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Well, you've really given us nothing to work with here (and are you sure you don't know the answers to any of those questions? You have root shell access, but don't know what OS you're running?), so all I can suggest is, "whatever you did to get the certificate in the first place, do it again."
If you have a shared IP address, I don't think you have root shell access. Instead, you're using some sort of shared hosting--you'll need to ask your hosting provider why the automatic renewal didn't work. I'd expect you could force a renewal through cPanel, but it should be happening automatically.
