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How to manage deploying database scripts that exceed workflow step timeout

Sometimes when we execute MSSQL or Oracle scripts they exceed the workflow step timeout.  When this happens we have no way of knowing if the script is still running... or when it completes.  This most offen happens on large Deploy to PROD updates.   We recently ran into a situation where a package line timed out and the user ended up cancelling the pkg line the following day.   A week later, either the DBA or the application team noticed that our PPM connection was still running but in a stuck state.  They had to manually kill the process.  This is the first time I have run into something that extreme.  However we need to improve our process.   Has anyone run into this?

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