Tons of Errors when using Disk Repair

Sorry for the long reply... not sure if you still have this problem, but I have a solution. I recently came across this problem. It is caused (in my case) by corrupted snapshots of the TimeMachine Backup. (in my case, I used a 3rd party utility called CleanMyMac X to clean up files, clutter, etc., and it corrupted the TimeMachine Backup).

The way to fix it is to follow these directions that I got a long time ago from another site (sorry original author, I can't remember where it came from); once you follow these directions, restart(reboot) the Mac and run a FirstAid in Disk Utility and you will see all the errors that you had have gone (it's been fixed).

**IMPORTANT**-- when you delete the snapshots (as described below) you need to understand that your TimeMachine backups are GONE. So... AFTER you follow the procedure below and restart/reboot, you will need to create a NEW TimeMachine backup for protection.

AND.... these instructions are provided to you "AS IS".... no guarantee they will work... no guarantee that they won't cause other problems. In my case, all works normally after doing it, but I can't attest that nothing bad will happen. If you're nervous about following the directions, then don't (and take it to an Apple/Mac repair place).

Here's the directions:

DELETE LOCAL SNAPSHOTS

• Launch the Terminal (from Applications > Utilities), and then copy and paste this command and press Return:

tmutil listlocalsnapshots /

• The Terminal will show a list of local snapshots with names like: com.apple.TimeMachine.2018-03-01-002010

To remove a snapshot:

• Copy and paste this command: sudo tmutil deletelocalsnapshots
• DO NOT HIT RETURN/ENTER YET... BUT... at this point at the end of the line above, type a space and then paste in the date portion of the snapshot.
• Press Return, and finally press Return.

Altogether, using the example snapshot above, that looks like:

• sudo tmutil deletelocalsnapshots 2018-03-01-002010

If it deletes properly, you’ll see: Delete local snapshot '2018-03-01-002010' in the Terminal as the response. This means the command completed successfully.

For more than one snapshot, repeat the steps as needed above until they are all gone.

Keep in mind that you may not know which snapshot caused the problem; it could be any or all of them.

Good luck!

~~Russ.

Volume could not be unmounted.

Using live mode.

You are still mounted to volume.

Boot into Internet Recovery mode and run your First Aid again on your Macintosh HD.

Internet Recovery http://support.apple.com/kb/HT4718

or from a bootable installerUSB and run Disk Utility from there, and try again.

If errors are found and repaired, run it again until it reports no errors.

If this does not sort your issue—restore from a current backup.

fs tree invalid on APFS

Download and run Etrecheck.  Copy and paste the results into your reply. Etrecheck is a diagnostic tool that was developed by one of the most respected users here in the ASC and recommended by Apple Support  to provide a snapshot of the system and help identify the more obvious culprits that can adversely affect a Mac's performance.

Use the Add Text button to include the report in your reply:

Same error codes although slightly better off than you. Bluetooth repeatedly fails for me however, everything else seems to be running normally still. Disk Utility's first aid function doesn't fix the problem although it appears to speed up the process slightly each time.

I have done six or seven runs after booting to recovery mode, and three from single-user mode.

The same error messages show up every time. That is, Disk Utility is not clearing the errors.

Now to be fair, it's calling them "warnings" but the message that extents listed in an extents tree cannot be found in the actual extents storage. I have some directories that are acting corrupted and I want to fix them.

My disk is 1 GB and takes quite a while to back up or restore - on the order of 12+ hours on my slow old machine. I do have a Time Machine backup on a NAS and I'm not really looking forward to using it. Doing a restore is not desirable.

Same problem here, and I have many folder corrupted, I can no longer access my 900 GB Photos library.

Disk Utility is unable to repair, and no other tool supports APFS (DiskWarrior, Techtool Pro, etc.).

My corrupted volume is a Fusion Drive that was automatically converted to APFS with Mojave install in October. Was working fine and had no Disk Util error until today.

Checking the container superblock.

Checking the fusion superblock.

Checking the EFI jumpstart record.

Checking the space manager.

Checking the space manager free queue trees.

Checking the object map.

Checking the Fusion data structures.

Checking volume.

Checking the APFS volume superblock.

The volume iMacSSD was formatted by hfs_convert (945.200.129) and last modified by apfs_kext (945.230.6).

Checking the object map.

Checking the snapshot metadata tree.

Checking the snapshot metadata.

Checking snapshot 1 of 13.

warning: Cross Check : FSroot tree references extent (0x40000315d5724 + 2) which is not present in the ExtentRef tree

warning: fe_val: object (oid 0x17): fext (phys_block_num 1125900735043364 len 2) not found in extentref tree

warning: Cross Check : FSroot tree references extent (0x40000315d5722 + 2) which is not present in the ExtentRef tree

warning: fe_val: object (oid 0x19): fext (phys_block_num 1125900735043362 len 2) not found in extentref tree

warning: Cross Check : FSroot tree references extent (0x40000005a12ea + 2) which is not present in the ExtentRef tree

warning: fe_val: object (oid 0x7b): fext (phys_block_num 1125899912745706 len 2) not found in extentref tree

warning: Cross Check : FSroot tree references extent (0x40000005a12f0 + 2) which is not present in the ExtentRef tree

warning: fe_val: object (oid 0xe1): fext (phys_block_num 1125899912745712 len 2) not found in extentref tree

warning: Cross Check : FSroot tree references extent (0x40000112320c5 + 1) which is not present in the ExtentRef tree

warning: fe_val: object (oid 0x1b6): fext (phys_block_num 1125900194357445 len 1) not found in extentref tree

warning: Cross Check : FSroot tree references extent (0x400001d1706d8 + 24) which is not present in the ExtentRef tree

warning: fe_val: object (oid 0x1b9): fext (phys_block_num 1125900394890968 len 24) not found in extentref tree

warning: Cross Check : FSroot tree references extent (0x400003339a4f6 + 2) which is not present in the ExtentRef tree

warning: fe_val: object (oid 0x1b58): fext (phys_block_num 1125900766258422 len 2) not found in extentref tree

warning: Cross Check : FSroot tree references extent (0x400003339a4f8 + 2) which is not present in the ExtentRef tree

warning: fe_val: object (oid 0x1b59): fext (phys_block_num 1125900766258424 len 2) not found in extentref tree

warning: Cross Check : FSroot tree references extent (0x400003339a4fa + 2) which is not present in the ExtentRef tree

warning: fe_val: object (oid 0x1b5a): fext (phys_block_num 1125900766258426 len 2) not found in extentref tree

warning: Cross Check : FSroot tree references extent (0x400003339a4fc + 4) which is not present in the ExtentRef tree

warning: fe_val: object (oid 0x1b5b): fext (phys_block_num 1125900766258428 len 4) not found in extentref tree

warning: Cross Check : FSroot tree references extent (0x400003339a504 + 2) which is not present in the ExtentRef tree

warning: fe_val: object (oid 0x1b5f): fext (phys_block_num 1125900766258436 len 2) not found in extentref tree

warning: Cross Check : FSroot tree references extent (0x400003339a506 + 2) which is not present in the ExtentRef tree

warning: fe_val: object (oid 0x1b61): fext (phys_block_num 1125900766258438 len 2) not found in extentref tree

warning: Cross Check : FSroot tree references extent (0x400003339a508 + 4) which is not present in the ExtentRef tree

warning: fe_val: object (oid 0x1b62): fext (phys_block_num 1125900766258440 len 4) not found in extentref tree

warning: Cross Check : FSroot tree references extent (0x400003339a50c + 6) which is not present in the ExtentRef tree

warning: fe_val: object (oid 0x1b63): fext (phys_block_num 1125900766258444 len 6) not found in extentref tree

warning: Cross Check : FSroot tree references extent (0x400003339a512 + 18) which is not present in the ExtentRef tree

warning: fe_val: object (oid 0x1b64): fext (phys_block_num 1125900766258450 len 18) not found in extentref tree

too many warnings generated; suppressing subsequent ones.

Checking snapshot 2 of 13.

Checking snapshot 3 of 13.

...

I am also having these problems. I have run First Aid via Disk Utility in Recovery Mode multiple times, but the errors are not cleared.

Strangely, I have the same type of problem on two different MacBook Pro's (however with different FSroot and phys_block references). The second MacBook Pro was based on a Time Machine image of the first one, about a year ago, but since then they have been separate except for sharing Dropbox files. So if Disk Utility is reacting on corrupted files shared in Dropbox folders then that might explain it. I have run Disk Utility on both in the past without errors.

Has anyone contacted Apple support and asked for assistance?

Is it advisable not to use the computer if these errors occur?

Update:

I tried running Disk Utility on a third Mac of mine, a new 2018 Mac Mini, that also shares the Dropbox files with the other two MacBooks Pros.

While the Mac Mini showed no "FSroot tree references extent" warnings like the other two MacBooks Pros, it did show a warning saying: "warning: apfs_num_other_fsobjects (79) is not valid (80)".

The Mac Mini is not created from the same image as the others were a year ago.

I am having the same problem. Have done all the Disk Utility things, etc. Everything is running really slowly and and my HD is filling up by it self. Any advice?

Thanks

Running First Aid on “Macintosh HD” (disk1s1)

NOTE: First Aid will temporarily lock the startup volume.

Verifying file system.

Volume could not be unmounted.

Using live mode.

Performing fsck_apfs -n -l -x /dev/rdisk1s1

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 Macintosh HD was formatted by hfs_convert (945.200.129) and last modified by apfs_kext (945.230.6).

Checking the object map.

Checking the snapshot metadata tree.

Checking the snapshot metadata.

Checking snapshot 1 of 3.

warning: Cross Check : FSroot tree references extent (0x5d76a + 24) which is not present in the ExtentRef tree

warning: fe_val: object (oid 0x175c): fext (phys_block_num 382826 len 24) not found in extentref tree

warning: Cross Check : FSroot tree references extent (0x747a68 + 1) which is not present in the ExtentRef tree

warning: fe_val: object (oid 0x4cdc): fext (phys_block_num 7633512 len 1) not found in extentref tree

warning: Cross Check : FSroot tree references extent (0x6b79125 + 1) which is not present in the ExtentRef tree

warning: fe_val: object (oid 0x6248): fext (phys_block_num 112693541 len 1) not found in extentref tree

warning: Cross Check : FSroot tree references extent (0x6c790 + 1) which is not present in the ExtentRef tree

warning: fe_val: object (oid 0x6257d): fext (phys_block_num 114842042 len 1) not found in extentref tree

warning: Cross Check : FSroot tree references extent (0x210d81 + 19) which is not present in the ExtentRef tree

warning: fe_val: object (oid 0x62611): fext (phys_block_num 2166145 len 19) not found in extentref tree

warning: Cross Check : FSroot tree references extent (0x210d94 + 4) which is not present in the ExtentRef tree

warning: fe_val: object (oid 0x62612): fext (phys_block_num 2166164 len 4) not found in extentref tree

warning: Cross Check : FSroot tree references extent (0x210d98 + 1) which is not present in the ExtentRef tree

warning: fe_val: object (oid 0x62614): fext (phys_block_num 2166168 len 1) not found in extentref tree

warning: Cross Check : FSroot tree references extent (0x210d99 + 1) which is not present in the ExtentRef tree

warning: fe_val: object (oid 0x62615): fext (phys_block_num 2166169 len 1) not found in extentref tree

you have to be very careful with the spelling. Look:

for d in $(tmutil listlocalsnapshotdates); do tmutil deletelocalsnapshots $d; done

listlocalsnapshotdates has no S after the T. But deletelocalsnapshots has an S after the T

Thank you @dzmitry1, I was inputting the string wrong, didn’t read that correctly only numerals, anyway password worked! Thanks for your kind response. Now I’m on to the next problem, why my container is disk3 and not in the first one... whatever! Like I said, another set of problems. I’m running out of space and Ned to uproars my 2012 MacBook Pro Retina to a newer larger capacity version.

I agree Dr Wise answers should be the solved one, it works like a charm, thank you soooo much for posting!!! Started with me after the mojave upgrade and computer has been lagging ever since, not reacting to force quit etc.

I wonder if this is a thing between external cleaning programs, I'm using Onyx and Mojave?

cheers

It's not really acceptable to get warnings and not have a way to clear them.

have this error and bluetooth that craps out and is unavailable too. This was resolved but since the upgrade to 10.14.3 just saying and adding to the numbers