I executed the Ubuntu script at
https://developers.yubico.com/PGP/SSH_authentication/ for yubikey 4

I got this message:
gpg-connect-agent: no running gpg-agent - starting '/usr/bin/gpg-agent'

When the PGP agent is running run the following command:

ssh-add

It solved this issue for me.

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https://bugs.launchpad.net/bugs/1569019

Title:
  rsa ssh login fails with "sign_and_send_pubkey: signing failed: agent
  refused operation" error

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