Error: Bad file number

This error usually means you were unable to connect to the server. Often this is caused by firewalls and proxy servers.

When running remote Git commands or SSH, your connection might time out:

$ ssh -vT git@HOSTNAME
> OpenSSH_8.1p1, LibreSSL 2.7.3
> debug1: Connecting to HOSTNAME [207.97.227.239] port 22.
> debug1: connect to address 207.97.227.239 port 22: Connection timed out
> ssh: connect to host HOSTNAME port 22: Connection timed out
> ssh: connect to host HOSTNAME port 22: Bad file number

Solving the issue

Use HTTPS

Often, the simplest solution is to simply avoid SSH entirely. Most firewalls and proxies allow HTTPS traffic without issue. To take advantage of this, change the remote URL you're using:

$ git clone https://HOSTNAME/USERNAME/REPO-NAME.git
> Cloning into 'reponame'...
> remote: Counting objects: 84, done.
> remote: Compressing objects: 100% (45/45), done.
> remote: Total 84 (delta 43), reused 78 (delta 37)
> Unpacking objects: 100% (84/84), done.

Test from a different network

If you can connect the computer to another network that doesn't have a firewall, you can try testing your SSH connection to GitHub Enterprise Server. If everything works as it should, contact your network administrator for help on changing the firewall settings to allow your SSH connection to GitHub Enterprise Server to succeed.