCFReaderVariantProvider.java:38)
        at de.charite.compbio.jannovar.vardbs.base.AbstractDBAnnotationDriver.annotateVariantContext(AbstractDBAnnotationDriver.java:66)
        at de.charite.compbio.jannovar.vardbs.facade.DBVariantContextAnnotator.annotateVariantContext(DBVariantContextAnnotator.java:55)
        at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
        at java.util.Iterator.forEachRemaining(Iterator.java:116)
        at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
        at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
        at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
        at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
        at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
        at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
        at java.util.stream.ReferencePipeline.forEachOrdered(ReferencePipeline.java:490)
        at org.habush.varann.Test.annotateVCF(Test.java:134)
        at org.habush.varann.Test.main(Test.java:59)

How can I fix this?

P.S when I remove the code that is annotating using VariantContextAnnotator, it works, which is odd.