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I have FileVault turned on, which means that Time Machine won't back up my data while I'm logged in. Is there any way to get my MacBook to wake once at night, say 6 AM, to start a Time Machine backup and then go back to sleep when done? This way I can log out at night when I'm done with it and it can back up my home folder's sparsebundle file.

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Oops, forgot about apple.stackexchange. Can someone move this there? –  jasonh Jun 5 '11 at 19:33
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You're not off-topic here. I'd suggest you wait a day or two, and, if nobody answers, then flag for moderator attention. –  Daniel Beck Jun 5 '11 at 19:38
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When FileVault is activated, your home directory is automatically backed up upon log out (after compacting of the FileVault sparsebundle disk image) if the backup disk is connected. There's absolutely no need for you to wake your Mac. Just log out, and make sure your Mac goes to sleep afterwards with appropriate power settings. –  Daniel Beck Jun 5 '11 at 19:40
    
It won't wake up for a backup though right? Are there settings that will allow Time Machine to wake it for a backup? –  jasonh Jun 5 '11 at 19:51
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Why would you want to do that? Backup upon logout, and you're good. Since it's absolutely unnecessary, there's no such feature, AFAIK. –  Daniel Beck Jun 5 '11 at 20:16
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EDIT Whoops! Didn't read that you had to be logged out... well, I'll just leave this here, hopefully a starting point.

Not sure if this is what you want but try it and let me know:

Use Terminal to wake Mac at scheduled time:

pmset schedule wake "12/26/2009 00:00:00"

Set date as preferred. Exchange wake for sleep to put Mac to sleep at scheduled time.

UPDATE: I knew there was a way to do this with Automator: http://masonsklut.com/blog/customize-time-machine-backup-times/

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