How can I fix the Git error "object file ... is empty"?

When I try to commit changes, I get this error:

error: object file .git/objects/31/65329bb680e30595f242b7c4d8406ca63eeab0 is empty
fatal: loose object 3165329bb680e30595f242b7c4d8406ca63eeab0 (stored in .git/objects/31/65329bb680e30595f242b7c4d8406ca63eeab0) is corrupt

I tried git fsck I've got:

error: object file .git/objects/03/dfd60a4809a3ba7023cbf098eb322d08630b71 is empty
fatal: loose object 03dfd60a4809a3ba7023cbf098eb322d08630b71 (stored in .git/objects/03/dfd60a4809a3ba7023cbf098eb322d08630b71) is corrupt

How can I solve this error?

I had a similar problem. My laptop ran out of battery during a Git operation. Boo.

I didn't have any backups. (N.B. Ubuntu One is not a backup solution for Git; it will helpfully overwrite your sane repository with your corrupted one.)

To the Git wizards, if this was a bad way to fix it, please leave a comment. It did, however, work for me... at least temporarily.

Step 1: Make a backup of folder .git (in fact I do this in between every step that changes something, but with a new copy-to name, e.g., .git-old-1, .git-old-2, etc.):

cd ~/workspace/mcmc-chapter
cp -a .git .git-old

Step 2: Run git fsck --full

git fsck --full

error: object file .git/objects/8b/61d0135d3195966b443f6c73fb68466264c68e is empty
fatal: loose object 8b61d0135d3195966b443f6c73fb68466264c68e (stored in .git/objects/8b/61d0135d3195966b443f6c73fb68466264c68e) is corrupt

Step 3: Remove the empty file. I figured what the heck; it's blank anyway.

rm .git/objects/8b/61d0135d3195966b443f6c73fb68466264c68e

rm: remove write-protected regular empty file `.git/objects/8b/61d0135d3195966b443f6c73fb68466264c68e'? y

Step 3: Run git fsck again. Continue deleting the empty files. You can also cd into the .git directory and run find . -type f -empty -delete -print to remove all empty files. Eventually Git started telling me it was actually doing something with the object directories:

git fsck --full

Checking object directories: 100% (256/256), done.
error: object file .git/objects/e0/cbccee33aea970f4887194047141f79a363636 is empty
fatal: loose object e0cbccee33aea970f4887194047141f79a363636 (stored in .git/objects/e0/cbccee33aea970f4887194047141f79a363636) is corrupt

Step 4: After deleting all of the empty files, I eventually came to git fsck actually running:

git fsck --full

Checking object directories: 100% (256/256), done.
error: HEAD: invalid sha1 pointer af9fc0c5939eee40f6be2ed66381d74ec2be895f
error: refs/heads/master does not point to a valid object!
error: refs/heads/master.u1conflict does not point to a valid object!
error: 0e31469d372551bb2f51a186fa32795e39f94d5c: invalid sha1 pointer in cache-tree
dangling blob 03511c9868b5dbac4ef1343956776ac508c7c2a2
missing blob 8b61d0135d3195966b443f6c73fb68466264c68e
missing blob e89896b1282fbae6cf046bf21b62dd275aaa32f4
dangling blob dd09f7f1f033632b7ef90876d6802f5b5fede79a
missing blob caab8e3d18f2b8c8947f79af7885cdeeeae192fd
missing blob e4cf65ddf80338d50ecd4abcf1caf1de3127c229

Step 5: Try git reflog. Fail because my HEAD is broken.

git reflog

fatal: bad object HEAD

Step 6: Google. Find this. Manually get the last two lines of the reflog:

tail -n 2 .git/logs/refs/heads/master

f2d4c4868ec7719317a8fce9dc18c4f2e00ede04 9f0abf890b113a287e10d56b66dbab66adc1662d Nathan VanHoudnos <[email protected]> 1347306977 -0400    commit: up to p. 24, including correcting spelling of my name
9f0abf890b113a287e10d56b66dbab66adc1662d af9fc0c5939eee40f6be2ed66381d74ec2be895f Nathan VanHoudnos <[email protected]> 1347358589 -0400    commit: fixed up to page 28

Step 7: Note that from Step 6 we learned that the HEAD is currently pointing to the very last commit. So let's try to just look at the parent commit:

git show 9f0abf890b113a287e10d56b66dbab66adc1662d

commit 9f0abf890b113a287e10d56b66dbab66adc1662d
Author: Nathan VanHoudnos <nathanvan@XXXXXX>
Date:   Mon Sep 10 15:56:17 2012 -0400

    up to p. 24, including correcting spelling of my name

diff --git a/tex/MCMC-in-IRT.tex b/tex/MCMC-in-IRT.tex
index 86e67a1..b860686 100644
--- a/tex/MCMC-in-IRT.tex
+++ b/tex/MCMC-in-IRT.tex

It worked!

Step 8: So now we need to point HEAD to 9f0abf890b113a287e10d56b66dbab66adc1662d.

git update-ref HEAD 9f0abf890b113a287e10d56b66dbab66adc1662d

Which didn't complain.

Step 9: See what fsck says:

git fsck --full

Checking object directories: 100% (256/256), done.
error: refs/heads/master.u1conflict does not point to a valid object!
error: 0e31469d372551bb2f51a186fa32795e39f94d5c: invalid sha1 pointer in cache-tree
dangling blob 03511c9868b5dbac4ef1343956776ac508c7c2a2
missing blob 8b61d0135d3195966b443f6c73fb68466264c68e
missing blob e89896b1282fbae6cf046bf21b62dd275aaa32f4
dangling blob dd09f7f1f033632b7ef90876d6802f5b5fede79a
missing blob caab8e3d18f2b8c8947f79af7885cdeeeae192fd
missing blob e4cf65ddf80338d50ecd4abcf1caf1de3127c229

Step 10: The invalid sha1 pointer in cache-tree seemed like it was from a (now outdated) index file (source). So I killed it and reset the repository.

rm .git/index
git reset

Unstaged changes after reset:
M    tex/MCMC-in-IRT.tex
M    tex/recipe-example/build-example-plots.R
M    tex/recipe-example/build-failure-plots.R

Step 11: Looking at the fsck again...

git fsck --full

Checking object directories: 100% (256/256), done.
error: refs/heads/master.u1conflict does not point to a valid object!
dangling blob 03511c9868b5dbac4ef1343956776ac508c7c2a2
dangling blob dd09f7f1f033632b7ef90876d6802f5b5fede79a

The dangling blobs are not errors. I'm not concerned with master.u1conflict, and now that it is working I don't want to touch it anymore!

Step 12: Catching up with my local edits:

git status

# On branch master
# Changes not staged for commit:
#   (use "git add <file>..." to update what will be committed)
#   (use "git checkout -- <file>..." to discard changes in working directory)
#
#    modified:   tex/MCMC-in-IRT.tex
#    modified:   tex/recipe-example/build-example-plots.R
#    modified:   tex/recipe-example/build-failure-plots.R
#
< ... snip ... >
no changes added to commit (use "git add" and/or "git commit -a")


git commit -a -m "recovering from the git fiasco"

[master 7922876] recovering from the git fiasco
 3 files changed, 12 insertions(+), 94 deletions(-)

git add tex/sept2012_code/example-code-testing.R
git commit -a -m "adding in the example code"

[master 385c023] adding in the example code
 1 file changed, 331 insertions(+)
 create mode 100644 tex/sept2012_code/example-code-testing.R

The Git object files have gone corrupt (as pointed out in other answers as well). This can happen during machine crashes, etc.

I had the same thing. After reading the other top answers here I found the quickest way to fix the broken Git repository with the following commands (execute in the Git working directory that contains the .git folder):

(Be sure to back up your Git repository folder first!)

find .git/objects/ -type f -empty | xargs rm
git fetch -p
git fsck --full

This will first remove any empty object files that cause corruption of the repository as a whole, and then fetch down the missing objects (as well as latest changes) from the remote repository, and then do a full object store check. Which, at this point, should succeed without any errors (there may be still some warnings though!)

PS. This answer suggests you have a remote copy of your Git repository somewhere (e.g. on GitHub) and the broken repository is the local repository that is tied to the remote repository which is still intact. If that is not the case, then do not attempt to fix it the way I recommend.

This error happens to me when I am pushing my commit and my computer hangs.

This is how I've fix it.

Steps to fix

git status

Show the empty/corrupt object file

rm .git/objects/08/3834cb34d155e67a8930604d57d3d302d7ec12

remove it

git status

I got fatal: bad object HEAD message

rm .git/index

I remove the index for the reset.

git reset

fatal: Could not parse object 'HEAD'.

git status
git pull

Just to check what's happening

tail -n 2 .git/logs/refs/heads/MY-CURRENT-BRANCH

It prints the last two lines, tail -n 2, of the log branch to show my last two commit hashes.

git update-ref HEAD 7221fa02cb627470db163826da4265609aba47b2

I pick the last commit hash

git status

It shows all my file as deleted, because i removed the .git/index file

git reset

Continue to the reset

git status

Verify my fix