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SQL Compare hangs on the "Owner mapping" tab

I am comparing two database with different schema name. The database has around 50k tables but i need to compare only 100 tables. After entering Source and Target database, when I click the tab "Owner mapping", it start to process but hangs at the step "Analyzing your mappings: 0%". I am thinking it is due to large number of tables. Is there a way or options to make it look for only 100 tables which i am concerned about?

I am checking out command line, but I see option to compare only one table and I do not see syntax to specify comparing two different schemas.
Ratha
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