I have found following issue in my data:

A p.value is quite low (6.12215783498127e-12) but the p.adjusted is NA. Why could this happen? 
 

ENSMUSG00000052837.4/Junb 1512.65617045918 0.453974583706133 0.0660155978404382 6.87677758828155 6.12215783498127e-12 NA

DESeq2 performs independent filtering based on the average logCPM values. This gene likely has a very low average abundance and fell below the automatically-determined filtering threshold. You could re-run DESeq2 with independent filtering disabled and see what difference that makes.

hi,

Yes, Ryan has the answer above, but I'd just mention that we have a section in our vignette...

vignette("DESeq2")

...for Frequently Asked Questions, one of which is "Why are some p values set to NA?"