My primary disk is almost full (~250GB free 19GB), checking System Information on Storage tab I see that System takes ~196GB: enter image description here

Clicking on Manage I can confirm that most the space used is assigned to System: enter image description here

Report using df

df -h
Filesystem      Size  Used Avail Use% Mounted on
/dev/disk2s1    233G  215G   18G  93% /
/dev/disk2s4    233G   20K   18G   1% /private/var/vm

And du:

sudo du -xhd 1 /
0   /.HFS+ Private Directory Data
4.1G    /usr
913M    /.Spotlight-V100
0   /.PKInstallSandboxManager-SystemSoftware
2.7M    /bin
0   /Network
1.2M    /sbin
3.8G    /Library
7.3G    /System
1.8M    /.fseventsd
5.4G    /private
1.1G    /.DocumentRevisions-V100
0   /.vol
19G /Users
18G /Applications
177M    /opt
0   /Volumes
0   /cores
59G /

This simply does not add up. I'm not able to understand where those 196GB come from...

I've run diskutil to ckeck for errors:

Verifying file system.
Volume could not be unmounted.
Using live mode.
Performing fsck_apfs -n -l -x /dev/rdisk2s1
Checking volume.
Checking the container superblock.
Checking the EFI jumpstart record.
Checking the space manager.
Checking the object map.
Checking the APFS volume superblock.
Checking the object map.
Checking the fsroot tree.
Checking the snapshot metadata tree.
error: btn:1: invalid key order (1) oid 631545 / oxid 288900
Snapshot metadata tree is invalid.
The volume /dev/rdisk2s1 could not be verified completely.
File system check exit code is 0.
Restoring the original state found as mounted.
Operation successful.

The test passes but there is an error Snapshot metadata tree is invalid. which googling relates to Timemachine, which I never used, just to be sure run tmutil listlocalsnapshots / which outputs nothing.

Any ideas how to track what's messing with the disk?

  • The test didn't pass, it just completed. Try restarting in recovery mode (holding down ⌘ and R at the chime). Open the disk utility from there and then try to verify and repair the disk. Maybe the metadata isn't reporting the disk space correctly. – MJ Walsh Feb 5 '19 at 11:56

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