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Snapshot invalid?

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Jan 24, 2016
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Motherboard
z170i
CPU
6700K
Graphics
Radeon 580
Mac
  1. MacBook Pro
Classic Mac
  1. Power Mac
Mobile Phone
  1. iOS
I recently noticed that my main drive was severely low on space. Checking the storage tab, I noticed that the System was taking 180GB of space. daisyDisk tells me there is around 100GB of "still hidden" stuff which I can't seem to get eyes on.

Running tmutil listlocalsnapshots / returns an empty list, so there are no snapshots. BUT, running fsck_apfs -ln:

** Checking the container superblock.
** Checking the EFI jumpstart record.
** Checking the space manager.
** Checking the space manager free queue trees.
** Checking the object map.
** Checking volume.
** Checking the APFS volume superblock.
** The volume Eren was formatted by hfs_convert (748.31.8) and last modified by apfs_kext (945.250.134).
** Checking the object map.
** Checking the snapshot metadata tree.
** Checking the snapshot metadata.
** Checking snapshot 1 of 1.
error: apfs_extentref: btn: invalid o_oid (0x0)
Snapshot is invalid.
** The volume /dev/disk2 could not be verified completely.

So, it looks like there is a snapshot, but tmutil doesn't see it? I've tried running fsck_apfs -y after dropping to single user mode (command-s on startup) to no avail. Any other suggestions?
 
Maybe a dumb question, but have you used ShowAllFiles to check out your file system? I had a similar problem recently and discovered a nearly complete duplicate of all my system files in a hidden folder, plus a lot of other folders that looked like garbage taking up a huge amount of space. I saw all this about 2 weeks ago when Time Machine stopped making new backups AND SuperDuper clone failed, returning a lengthy error log. I sent error log to SuperDuper and they said my disk was corrupt which got me looking more closely at my file system. I tried First Aid and fsck repairs but couldn’t get it to verify or repair. I decided to wipe and do a fresh install as my important data is stored on non-system drives and I didn’t have time to mess around with the strange mess of hidden folders & files. If this is similar to your situation, you might be able to get rid of some of the hidden files and get it repaired vs a fresh install. Good luck.
 
Yeah, its not a hidden file issue. I'm fairly sure the invalid snapshot is the real problem. Even if it is a red herring, I'd like to clean it up.
 
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