How to deal with large files already deleted?

If you see errors like this:

> git push --set-upstream origin plp_design_package
....
remote: Resolving deltas: 100% (24/24), completed with 3 local objects.
remote: error: Trace: .......123231laksjdksjlasd
remote: error: See https://gh.io/lfs for more information.
remote: error: File codes/Mus.fa is 315.77 MB; this exceeds GitHub's file size limit of 100.00 MB
remote: error: File codes/Mus_musculus.GRCm39.dna.chromosome.1.fa is 189.22 MB; this exceeds GitHub's file size limit of 100.00 MB
remote: error: File codes/Mus_musculus.GRCm39.dna.chromosome.10.fa is 126.56 MB; this exceeds GitHub's file size limit of 100.00 MB
remote: error: GH001: Large files detected. You may want to try Git Large File Storage - https://git-lfs.github.com.
To https://github.com/account/repo.git
 ! [remote rejected] branch -> branch (pre-receive hook declined)
error: failed to push some refs to 'https://github.com/account/repo.git'

Step 1: Install BFG Repo Cleaner

wget https://repo1.maven.org/maven2/com/madgag/bfg/1.14.0/bfg-1.14.0.jar

Step 2: Remove Large Files

Remove all large files (.fa) files from history:

cd ~/repo/
java -jar bfg-1.14.0.jar --delete-files "*.fa"

Step 3: Clean Up Git

After running BFG, clean up the repository:

git reflog expire --expire=now --all
git gc --prune=now --aggressive

Step 4: Force Push the Cleaned Repo

Finally, force push your changes to rewrite history:

 git push --set-upstream origin branch

Note: In this case I am pushing to a new branch which exists locally but not remotely.

Git Cheatsheet

Beginner

| Command | Function / Outcome | |——–|———————| | git init | Create a new local Git repository in the current folder. | | git clone <url> | Download a remote repository to your local machine. | | git status | Show what has changed, what is staged, and what is untracked. | | git add <file> | Stage a specific file for the next commit. | | git add . | Stage all modified and new files. | | git commit -m "message" | Save staged changes as a new commit in the local repo. | | git log | Show the commit history. | | git diff | Show the changes in files (working directory vs last commit). | | git branch | List local branches. | | git branch <name> | Create a new branch. | | git switch <branch> | Switch to another branch. | | git switch -c <branch> | Create and switch to a new branch. | | git merge <branch> | Merge another branch into the current branch (creates a merge commit if needed). | | git pull | Fetch from remote and integrate changes (merge or rebase, depending on config). | | git push | Upload your local commits to the remote repository. | | git remote -v | Show the remote repositories linked to this repo. | | git restore <file> | Restore a file to the last committed version. | | git restore --staged <file> | Unstage a file but keep its changes. | | git reset <file> | Older way to unstage; similar to git restore --staged. | | git rm <file> | Remove a file and stage its deletion. | | git stash | Temporarily save uncommitted changes and clean the working directory. | | git stash pop | Re-apply the stashed changes and drop them from the stash. |

Rebase & pull behaviour

| Command | Function / Outcome (Beginner-speak) | |——–|————————————–| | git rebase <branch> | Replay your current branch’s commits on top of <branch> (rewrites history; keeps it linear). | | git pull --rebase | Fetch remote changes and then reapply your local commits on top (no merge commit; history is rewritten). | | git pull --no-rebase | Fetch remote changes and merge them into your branch (creates a merge commit if needed; no history rewrite). | | git pull --ff-only | Only update your branch if it can be fast-forwarded (no merge commit, no rebase); fails if histories have diverged. |

One-line rule of thumb

Private or local work → git pull –rebase
Shared or published work → git pull –no-rebase

Configuring default pull strategy

| Command | What it configures / When to use | |——–|———————————–| | git config pull.rebase false | Make git pull use merge by default in this repo. Preserves your existing commits (no history rewrite). | | git config pull.rebase true | Make git pull use rebase by default (linear history, but your local commits get new hashes). | | git config pull.ff only | Make git pull only do fast-forward updates (no merge commits; fails if local & remote have diverged). | | git config --global pull.rebase false | Same as above, but applies to all repositories for your user. | | git config --global user.name "<name>" | Set your global Git username (for commit metadata). | | git config --global user.email "<email>" | Set your global Git email (for commit metadata). |