java.lang.NullPointerException

[visze]

I get a null pointer exception when I try to annotate the recent clinvar (hg38m, clinvar_20190603) version. I removed the contigs in the vcf header because they had no length (but I guess then this should still work). here is the error:
(jannovar load by bioconda, version 0.31)

jannovar annotate-vcf -d data/hg38_ensembl.ser -i clinvar_20190603.vcf.gz -o clinvar_20190603.ensembl.vcf.gz 
Options
JannovarAnnotateVCFOptions [escapeAnnField=true, pathInputVCF=clinvar_20190603.vcf.gz, interval=, pathOutputVCF=clinvar_20190603.ensembl.vcf.gz, pathVCFDBSNP=null, prefixDBSNP=DBSNP_, pathFASTARef=null, pathVCFExac=null, prefixExac=EXAC_, pathVCFGnomadExomes=null, prefixGnomadExomes=GNOMAD_EXOMES_, pathVCFGnomadGenomes=null, prefixGnomadGenomes=GNOMAD_GENOMES_, pathVCFUK10K=null, prefixUK10K=UK10K_, pathThousandGenomes=null, prefixThousandGenomes=G1K_, pathClinVar=null, prefixClinVar=CLINVAR_, pathCosmic=null, prefixCosmic=COSMIC_, pathPedFile=null, annotateAsSingletonPedigree=false, useThresholdFilters=false, useAdvancedPedigreeFilters=false, threshFiltMinGtCovHet=8, threshFiltMinGtCovHomAlt=4, threshFiltMaxCov=10000, threshFiltMinGtGq=20, threshFiltMinGtAafHet=0.2, threshFiltMaxGtAafHet=0.8, threshFiltMinGtAafHomAlt=0.7, threshFiltMaxGtAafHomRef=0.3, threshFiltMaxExacHomAlt=20, threshFiltMaxThousandGenomesHomAlt=10, threshFiltMaxAlleleFrequencyAd=0.01, threshFiltMaxAlleleFrequencyAr=0.01, offTargetFilterEnabled=false, offTargetFilterUtrIsOffTarget=false, offTargetFilterIntronicSpliceIsOffTarget=false, oneParentGtFilteredFiltersAffected=false, inheritanceAnnoUseFilters=false, useParentGtIsFiltered=true, threshDeNovoParentAd2=1, bedAnnotationOptions=[], dbNsfpColContig=1, dbNsfpColPosition=2, prefixDbNsfp=DBNSFP_, pathDbNsfp=null, columnsDbNsfp=[], tsvAnnotationOptions=[], vcfAnnotationOptions=[]]
Deserializing transcripts...
INFO Deserializing JannovarData from data/hg38_ensembl.ser
INFO Deserialization took 7.56 sec.
Progress reporting does not work because VCF file is missing the contig lines in the header.
Annotating VCF...
Will read full input file
Exception in thread "main" java.lang.NullPointerException
	at de.charite.compbio.jannovar.annotation.VCFAnnotationData.setAnnoLoc(VCFAnnotationData.java:105)
	at de.charite.compbio.jannovar.annotation.Annotation.toVCFAnnoString(Annotation.java:285)
	at de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator.applyAnnotations(VariantContextAnnotator.java:400)
	at de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator.dispatchAnnotateVariantContext(VariantContextAnnotator.java:337)
	at de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator.annotateVariantContext(VariantContextAnnotator.java:296)
	at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:195)
	at java.base/java.util.Iterator.forEachRemaining(Iterator.java:133)
	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
	at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484)
	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474)
	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
	at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
	at java.base/java.util.stream.ReferencePipeline.forEachOrdered(ReferencePipeline.java:502)
	at de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotateVCFCommand.run(AnnotateVCFCommand.java:411)
	at de.charite.compbio.jannovar.Jannovar.main(Jannovar.java:64)