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Error on running ReadBasedPhasing tool

I got a Contig X does not have a length field error when I run the phasing tool. By digging in more, it seems a user exception from htsjdk code, here is the trace of the coding line, has anyone experienced this issue before? Is it a problem in contig reference sequence or bad VCF file, or bad bam file?

Thanks for any help,

--------------------------------error exception raised in following code line-------------------------------------------------------------------

public SAMSequenceRecord getSAMSequenceRecord() {
final String lengthString = this.getGenericFieldValue("length");
if (lengthString == null) throw new TribbleException("Contig " + this.getID() + " does not have a length field.");

which is called by RMDTrackBuilder.java validateVariantAgainstSequenceDictionary(final String name, final String descriptorName, final AbstractFeatureReader reader, final SAMSequenceDictionary dict )

in vcfContigRecords.add(contig.getSAMSequenceRecord()); -- crashed here

Answers

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