While running the scripts from the command line with --job_id, I noticed that each step skips the first set of chromosomes/coordinates in the chrsize.tsv and chrsize_index.tsv. Digging into this, it looks like these are not being read in as 0-base index, rather than a 1-base index.
While running the scripts from the command line with --job_id, I noticed that each step skips the first set of chromosomes/coordinates in the chrsize.tsv and chrsize_index.tsv. Digging into this, it looks like these are not being read in as 0-base index, rather than a 1-base index.