how to stop a file from running after its executed

[bibhor dhungel]

hi,
i ran a query on mysql server which affected certain tables. after a while i figured that the program did not correctly execute and i deleted the file containing the query. But, it seems that the query is still running and i am not sure how to stop the file from executing. i have already rebooted the server once and i am not sure that it worked. is there a way to do this. btw the server is operating under a linux machine.

thanks