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I have just inherited a server and qmail is set up as the default mailserver. It is running however there is also a postfix mail server installed and all mails are being queued in it's mailqueue skipping the qmail.

Since postfix is not running, these emails are not getting delivered.

I have been searching for 2 days looking for a solution, The thing is this is a live server and emails being using pop or imap are working. Just not those that are sent using using scripts.

Does anybody have any idea how stop the system messages going into the wrong mail queue, and why they would even be doing so?

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Scripts etc are normally queued using /usr/sbin/sendmail. In your case, that's still the postfix local mail agent. You need to make sure that that is a symlink to /var/qmail/bin/sendmail instead.

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