Github cannot connect using ssh

Question

I am setting up my SSH keys with github. Did it numerous times earlier so i am pretty much sure that i am doing it right. But its not working. whenever i clone it just gets stuck there for around 5-10 mins and then returns this

Cloning into 'sentry-python'...
Connection to github.com closed by remote host.
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.

Ran this command to check what's going on ssh -vT [email protected]. One of the many lines in output has this

Authenticated to github.com ([13.234.176.102]:22) using "publickey".

Followed official documentation for setting up keys. I believe its something else.

UPDATE: HTTPs works fine

Output from: ssh -vT [email protected]

OpenSSH_8.9p1 Ubuntu-3, OpenSSL 3.0.2 15 Mar 2022
debug1: Reading configuration data /etc/ssh/ssh_config
debug1: /etc/ssh/ssh_config line 19: include /etc/ssh/ssh_config.d/*.conf matched no files
debug1: /etc/ssh/ssh_config line 21: Applying options for *
debug1: Connecting to github.com [13.234.176.102] port 22.
debug1: Connection established.
debug1: identity file /home/user/.ssh/id_rsa type 0
debug1: identity file /home/user/.ssh/id_rsa-cert type -1
debug1: identity file /home/user/.ssh/id_ecdsa type -1
debug1: identity file /home/user/.ssh/id_ecdsa-cert type -1
debug1: identity file /home/user/.ssh/id_ecdsa_sk type -1
debug1: identity file /home/user/.ssh/id_ecdsa_sk-cert type -1
debug1: identity file /home/user/.ssh/id_ed25519 type -1
debug1: identity file /home/user/.ssh/id_ed25519-cert type -1
debug1: identity file /home/user/.ssh/id_ed25519_sk type -1
debug1: identity file /home/user/.ssh/id_ed25519_sk-cert type -1
debug1: identity file /home/user/.ssh/id_xmss type -1
debug1: identity file /home/user/.ssh/id_xmss-cert type -1
debug1: identity file /home/user/.ssh/id_dsa type -1
debug1: identity file /home/user/.ssh/id_dsa-cert type -1
debug1: Local version string SSH-2.0-OpenSSH_8.9p1 Ubuntu-3
debug1: Remote protocol version 2.0, remote software version babeld-92f10f70
debug1: compat_banner: no match: babeld-92f10f70
debug1: Authenticating to github.com:22 as 'git'
debug1: load_hostkeys: fopen /home/user/.ssh/known_hosts2: No such file or directory
debug1: load_hostkeys: fopen /etc/ssh/ssh_known_hosts: No such file or directory
debug1: load_hostkeys: fopen /etc/ssh/ssh_known_hosts2: No such file or directory
debug1: SSH2_MSG_KEXINIT sent
debug1: SSH2_MSG_KEXINIT received
debug1: kex: algorithm: curve25519-sha256
debug1: kex: host key algorithm: ssh-ed25519
debug1: kex: server->client cipher: [email protected] MAC: <implicit> compression: none
debug1: kex: client->server cipher: [email protected] MAC: <implicit> compression: none
debug1: expecting SSH2_MSG_KEX_ECDH_REPLY
debug1: SSH2_MSG_KEX_ECDH_REPLY received
debug1: Server host key: <SERVER HOST KEY HERE>
debug1: load_hostkeys: fopen /home/user/.ssh/known_hosts2: No such file or directory
debug1: load_hostkeys: fopen /etc/ssh/ssh_known_hosts: No such file or directory
debug1: load_hostkeys: fopen /etc/ssh/ssh_known_hosts2: No such file or directory
debug1: Host 'github.com' is known and matches the ED25519 host key.
debug1: Found key in /home/user/.ssh/known_hosts:1
debug1: rekey out after 134217728 blocks
debug1: SSH2_MSG_NEWKEYS sent
debug1: expecting SSH2_MSG_NEWKEYS
debug1: SSH2_MSG_NEWKEYS received
debug1: rekey in after 134217728 blocks
debug1: get_agent_identities: bound agent to hostkey
debug1: get_agent_identities: agent returned 1 keys
debug1: Will attempt key: /home/user/.ssh/id_rsa RSA <KEY HERE> agent
debug1: Will attempt key: /home/user/.ssh/id_ecdsa 
debug1: Will attempt key: /home/user/.ssh/id_ecdsa_sk 
debug1: Will attempt key: /home/user/.ssh/id_ed25519 
debug1: Will attempt key: /home/user/.ssh/id_ed25519_sk 
debug1: Will attempt key: /home/user/.ssh/id_xmss 
debug1: Will attempt key: /home/user/.ssh/id_dsa 
debug1: SSH2_MSG_EXT_INFO received
debug1: kex_input_ext_info: server-sig-algs=<[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],ssh-ed25519,ecdsa-sha2-nistp521,ecdsa-sha2-nistp384,ecdsa-sha2-nistp256,rsa-sha2-512,rsa-sha2-256,ssh-rsa>
debug1: SSH2_MSG_SERVICE_ACCEPT received
debug1: Authentications that can continue: publickey
debug1: Next authentication method: publickey
debug1: Offering public key: /home/user/.ssh/id_rsa RSA <KEY HERE> agent
debug1: Server accepts key: /home/user/.ssh/id_rsa RSA <KEY HERE> agent
Authenticated to github.com ([13.234.176.102]:22) using "publickey".
debug1: channel 0: new [client-session]
debug1: Entering interactive session.
debug1: pledge: filesystem
debug1: client_input_global_request: rtype [email protected] want_reply 0
debug1: client_input_hostkeys: searching /home/user/.ssh/known_hosts for github.com / (none)
debug1: client_input_hostkeys: searching /home/user/.ssh/known_hosts2 for github.com / (none)
debug1: client_input_hostkeys: hostkeys file /home/user/.ssh/known_hosts2 does not exist
debug1: client_input_hostkeys: no new or deprecated keys from server
debug1: Sending environment.
debug1: channel 0: setting env LANG = "en_IN"

Okay. So earlier logs where till LANG = "en_IN". Now after altering some permission of my keys here's the updated log.

OpenSSH_8.9p1 Ubuntu-3, OpenSSL 3.0.2 15 Mar 2022
debug1: Reading configuration data /etc/ssh/ssh_config
debug1: /etc/ssh/ssh_config line 19: include /etc/ssh/ssh_config.d/*.conf matched no files
debug1: /etc/ssh/ssh_config line 21: Applying options for *
debug1: Connecting to github.com [13.234.210.38] port 22.
debug1: Connection established.
debug1: identity file /home/user/.ssh/id_rsa type 0
debug1: identity file /home/user/.ssh/id_rsa-cert type -1
debug1: identity file /home/user/.ssh/id_ecdsa type -1
debug1: identity file /home/user/.ssh/id_ecdsa-cert type -1
debug1: identity file /home/user/.ssh/id_ecdsa_sk type -1
debug1: identity file /home/user/.ssh/id_ecdsa_sk-cert type -1
debug1: identity file /home/user/.ssh/id_ed25519 type -1
debug1: identity file /home/user/.ssh/id_ed25519-cert type -1
debug1: identity file /home/user/.ssh/id_ed25519_sk type -1
debug1: identity file /home/user/.ssh/id_ed25519_sk-cert type -1
debug1: identity file /home/user/.ssh/id_xmss type -1
debug1: identity file /home/user/.ssh/id_xmss-cert type -1
debug1: identity file /home/user/.ssh/id_dsa type -1
debug1: identity file /home/user/.ssh/id_dsa-cert type -1
debug1: Local version string SSH-2.0-OpenSSH_8.9p1 Ubuntu-3
debug1: Remote protocol version 2.0, remote software version babeld-92f10f70
debug1: compat_banner: no match: babeld-92f10f70
debug1: Authenticating to github.com:22 as 'git'
debug1: load_hostkeys: fopen /home/user/.ssh/known_hosts2: No such file or directory
debug1: load_hostkeys: fopen /etc/ssh/ssh_known_hosts: No such file or directory
debug1: load_hostkeys: fopen /etc/ssh/ssh_known_hosts2: No such file or directory
debug1: SSH2_MSG_KEXINIT sent
debug1: SSH2_MSG_KEXINIT received
debug1: kex: algorithm: curve25519-sha256
debug1: kex: host key algorithm: ssh-ed25519
debug1: kex: server->client cipher: [email protected] MAC: <implicit> compression: none
debug1: kex: client->server cipher: [email protected] MAC: <implicit> compression: none
debug1: expecting SSH2_MSG_KEX_ECDH_REPLY
debug1: SSH2_MSG_KEX_ECDH_REPLY received
debug1: Server host key: <SERVER HOST KEY>
debug1: load_hostkeys: fopen /home/user/.ssh/known_hosts2: No such file or directory
debug1: load_hostkeys: fopen /etc/ssh/ssh_known_hosts: No such file or directory
debug1: load_hostkeys: fopen /etc/ssh/ssh_known_hosts2: No such file or directory
debug1: Host 'github.com' is known and matches the ED25519 host key.
debug1: Found key in /home/user/.ssh/known_hosts:1
debug1: rekey out after 134217728 blocks
debug1: SSH2_MSG_NEWKEYS sent
debug1: expecting SSH2_MSG_NEWKEYS
debug1: SSH2_MSG_NEWKEYS received
debug1: rekey in after 134217728 blocks
debug1: get_agent_identities: bound agent to hostkey
debug1: get_agent_identities: agent returned 1 keys
debug1: Will attempt key: /home/user/.ssh/id_rsa <KEY HERE> agent
debug1: Will attempt key: /home/user/.ssh/id_ecdsa 
debug1: Will attempt key: /home/user/.ssh/id_ecdsa_sk 
debug1: Will attempt key: /home/user/.ssh/id_ed25519 
debug1: Will attempt key: /home/user/.ssh/id_ed25519_sk 
debug1: Will attempt key: /home/user/.ssh/id_xmss 
debug1: Will attempt key: /home/user/.ssh/id_dsa 
debug1: SSH2_MSG_EXT_INFO received
debug1: kex_input_ext_info: server-sig-algs=<[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],ssh-ed25519,ecdsa-sha2-nistp521,ecdsa-sha2-nistp384,ecdsa-sha2-nistp256,rsa-sha2-512,rsa-sha2-256,ssh-rsa>
debug1: SSH2_MSG_SERVICE_ACCEPT received
debug1: Authentications that can continue: publickey
debug1: Next authentication method: publickey
debug1: Offering public key: /home/user/.ssh/id_rsa RSA <KEY HERE> agent
debug1: Server accepts key: /home/user/.ssh/id_rsa RSA <KEY HERE> agent
Authenticated to github.com ([13.234.210.38]:22) using "publickey".
debug1: channel 0: new [client-session]
debug1: Entering interactive session.
debug1: pledge: filesystem
debug1: client_input_global_request: rtype [email protected] want_reply 0
debug1: client_input_hostkeys: searching /home/user/.ssh/known_hosts for github.com / (none)
debug1: client_input_hostkeys: searching /home/user/.ssh/known_hosts2 for github.com / (none)
debug1: client_input_hostkeys: hostkeys file /home/user/.ssh/known_hosts2 does not exist
debug1: client_input_hostkeys: no new or deprecated keys from server
debug1: Sending environment.
debug1: channel 0: setting env LANG = "en_IN"
PTY allocation request failed on channel 0
debug1: client_input_channel_req: channel 0 rtype exit-status reply 0
Hi targhs! You've successfully authenticated, but GitHub does not provide shell access.
debug1: channel 0: free: client-session, nchannels 1
Connection to github.com closed.
Transferred: sent 3888, received 2812 bytes, in 0.6 seconds
Bytes per second: sent 6234.8, received 4509.3
debug1: Exit status 1

Answer 1

TL;DR link to what might as well be a duplicate here.

Explanation (long-ish)

You have something new in your edit: agent refused operation. That's the problem here. You are using an ssh agent, and it's the agent that must pass the private key (of the public/private key-pair) to ssh so that your ssh can decrypt the challenge that GitHub have sent to your ssh.

The way ssh authentication works (boiled down a bit) is this:

• Your ssh client (ssh command) opens a channel to the host (in this case GitHub).
• Your client tells them you'd like to log in as some user name (in this case git: GitHub always requires this as a constant).
• Their ssh server then says: I might let you in, provided you prove to me that you have permission. Send me a public key.
• Your client then pokes around to look for a public key to send. It finds one and sends it.
• Their server checks to see if that ssh key is a valid key. It is; it's registered to you. But maybe you're not targhs. Maybe you've snagged the public key from the real targhs, and this connection is from an imposter! So they want to make sure you're really targhs. They use the public key to encrypt a random value, and send you—or rather, your client ssh—the value, challenging you to decrypt it.
• Your client now requires the private key.

It's pretty common to have both public and private keys stored in a file on your computer (e.g., on your laptop). When this is the case, your ssh client can just open and read the private key file, giving it access to that private key. For security purposes, though, you can do one or both of these two things:

• Not supply the private key at all. Keep it only in an agent.
• Keep the private key in an encrypted file, so that a decryption key—separate from the public and private key—is required to read the private key.

If you've done either or both of these, your ssh client now needs help.

To get that help, your ssh client can:

• interact directly with you, the user, via the keyboard: this may or may not be permitted; or
• consult an ssh agent.

The ssh agent enables ssh clients to interact with you, the user, and provide the (secret) private key, even if it's not on the computer on which you're running ssh, or if it's just encrypted, or whatever. To do that, the ssh client asks the ssh agent for the key.

Your ssh agent says: Nuh-uh, not gonna give you the key!

Why does your ssh agent say that? That's the mystery here; that's what you have to figure out. There are multiple possible reasons. Fortunately, they're all pretty well covered in a separate StackOverflow question and answers: see How to solve "sign_and_send_pubkey: signing failed: agent refused operation"?