Disk space - huge portion not accounted for

Question

I am running a mini server (mac 3,1). 10.9.2 ans server 3.0. My server service data is on an external disk. The startup drive is a 500GB drive. Doing Get info on that drive shows a capacity of 499 GB. 412 GB used, 86 GB free.
Looking at all the files on the Starup drive, the tolal space used according to Finder is 245 GB. I used a utility (InVisible) to show all invisible files, and an additional 13 GB of content appeared (private, usr). This gives me a total of close to 260 GB. Why is my drive showing only 86 Gb free, it should be closer to 245 - 250 GB.
I did maintenance and cleaning on the startup drive using Onyx before taking these stats, that freed up about 4 GB.
Any suggestions on how to free or see what is taking all this space? Thanks in advance.

Answer 1

You can use a tool such as OmniDiskSweeper (ODS) or GrandPerspective (GP) to explore the volume and find out what's taking up the space. You can also delete files with it, but don't do that unless you're sure that you know what you're deleting and that all data is safely backed up. That means you have multiple backups, not just one. Note that ODS only works with OS X 10.8 or later. If you're running an older OS version, use GP.
ODS or GP can't see the whole filesystem when you run it just by double-clicking; it only sees files that you have permission to read. To see everything, you have to run it as root.
Back up all data now.
If you have more than one user account, make sure you're logged in as an administrator. The administrator account is the one that was created automatically when you first set up the computer.
Install the app you downloaded in the Applications folder as usual. Quit it if it's running.
Triple-click anywhere in the corresponding line of text below on this page to select it, then copy the selected text to the Clipboard by pressing the key combination command-C:
sudo /Applications/OmniDiskSweeper.app/Contents/MacOS/OmniDiskSweeper
sudo /Applications/GrandPerspective.app/Contents/MacOS/GrandPerspective
Launch the built-in Terminal application in any of the following ways:
☞ Enter the first few letters of its name into a Spotlight search. Select it in the results (it should be at the top.)
☞ In the Finder, select Go ▹ Utilities from the menu bar, or press the key combination shift-command-U. The application is in the folder that opens.
☞ Open LaunchPad. Click Utilities, then Terminal in the icon grid.
Paste into the Terminal window by pressing command-V. You'll be prompted for your login password, which won't be displayed when you type it. You may get a one-time warning to be careful. If you see a message that your username "is not in the sudoers file," then you're not logged in as an administrator.
The application window will open, eventually showing all files in all folders, sorted by size. It may take a few minutes for the app to finish scanning.
I don't recommend that you make a habit of doing this. Don't delete anything as root. If something needs to be deleted, make sure you know what it is and how it got there, and then delete it by other, safer, means. When in doubt, leave it alone or ask for guidance.
When you're done with the app, quit it and also quit Terminal.