Updating fails with "fatal: You are attempting to fetch c2b5b05b2d0fd7a40b9f89b4032c9695e411a388, which is in the commit graph file but not in the object database."

[reftel]

Output of brew config

HOMEBREW_VERSION: 5.1.11
ORIGIN: https://github.com/Homebrew/brew
HEAD: 6f293daa9f9f5832e13b497976335e90509886d7
Last commit: 8 days ago
Branch: stable
Core tap JSON: 18 May 07:58 UTC
Core cask tap JSON: 18 May 07:58 UTC
HOMEBREW_PREFIX: /opt/homebrew
HOMEBREW_CASK_OPTS: ["--appdir=~/Applications"]
HOMEBREW_DOWNLOAD_CONCURRENCY: 24
HOMEBREW_FORBID_PACKAGES_FROM_PATHS: set
HOMEBREW_MAKE_JOBS: 12
Homebrew Ruby: 4.0.3 => /opt/homebrew/Library/Homebrew/vendor/portable-ruby/4.0.3/bin/ruby
CPU: dodeca-core 64-bit arm_lobos
Clang: 21.0.0 build 2100
Git: 2.54.0 => /opt/homebrew/bin/git
Curl: 8.7.1 => /usr/bin/curl
macOS: 26.5-arm64
CLT: 26.5.0.0.1777544298
Xcode: 26.5
Metal Toolchain: N/A
Rosetta 2: false

Output of brew doctor

Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry or file an issue; just ignore this. Thanks!

Warning: Some installed formulae are deprecated or disabled.
You should find replacements for the following formulae:
  icu4c@77
  node@18
  pypy3.9

Warning: You have the following deprecated, official taps tapped:
  Homebrew/homebrew-bundle
Untap them with `brew untap`.

Warning: The following repositories are on the deprecated "master" branch.
The "master" branch sync will stop and this warning will become an error
when Homebrew 5.2.0 is released (no earlier than 2026-06-10).
Run `brew update` to migrate to "main":
  homebrew/bundle

Description of issue

The command brew update fails with the following error message:

==> Updating Homebrew...
fatal: You are attempting to fetch c2b5b05b2d0fd7a40b9f89b4032c9695e411a388, which is in the commit graph file but not in the object database.
This is probably due to repo corruption.
If you are attempting to repair this repo corruption by refetching the missing object, use 'git fetch --refetch' with the missing object.
Error: Fetching /opt/homebrew failed!

The commit mentioned is according to GitHub not reachable from any branch or tag, and appears to point to a non-existent tree in my git:

% pwd && git show c2b5b05b2d0fd7a40b9f89b4032c9695e411a388
/opt/homebrew
fatal: unable to read tree (bfd25b56bf422d1b4d9e8d868788c86b2935a11b)

Does anyone here have an idea of how my git could have ended up in this state?

[sueun-dev]

This looks like the local Git object DB and commit-graph got out of sync, not that Homebrew is serving a bad commit. That commit and its tree are still readable from GitHub.

I could repro the same kind of failure in a throwaway repo by writing a commit-graph, deleting the commit object, then running git fetch. git fetch --refetch restored it for me.

I’d try this first:

cd "$(brew --repo)"
git commit-graph verify
git fetch --refetch origin
brew update

If fetch still trips over the graph before it can repair things, drop the local commit-graph cache and refetch:

cd "$(brew --repo)"
rm -f .git/objects/info/commit-graph
rm -rf .git/objects/info/commit-graphs
git fetch --refetch origin
brew update

brew update-reset is the heavier fallback. It may be fine here, but I’d only use it after checking there are no local changes under /opt/homebrew, since it resets the repo.

[reftel]

Spot on! git fetch --refetch origin fixed the problem. Thank you! =)