I ran into a similar issue. Since it is a "Custom File Source", the first source just listing folder/file path for all existing files. Next operator "Split Reader" will read the content of the file. "Custom File Source" went to "finished" state after first couple secs. That's way we got this error message "Custom File Source (1/1) is not being executed at the moment. Aborting checkpoint". Because the "Custom File Source" finished already.
Is this by design? Although the "Custom File Source" finished in secs, the rest of the pipeline can running for hours or days. Whenever anything went wrong, the pipeline will restart and start to reading from the beginning again, since there is not any checkpoint. -- Sent from: http://apache-flink-user-mailing-list-archive.2336050.n4.nabble.com/