Everytime when I delete a file, a popup pops up

everytime when I delete a file, this will pops up.

Does it still come up when you do it as root?

If I do this from terminal, it will not pops up, no mater by which user.
but if I do this from mouse right click to delete, it will pops up.

Have you changed any permissions or installed any new software recently? Also, try chmod +w nohup.out in the Terminal.

when nohup.out will be created? I have not this file.

Hmm, can you log in as root through the GUI and then try it?