Be careful with sentences that have an all … not … form. They may be hazardous to your clarity. The sentence All of the departments did not file a report may mean that some departments did not file or that none did. If you want the first meaning, you can express it unambiguously by saying Not all of the departments filed a report.

If you want the second meaning, try a paraphrase such as None of the departments filed a report or All of the departments failed to file a report. Note that the same problem can arise with other universal terms like every in negated sentences, as in the ambiguous Every department did not file a report