How do I fix "remote: fatal error in commit_refs" errors trying to push with Git?

Question

When I try to push to master branch that is hosted on https://github.com I get:

remote: fatal error in commit_refs

How can I solve this?

Where is the remote repository hosting/located? Might be that this is corrupt? — André Schild, May 20 '16 at 08:51
Thank you for helping! The remote is github. Seems it was a local error (none of the others working against the same repo have had this issue). — Tomas Skogberg, May 20 '16 at 13:21
This seems to be a recent GitHub issue, see also http://pastebin.com/50BL9YTF and http://blastedbio.blogspot.co.uk/2016/05/sync-github-mirror-with-cron.html also from 20 May 2016. — Peter Cock, May 23 '16 at 13:39
None of the above solved my issue. However, a good old system restart did. — Balázs Koskóci, Sep 25 '17 at 21:44
same here, it seems to happen once in a while. restarting the system and just trying the next day makes the problem go away for me. — Peter Kunszt, May 05 '23 at 06:26

score 1065 · Answer 1 · edited May 04 '23 at 15:57

1065

In my case, GitHub was down by the time I was trying to push.

Just check https://www.githubstatus.com to know about GitHub site status.

When it's up you'll be able to push.

edited May 04 '23 at 15:57

Benjamin Loison

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answered Jun 05 '17 at 19:17

vicke4

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I waited 10 minutes while https://www.githubstatus.com/ was reporting OK status – mirelon Mar 27 '23 at 12:34
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Waiting worked for me, even though everything was shown as online – Cyrill Mar 27 '23 at 13:55
I went to githubstatus.com, read "All Systems Operational", and then assumed that wasn't it. 15 minutes later, githubstatus.com showed that GitHub was down. – Throw Away Account May 17 '23 at 04:58

score 155 · Answer 2 · answered May 20 '16 at 08:41

155

This fixed it for me:

git gc

That will start a garbage collection that resolved my error.

answered May 20 '16 at 08:41

Tomas Skogberg

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`git gc` didn't solve it for me, but `git fsck` and then `git gc` did it. – dchest Jun 02 '17 at 14:24
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docs: [git fsck](https://git-scm.com/docs/git-fsck) and [git gc](https://git-scm.com/docs/git-gc) – djvg Dec 01 '21 at 08:28
This worked for me also. Good to do some preventative maintenance on a regular basis. – Chris Ballance May 04 '23 at 16:58

score 16 · Answer 3 · answered Nov 16 '16 at 22:31

16

Make sure your repo is online.

I got this error today when attempting to push to github and then couldn't even browse the site without getting their unicorn error message.

answered Nov 16 '16 at 22:31

sirclesam

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score 5 · Answer 4 · answered Aug 02 '16 at 02:00

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Try rebase the current branch on top of the upstream branch after pull, e.g.

git pull origin master -r

then push it again:

git push origin master

answered Aug 02 '16 at 02:00

kenorb

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Lol i tried that earlier today, and my repository got absolutely empty cuz it didn't want to push it back, luckily I have all my files saved in my code editor and in backup, but yeah apparently github's down... – PrezOfTheUnitedIdiots Aug 10 '21 at 15:48

score 4 · Answer 5 · answered Jun 01 '16 at 15:52

I raised this with GitHub in relation to http://blastedbio.blogspot.co.uk/2016/05/sync-github-mirror-with-cron.html and it turned out to be due to protected branch settings. GitHub have improved the error message:

$ git push mirror master
Counting objects: 391, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (391/391), done.
Writing objects: 100% (391/391), 99.28 KiB | 0 bytes/s, done.
Total 391 (delta 298), reused 0 (delta 0)
remote: error: GH006: Protected branch update failed for refs/heads/master.
remote: error: You're not authorized to push to this branch. Visit https://help.github.com/articles/about-protected-branches/ for more information.
To git@github.com:HuttonICS/biopython.git
 ! [remote rejected] master -> master (protected branch hook declined)
error: failed to push some refs to 'git@github.com:HuttonICS/biopython.git'

If you try again now you ought to get a more constructive error report. In my case I needed to adjust my protected branch settings as per https://help.github.com/articles/about-protected-branches/

In my case the problem was also caused by protected branch settings. — Mouse, Nov 01 '16 at 03:50

score 3 · Answer 6 · answered Apr 30 '19 at 16:54

From my experience, there is now (2019) some rate limit on GitHub that causes this problem for me when mass-pushing tens of huge repositories. It can also cause "cannot read" problem in random cases.

When I delay for 30 seconds before each push, both problems go away and I can continue with hundreds of repos without a glitch (sigh, don't even ask).

score 3 · Answer 7 · answered Aug 10 '21 at 16:26

3

Opening a new terminal and trying worked for me.

answered Aug 10 '21 at 16:26

Brian F

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May have just been lucky and done this as github went back up. – Smern Aug 10 '21 at 18:17

score 0 · Answer 8 · answered Jun 08 '17 at 21:49

0

In my case I suspect a hung git process was causing the problem; I killed it and retried and the problem went away.

answered Jun 08 '17 at 21:49

rakslice

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This was the most similar to my issue - I just needed to close VSCode, which likely had a git process working in the background that was hung for some reason. – Pro Q May 04 '23 at 16:06

score -3 · Answer 9 · answered Jun 05 '17 at 19:15

-3

Pulling down latest code from the branch solved it for me:

git pull origin master
git push origin master

answered Jun 05 '17 at 19:15

Fellow Stranger

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How do I fix "remote: fatal error in commit_refs" errors trying to push with Git?

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