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Weird Behaviour of Oracle 11g to 12C

My application runs select sql queries using JDBC driver on Oracle and stores the data in Result set. Then by using buffer writer/file writer writes information to xml.

** Weird Behaviour : Same code when runs with Oracle 11g takes 2 hrs to complete and for 12 C it takes @ 12 hrs.

** JDBC driver I am using is compatible with 11g and 12c. Data is same on both the DBs. Both DB are independent instance, so no question of migration problems. Can somebody please help, what how can I debug for this ?

** select queries uses bind parameter IN clause and has 1000 values in it.

IT seems, there is a bug with Oracle 12C. Working with Oracle support.

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