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Use fsck in Single-User Mode
In some cases, even Safe Mode or Disk Utility in OS X Recovery won’t be enough to fix problems. You may need to boot your Mac into single-user mode and run the fsck (file system check) command the old-fashioned way. You don’t need to do this if any of the above steps worked. This is the thing you should try last, as Disk Utility in the recovery environment may work better and be more capable.
To do this, start your Mac in single-user mode. Restart it, and then press and hold the Command+S keys while it boots.
You’ll enter single-user mode, which will provide you with a text-mode terminal. Type the following command into the terminal and press Enter to start a file system check:
/sbin/fsck -fy
The command will run through several phases of checks. When it’s done, you’ll see a message saying “** The volume [name] appears to be OK” if everything is fine.
If it found problems, you’ll see a “***** FILE SYSTEM WAS MODIFIED *****” message. This indicates the fsck command found and fixed problems. The fsck command may find additional errors after repairing the first batch of errors, so Apple recommends you run the fsck command again if it found and fixed problems. Run the above fsck command over and over until you see a “** The volume [name] appears to be OK” message.
When the fsck command says your disk is okay, type the following command at the terminal and press Enter:
reboot
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