The whole chromosome is output instead of blacklist

[KRhoDomb]

Hi,

I need help with building blacklist for my small plant genome (Marchantia polymorpha, ~280 Mbp total, 9 chromosoms between 30 and 7.5 Mbp). I tried Blacklist on demo data and it runs ok. When I run it on any of my chromosomes, using its respective input bam file and umap mappability file, it outputs the whole chromosome (e.g. chr1 0 30584100 High Signal Region). I know there are a few regions with excessive coverage in the genome, because I see them in genome browser in every CHIP-seq input file. Do you have any idea? I'll be really grateful for any help!

Best, Rotem