Clean combustion parts, clean air intake, get more air to water heater and see if problem continues.
Look at color of burner flame and pilot flame: if flame has yellow-and-orange instead of clear blue flame, then combustion parts need cleaning.
Pilot and burner problems can be caused by bad thermocouple, thermocouple not sitting in flame, weak pilot flame due to dirty tube or low gas pressure, air in gas line, no draft up vent, backdraft coming down vent, dirty combustion parts, clogged air intake, insufficient air, insufficient air quality, hot attic, bad gas control valve, etc.
Open following link for pdf resources, and illustrations for cleaning combustion parts, and some service manuals:http://waterheatertimer.org/How-to-install-gas-water-heater.html#troubleshoot
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