I had the same problem. MacOS Mojave keychain keeps asking for the passphrase. Your id_rsa should be encrypted with a passphrase for security.
Then try adding it to the keychain ssh-add -K ~/.ssh/id_rsa
If your key is in another folder than ~/.ssh then substitute with the correct folder.
Keychain now knows your ssh key, hopefully, all works now.
If you are still facing the issue then try
1. brew install keychain
2. echo '/usr/local/bin/keychain $HOME/.ssh/id_rsa' >> ~/.bash_profile
echo 'source $HOME/.keychain/$HOSTNAME-sh' ~/.bash_profile
3. ssh-add -K ~/.ssh/id_rsa
Hopefully, it should work now.