The name of the virtual environment and repository is the same because Windows paths are not case-sensitive.
PS C:\Users\dstr7320> py -m venv kronos
PS C:\Users\dstr7320> .\kronos\Scripts\activate
(kronos) PS C:\Users\dstr7320> git clone https://github.com/mahmoodlab/KRONOS.git
fatal: destination path 'KRONOS' already exists and is not an empty directory.
The instruction in Step 1 should use a different name for the environment.
# for Windows
py -m venv kronos