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Resolving GitHub's "Permission Denied (publickey)" Error

Comprehensive Guide to Authenticate and Clone Repositories Successfully

developer coding with terminal and SSH keys

Key Takeaways

  • Ensure SSH keys are correctly generated and added to both your local machine and GitHub account.
  • Verify your SSH agent is running and properly configured to use your SSH keys.
  • Double-check repository URLs and permissions to prevent access issues.

Understanding the "Permission Denied (publickey)" Error

Permission denied (publickey) indicates that GitHub cannot authenticate your connection using the provided SSH key. This authentication failure prevents you from accessing the desired repository. This guide will walk you through the steps to troubleshoot and resolve this issue comprehensively.

Step-by-Step Resolution

1. Verify Existing SSH Keys on Your Machine

Start by checking if you already have SSH keys generated on your local machine. Open your terminal and execute the following command:

ls -al ~/.ssh

Look for files named id_rsa and id_rsa.pub or id_ed25519 and id_ed25519.pub. These are your private and public SSH keys, respectively.

If you find these files, you have existing SSH keys. If not, proceed to generate a new SSH key pair.

2. Generate a New SSH Key Pair

If no SSH keys exist, generate a new SSH key pair using the following command:

ssh-keygen -t ed25519 -C "your_email@example.com"
  • Replace your_email@example.com with your GitHub-associated email address.
  • Press Enter to accept the default file location (~/.ssh/id_ed25519).
  • Optionally, set a passphrase for added security when prompted.

If your system does not support Ed25519, use RSA with:

ssh-keygen -t rsa -b 4096 -C "your_email@example.com"

3. Add Your SSH Key to the SSH Agent

Ensure that the SSH agent is running and add your private SSH key to it:

eval "$(ssh-agent -s)"
ssh-add ~/.ssh/id_ed25519

If you used a different filename for your key, replace id_ed25519 with your key’s name.

4. Add Your SSH Public Key to Your GitHub Account

To allow GitHub to recognize your machine, you need to add the public SSH key to your GitHub account. Follow these steps:

  1. Copy your public key to the clipboard using:

    cat ~/.ssh/id_ed25519.pub

    Select and copy the output.

  2. Log in to your GitHub account and navigate to Settings > SSH and GPG keys.

  3. Click on New SSH key, provide a descriptive title (e.g., "Personal Laptop"), and paste your public key into the "Key" field.

  4. Save the changes by clicking Add SSH key.

5. Test Your SSH Connection to GitHub

Verify that your SSH key is correctly set up by testing the connection:

ssh -T git@github.com

Upon successful authentication, you should see a message similar to:

Hi username! You've successfully authenticated, but GitHub does not provide shell access.

If you still encounter the Permission denied (publickey) error, proceed to the next steps.

6. Verify Your Git Remote Repository URL

Ensure that your Git remote URL is using the correct SSH format. Check your remote URL with:

git remote -v

The output should display URLs starting with git@github.com:. If you see https:// URLs instead, update them using:

git remote set-url origin git@github.com:username/repo.git

Replace username and repo.git with your GitHub username and repository name, respectively.

7. Reattempt Cloning the Repository

With the SSH key correctly configured and the remote URL verified, try cloning the repository again:

git clone git@github.com:keli/ctp-python.git

If the setup is correct, the cloning process should proceed without the previous permission error.

Common Issues and Additional Troubleshooting

Incorrect SSH URL

Using an incorrect SSH URL is a common cause of authentication failures. Always ensure that your repository URL follows the SSH format:

git@github.com:username/repository.git

Multiple SSH Keys

If you have multiple SSH keys, Git might not be using the correct one. List the keys loaded in the SSH agent with:

ssh-add -l

If your desired key isn't listed, add it using:

ssh-add ~/.ssh/your_key_name

SSH Config File Misconfiguration

A misconfigured ~/.ssh/config file can prevent Git from using the correct SSH key. Ensure your config file includes the following for GitHub:


Host github.com
  HostName github.com
  User git
  IdentityFile ~/.ssh/id_ed25519

Incorrect File Permissions

SSH requires specific file permissions for security reasons. Set the correct permissions using:

chmod 700 ~/.ssh
chmod 600 ~/.ssh/id_ed25519
chmod 644 ~/.ssh/id_ed25519.pub

Proxy or Firewall Interference

Network proxies or firewalls might block SSH connections. If you're on a restricted network, consider switching to HTTPS for cloning:

git clone https://github.com/keli/ctp-python.git

Repository Permissions

Ensure that your GitHub account has the necessary permissions to access the repository, especially if it's private. You might need to request access from the repository owner.

Alternative Solutions

Using HTTPS Instead of SSH

If SSH continues to present challenges, you can use HTTPS to clone repositories. This method uses your GitHub username and password or a personal access token for authentication:

git clone https://github.com/keli/ctp-python.git

While HTTPS is often simpler, it requires entering credentials more frequently unless a credential manager is used.

Regenerating SSH Keys

If your SSH key pair is compromised or you suspect it's malfunctioning, regenerate a new pair and update GitHub with the new public key:

  1. Generate a new SSH key:

    ssh-keygen -t ed25519 -C "your_email@example.com"
  2. Add the new key to the SSH agent and GitHub as previously described.

Best Practices for Managing SSH Keys

Use Strong Passphrases

Protect your SSH keys with strong, unique passphrases to enhance security.

Regularly Rotate Keys

Periodically rotate your SSH keys to minimize security risks in case of key compromise.

Limit Key Scope

Use different SSH keys for different devices or purposes to limit access scopes.

Secure Storage of Private Keys

Never share your private SSH keys. Store them securely and back them up if necessary.

Conclusion

The Permission denied (publickey) error is a common hurdle when working with GitHub repositories via SSH. By following the comprehensive steps outlined above, you can effectively troubleshoot and resolve this authentication issue. Ensuring your SSH keys are correctly set up, your Git remote URLs are accurate, and your network configurations are conducive will pave the way for seamless repository interactions.

References


Last updated January 23, 2025
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