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In virtualmin each virtual-server is configured to run under its own user/group, so if you get permission error when working with your script or FTP the permissions are not set properly.

This can be easily fixed by running Virtualmin permission fix script. To do so, login to your Virtualmin panel and navigate to Limits and Validation -> Validate Virtual servers -> Fix permissions, set Also fix sub-servers to Yes and finally click on Fix Permissions now