While most of these commands are running, it is not possible to perform other commands simultaneously because of a risk of conflict. For this reason, you will see the message "Application not responding" in the shortcut menu of the Dock or "OnyX (not responding)" if you try to force OnyX to quit.
Some operations take a long time (such as verifying the structure of the system files or rebuilding the locate database).
Wait for the tasks to finish!