System software updates require a stock phone with stock recovery. Rooting and/or custom recovery will break OTA updates. You'll have to unroot or temporarily disable root (if your SU supports it) and try that way. If you deleted system apps (bloat), that can also break OTA.
Samsung Galaxy S® 4 MJA Rooted with CF Auto-Root Tutorial
HTC EVO Design 4G™ v4.0.3 Bootloader Unlocked & Rooted with HTC SuperTool v3
If it ain't broke, use a sledge hammer.