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Why is there a progress bar when my Mac is starting up?

Update: As several of our commenters pointed out, the OS is probably running the fsck utility in the background to repair directory problems, while showing the progress bar to the end user so they know there's something going on (fsck can take quite a while). Here's an older Apple support article that explains the disk repair process very well. We will update you if we find a support article with more information.

Here's a story for anyone who's come across an unusual progress bar during boot and my best guess at what it really is. The moral of my story: backup frequently and try not to turn off your Mac while it is starting up.

Five days ago, I was prepping my late 2008 MacBook Pro for resale when I encountered the ever-spinning gear at boot. Ridiculously enough, I hadn't kept up any of my backups in a month and I hard powered off the machine while it was booting because I forgot to select the boot drive (yes -- I'm a technician and I did something dumb -- I know). Many thoughts went through my head: I've lost the last month's worth of work, I have to waste hours trying to recover data from my drive, why did this have to happen while I was trying to back it up? It goes to show that it can happen to anyone at any time and that the only real solution is to keep a current backup (if not several) of all your information.

Now for a quick word on backups. I usually keep a continuous Time Machine backup of everything and clone my internal drive every couple weeks. The cloned drive is kept in a fireproof safe here in my house. Also, as much as I love Time Machine, in my profession, I've seen several instances where Time Machine backups don't restore properly. I always suggest having a manual clone as a backup to your backup.
So, I didn't have a good backup, my clone was old and now my computer wouldn't boot into the operating system -- it just hung at the spinning gear. As any technician would, I booted to my diagnostic drive and tried to repair the disk with Disk Utility. Repair failed! After being told that Disk Utility couldn't fix my drive and that I would have to restore my computer from a backup, I was pretty frustrated. I restarted the machine and went to get a drink. 5 minutes later, I'm back to the computer and I see a progress bar at the bottom of the screen. It took 20 minutes, but after it was done, the machine loaded back to my desktop and life was good again. Impressive.

Until the introduction of Snow Leopard, I would have ran Disk Warrior or "archive and install" the operating system in hopes to fix the software issue, but this automated solution was relatively painless and built into the OS. I began looking for an explanation of what it's doing during that progress bar, but didn't find much. What I read were incorrect guesses about firmware. While firmware updates use a similar progress bar, my situation had nothing to do with firmware but software corruption that it appeared to fix on its own. TUAW's Joachim Bean noticed this support article show up on Apple's website today but it's still very vague on details. In fact, it just tells you what it is and why it appears, but not what it's doing. Obviously something is fixing the software corruption I caused by killing the machine mid-boot. Why can this startup procedure fix it when Disk Utility's repair disk function could not?

So, what can my experience pass on to the Mac newbies in the audience? Don't turn off your computer mid-boot and never skimp on your backup. If you find yourself in a situation where the progress bar shows up during boot, stay the course and let it finish. In the support article, it says it's possible that you may encounter this every time you boot -- in that instance, you probably have a hardware issue. If it only appears once, don't fret but instead make sure you have a good backup in case something goes awry. When in doubt, consult with your local Genius Bar or Apple Authorized Service Provider.

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Update: As several of our commenters pointed out, the OS is probably running the fsck utility in the background to repair directory...