Be sure to run HMMRATAC using the executable file, found here: https://github.com/LiuLabUB/HMMRATAC/releases The source files are uploaded for users to see how the program works. They do not contain the required manifest file needed to actually run. For details on HOW to run HMMRATAC, see the quick start guide, which contains a thorough runthrough of all parameters, output files and input requirements.