Had similar problem with similar message. This is how we found out what was wrong:

 1. Executed `check50 -h` to see what logging options there were. Discovered we can turn on debug logging using `--log-level` option.

 2. Executed `check50 --log-level debug path/to/folder...`. In the output noticed:
`fatal: repository 'https:///github.com/me50/$USERNAME' not found`.

3. Navigated to the repository URL in the browser: `https:///github.com/me50/$USERNAME`

4. Had to click "Accept Invitation" from `bot50`.

5. Executed `check50 path/to/folder/...` and it worked fine using username and GitHub personal access token (instead of password).