ZipperBams failed. Error: processed all unmapped reads but there are mapped reads remaining to be read.

[teryyoung]

hello! I'm doing with sequencing data with UMI, I followed #fgbio-best-practise-fastq---consensus-pipeline When I run fgbio ZipperBams to merge my consensus.ubam and consensus.mapped.bam, there is an exception: Exception in thread "main" java.lang.IllegalStateException: Error: processed all unmapped reads but there are mapped reads remaining to be read.

and I check my two bam files; they all are queryname sorted, have same number of reads, the difference between them is all of queryname of ubam have suffix "/A". like this: I found it is caused by fgbio CallConsensusReads...

I wanna know whether this is the problem caused ZipperBams failed, or how to deal with this problem(ZipperBams)? #my fgbio version is 2.2.2-3a74fd2-SNAPSHOT