the two links your provide in the read.me file for the human data differ from each other: the first link shows much less regions than the ENCODE file. What is the difference between them? is the first one just a truncated version of the "right" one available on ENCODE?
HUMAN (hg19/GRCh38): http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg38-human/hg38.blacklist.bed.gz ENCODE portal link: https://www.encodeproject.org/annotations/ENCSR636HFF/ (Select GRCh38).