Attempting to renew cert from /etc/letsencrypt/renewal/domain.conf produced an unexpected error: urn:ietf:params:acme:error:malformed :: The request message was malformed :: Method not allowed. Skipping

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Check python --version.

I had 2yrs old server installed by ansible for py2 so i set that as default. Unfortunately didn't change back to version 3.

In my case fixed problem by:

update-alternatives --install /usr/bin/python python /usr/bin/python3.5 1

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