MacOS Sierra 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 and, hopefully, all works now.

Also see this solution:
MacOS Sierra doesn’t seem to remember SSH keys between reboots
https://apple.stackexchange.com/questions/254468/macos-sierra-doesn-t-seem-to-remember-ssh-keys-between-reboots