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It sounds like the JDBC Query Consumer origin is in Full mode, and is configured to repeat the query according to the configured Query Interval. It's doing exactly what it's supposed to do with this configuration. This is intended for cases where you need to overwrite data in a destination periodically.

If you want the pipeline to stop once the query is complete, you need to add a Pipeline Finisher executor, triggered by the origin's no-more-data event. This case study shows how.