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The problem here is simply bad documentation on our part. Running certbot-auto both installs Certbot and runs it. In your case, Certbot was successfully installed, but encountered problems when it was running. This is because for your use case, Certbot needs additional commands on the command line.
Try continuing with the "Getting Started" instructions from your link above.
I started following the instructions for Ubuntu trusty + nginx and the auto install process failed.
Content of
letsencrypt.log
:The text was updated successfully, but these errors were encountered: