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Yesterday I deleted an ~80GB VMWare Fusion virtual machine on my hard disk (an inbuilt 256GB SSD.) It went to the Trash, and when I emptied the Trash the computer slowed almost to a halt showing a progress bar at about 99% for over an hour. Clicking Stop had no effect except that the progress bar changed to be indeterminate. After another half hour or so, I killed Finder.

I noticed while it was trying to empty that in About This Mac > More that the disk space was entirely - 100% - filled up with yellow Other usage. (This was a big increase from before I emptied the Trash; I didn't write down the numbers before but I had only a bit of yellow Other.) The purple Backups had also all gone. Ie, trying to empty the trash completely filled the hard drive's space with Other, to the extent of removing space used by backups too.

After killing Finder, I deleted the large VM file from the Trash manually in the Terminal, using rm in ~/.Trash/. That released a lot of disk space, and after that, emptying the remaining small items in the Trash occurred quickly as normal.

I didn't look at the disk usage after that since it all seemed to be working, and I went ahead to create a new 60GB VM image. However, I noticed I was running unexpectedly low on disk space and noticed there is still a lot of Other disk usage - 187GB, in fact: 187GB "Other" disk usage on a 256GB SSD

60GB of this will be the other VM image I created today before noticing the low disk space, 20GB max (or less) will be random files in my Documents and Pictures etc, but the rest, 100GB or so, I have no idea, and I would like to recover the space. It is far more Other usage than there was before I deleted the original VM.

Finder reports the same amount of free space, as do other apps. (In fact Fusion gave me an error because it needs 48GB for one operation.) I'm fairly sure that whatever the Other is, it really exists.

I have tried:

  • Emptying the Trash in all user accounts
  • Booting in Safe Mode
  • Verifying the hard disk in Disk Utility. It found two things: "Volume bitmap needs minor repair for orphaned blocks" and "Invalid volume free block count" ("should be 7479555 instead of 5451240"). Repairing the disk (booting holding Cmd-R to boot from the repair partition) added an extra 10GB to the free disk space. (You can see there's about 30GB free; it was 20GB before repairing.)
  • Disabled Time Machine
  • Reindexed the entire hard disk in Spotlight
  • Searched the disk for large files using Grand Perspective. It only showed some system files and field in my user account (to be expected I suppose) and there was nothing unusual.
  • iPhoto and iTunes are and always have been on an external hard disk, hard-linked.

What is the cause of the huge Other usage? (Remember it increased greatly when trying to empty the Trash with the large VM image.) How can I fix it?

I am using a late-2011 model MBP with fully updated Mavericks, and a 256GB internal SSD. The virtual machines (deleted and current) are created by VMWare Fusion 6.

Update

Some time ago, during moving (not copying) a 60GB VM image from the local HDD to an external HDD, the yellow Other shrunk. I now have a reasonable amount of free space.

I still don't know what it was or how deleting from the Trash caused it, or what exactly I did to make it go away.

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