Github Permission denied (publickey) SSH keys in wrong directory? - linux

Question

I've recently installed this stack on AWS EC2:
https://aws.amazon.com/marketplace/pp/B00NO1HJ56/ref=srh_res_product_title?ie=UTF8&sr=0-2&qid=1461119036279
The instance's system log says that the SSH keys were installed here:
Generating public/private rsa key pair.
Your identification has been saved in /etc/ssh/ssh_host_rsa_key.
Your public key has been saved in /etc/ssh/ssh_host_rsa_key.pub.
I have added the public key to my Github account and the fingerprints match.
When cloning a repo I get:
Permission denied (publickey).
From the Github help section https://help.github.com/articles/error-permission-denied-publickey
I run: ssh -vT git#github.com and get:
OpenSSH_6.6.1, OpenSSL 1.0.1f 6 Jan 2014
debug1: Reading configuration data /etc/ssh/ssh_config
debug1: /etc/ssh/ssh_config line 19: Applying options for *
debug1: /etc/ssh/ssh_config line 56: Applying options for *
debug1: Connecting to github.com [192.30.252.122] port 22.
debug1: Connection established.
debug1: identity file /home/bitnami/.ssh/id_rsa type -1
debug1: identity file /home/bitnami/.ssh/id_rsa-cert type -1
debug1: identity file /home/bitnami/.ssh/id_dsa type -1
debug1: identity file /home/bitnami/.ssh/id_dsa-cert type -1
debug1: identity file /home/bitnami/.ssh/id_ecdsa type -1
debug1: identity file /home/bitnami/.ssh/id_ecdsa-cert type -1
debug1: identity file /home/bitnami/.ssh/id_ed25519 type -1
debug1: identity file /home/bitnami/.ssh/id_ed25519-cert type -1
debug1: Enabling compatibility mode for protocol 2.0
debug1: Local version string SSH-2.0-OpenSSH_6.6.1p1 Ubuntu-2ubuntu2.6
debug1: Remote protocol version 2.0, remote software version libssh-0.7.0
debug1: no match: libssh-0.7.0
debug1: SSH2_MSG_KEXINIT sent
debug1: SSH2_MSG_KEXINIT received
debug1: kex: server->client aes128-ctr hmac-sha1 none
debug1: kex: client->server aes128-ctr hmac-sha1 none
debug1: sending SSH2_MSG_KEX_ECDH_INIT
debug1: expecting SSH2_MSG_KEX_ECDH_REPLY
debug1: Server host key: RSA 16:27:ac:a5:76:28:2d:36:63:1b:56:4d:eb:df:a6:48
debug1: Host 'github.com' is known and matches the RSA host key.
debug1: Found key in /home/bitnami/.ssh/known_hosts:1
debug1: ssh_rsa_verify: signature correct
debug1: SSH2_MSG_NEWKEYS sent
debug1: expecting SSH2_MSG_NEWKEYS
debug1: SSH2_MSG_NEWKEYS received
debug1: SSH2_MSG_SERVICE_REQUEST sent
debug1: SSH2_MSG_SERVICE_ACCEPT received
debug1: Authentications that can continue: publickey
debug1: Next authentication method: publickey
debug1: Trying private key: /home/bitnami/.ssh/id_rsa
debug1: Trying private key: /home/bitnami/.ssh/id_dsa
debug1: Trying private key: /home/bitnami/.ssh/id_ecdsa
debug1: Trying private key: /home/bitnami/.ssh/id_ed25519
debug1: No more authentication methods to try.
I seems the ssh agent is searching /home/bitnami/.ssh/ but the keys are located in /etc/ssh
This is the contents of /home/bitnami/.ssh
authorized_keys
known_hosts
And this is the contents of /etc/ssh
moduli
ssh_host_dsa_key
ssh_host_ecdsa_key.pub
ssh_host_rsa_key
ssh_config
ssh_host_dsa_key.pub
ssh_host_ed25519_key
ssh_host_rsa_key.pub
sshd_config
ssh_host_ecdsa_key
ssh_host_ed25519_key.pub
ssh_import_id
If I check what keys are added to the ssh agent I get:
$ ssh-add -l I get:
The agent has no identities.
Is this simply a matter of adding my public key in /etc/ssh/ to the ssh agent by using ssh-add, so it knows where to look?
I don't understand why the keys are were not installed in /etc/hosts rather than the home directory.

Answer 1

The solution is simply to ignore the keys in /etc/ssh. These keys are used by AWS to access the instance and belongs to the system rather than a user.
So I just generated new keys for the bitnami user and those keys are now correctly sitting in /home/.ssh/
I can now pull my repo from Github.