'-v', '/tmp/clearml_agent.ssh.cbvchse1:/.ssh',

It's my bad, after that inside the container it does cp -Rf /.ssh ~/.ssh
The reason is that you cannot know the user home folder before spinning the container
Anyhow the point is, are you sure that you have ~/.ssh on the Host machine configured?
And if you do, are you saying this is part of your AMI? if not how did you put it there?