RTC does not run in deep sleep. You should manage to wake up every second, increase the RTC and go to sleep again.
Really thanks for your reply. So I need to wake up from WDT interrupt and then need to update the RTC. Is that right?
Yes; If you set your deep-sleep WDT to 1 second, and wakeup to increment the RTC each second that should fix the RTC not running while asleep.