The correct way to launch an application is
not through the `open` command. That is attempting to launch the passed file using the default file handler.
Apparently, `open -a AppName` will open an (optional) file using AppName, so you could do `open -a calibre`
...
BUT.
The proper way is to call the `calibre` command

-- you will find it in
Code:
/Applications/calibre.app/Contents/console.app/Contents/MacOS/
It is suggested to symlink these to /usr/bin/ so they are on your PATH.
Note: My auto-updater also creates those symlinks:
https://github.com/eli-schwartz/calibre-installer