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Based on the message you are receiving, I expect you have RDS running, but are not aware of it. Perhaps it's running in a different region from the one you normally use? Your AWS Bill should indicate if you have RDS running and what region it is running in. Go to the AWS Service "Billing" and select Bills in the left menu panel. In the tab Charges by Service, you should be able to find RDS (Relational Database Service). If you expand (click on the plus) the entry, it should tell you the region that the resources are running in.
If you decide to delete the RDS resources, by default RDS will attempt to make a final snapshot backup. If you do not want the backups, then you should unselect the final snapshot and also verify that any backups/snapshots of the database have been deleted.
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You are right, there was an instance running in another region. Thanks a lot.