wgbstools add_cpg_counts --verbose <filename.bam>
stops with
FileNotFoundError: [Errno 2] No such file or directory: './<filename>_chr15.output.bam'
(filename.bam only contains reads mapping on chr15).
It also creates an indexed output file <filename.counts.bam>
which is empty
samtools view <filename.counts.bam> | wc -l
0