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Not able to get result set object back to app with Select Query of more than 13 sec execution time

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I am using mysql server 5.5 , jdk 7 , mysql-connector-java-5.1.20 and apache tomcat server 7.0.27 in my application

When Select Query with more than 13 seconds of execution time has been passes to mysql server , i am not able to get result set back to application

Everything works fine with Query which takes shorter time then 13 sec.

I used mysql yog for same query execution which is passed from java code and its working fine there

There is not error at all on tomcat server log too can any one give me the clue for debugging

Consider Paul's rocket mass heater.
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