The disk usage on the destination doesn't match the source. Did CCC miss some files?

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The disk usage on your startup disk does not reflect the amount of data that needs to be backed up; disk usage on the destination should be lower than disk usage on the source after making an initial backup of your startup disk. Special filesystem devices (e.g. filesystem snapshots) and some macOS service data either cannot or should not be copied to another volume. CCC automatically excludes these items to avoid problems while booting from the backup and to avoid unnecessary disk usage. That list of exclusions is documented here: Some files and folders are automatically excluded from a backup task.

CCC doesn't copy virtual memory or the Trash

The largest and most notable excluded item is the /private/var/vm/sleepimage file. The sleepimage file contains the live state of your Mac's RAM, so it will be as large as the amount of RAM that you have installed. This file is potentially very large, changes constantly and it gets recreated on startup, so CCC excludes this file from every backup task.

CCC also excludes the contents of the Trash, so you may want to empty the Trash, then compare again the source and destination.

Disk usage math is not straightforward

Disk usage is not a simple matter of adding the size of every file on a volume. Special filesystem devices (e.g. hard links) have always complicated this math, but more recently Apple has introduced more special filesystem devices that complicate this even further. The cloning feature in Apple's new APFS filesystem can lead to a scenario where it appears that you have more data on the disk than it can possibly contain, and the filesystem snapshots feature can lead to scenarios where disk usage is higher than the total size of the files on that volume. APFS also supports "sparse" files, which consume less space on disk than their file size would suggest. CCC can preserve sparse files between APFS volumes, but HFS+ does not support sparse files, so these files consume more space on an HFS+ formatted backup disk. See these sections of CCC's documentation for additional details on working with these challenges:

So how can I tell that all of my data was actually copied?

For an APFS volume, you may never be able to get accurate disk usage values that can be meaningfully compared on the source and destination. You should, however, always be able to find your files at the same location on the source and destination – you should never find an item to be missing from the destination (unless you excluded it from the backup, of course). This video will help you compare the files on the source and destination so you can verify that you're able to find your files on your backup.

For HFS+ formatted source and destination volumes, a basic enumeration of the files and folders on those volumes will give you meaningful numbers to compare. The Volume Disk Usage Details tool can help you collect this kind of enumeration. When this tool has completed scanning the source and destination volumes, you can compare the reports to find any discrepancies. You can use this tool to enumerate individual folders as well if you need to get more granular details about a discrepancy in a particular folder.

If you find a discrepancy that you cannot explain, or that appears to be errant, please let us know and we'll help you get to the bottom of it.