This MitoScape version can be executed with the command:

mitoscape \
  --threads <number of threads> \
  --prob <classification probability> \
  --ld <path to mitomap.ld file> \
  --numt <path to NUMTs_hg38.txt file> \
  --classifier <path to MTClassifierModel.RF folder> \
  --prefix <prefix, see below for explanation> \
  --out <output prefix for bam file>

mitomap.ld, NUMTs_hg38.txt, and MTClassifierModel.RF are provided in the package in the $MITOSCAPE_DATA folder.

The prefix matches the prefix of the bam filenames generated as explained here. MitoScape will look for _MT_MD.bam and _NT.bam.