Unsupported filesystem layout. sites-available/enabled expected

I’m trying to install letsencrypt on Apache with ubuntu 12.04 (Yes, ubuntu 12.04. Please don’t lecture me on using an outdated OS. That would be OT. It’s on my todo list.)

I executed these commands:

wget https://dl.eff.org/certbot-auto

chmod a+x certbot-auto

sudo /home/dellfalconer/certbot-auto --apache

This is the output after answering all the questions:

Obtaining a new certificate
Performing the following challenges:
tls-sni-01 challenge for accordi-online.net
tls-sni-01 challenge for accordi-online.com
tls-sni-01 challenge for www.accordi-online.com
tls-sni-01 challenge for www.accordi-online.net
Waiting for verification…
Cleaning up challenges
Created an SSL vhost at /etc/apache2/conf.robb/vhosts-le-ssl.conf
Enabling NameVirtualHosts on *:443
Deploying Certificate for accordi-online.net to VirtualHost /etc/apache2/conf.robb/vhosts-le-ssl.conf
Unsupported filesystem layout. sites-available/enabled expected.

  • Unable to install the certificate
  • Congratulations! Your certificate and chain have been saved at:
    Your key file has been saved at:
    Your cert will expire on 2017-12-09. To obtain a new or tweaked
    version of this certificate in the future, simply run certbot-auto
    again with the “certonly” option. To non-interactively renew all
    of your certificates, run “certbot-auto renew”
  • Your account credentials have been saved in your Certbot
    configuration directory at /etc/letsencrypt. You should make a
    secure backup of this folder now. This configuration directory will
    also contain certificates and private keys obtained by Certbot so
    making regular backups of this folder is ideal.

I have:

So I see why the installation program couldn’t find sites-available/enabled. It’s not there.

What is my best course of action? Do I change my filesystem layout to suit letsencrypt, then uninstall and reinstall letsencrypt?


Hi @dellfalconer,

In this case, this means “both sites-available and sites-enabled”, not a directory called “sites-available/enabled”. So, you do have the layout it expects… partly. :slight_smile:

In this case I think that Certbot was alarmed by the use of /etc/apache2/conf.robb because Certbot assumed that all VirtualHosts that it needs to modify exist within /etc/apache2/sites-available. conf.robb is not sites-available so I assume that Certbot concluded that it didn’t know how to modify this file.

The simplest thing would be if you could shift any VirtualHosts out of conf.robb and instead sites-available (you can make appropriate symlinks from sites-enabled via ln -s or more officially a2ensite). There shouldn’t be a need to reinstall Certbot and it’s probably even possible to get it to proceed with the installation proceed via certbot install. However, you might instead choose to use certbot-auto certificates to find the old certificate and certbot-auto delete to delete it, and then start from scratch rerunning certbot-auto --apache.

In any case, there shouldn’t be a need to reinstall certbot-auto because there are no configuration options saved inside the certbot-auto program itself.

Aha. Thanks.

My apache2.conf contains these lines at the end:

# Include generic snippets of statements 
Include conf.d/
# Include the virtual host configurations:
Include sites-enabled/
# Added own directives by Robb on 2012-08-27.
include conf.robb/

conf.d contains:

(ref to) phpmyadmin.conf

sites-available doesn’t appear to get loaded and contains


sites-enabled contains nothing.

conf.robb contains:


Should I just move the 3 files in conf.robb to sites-enabled and delete the corresponding line in apache2.conf?


@bmw, would you be willing to take a look at this? I don’t have a clear intuition about this situation.


I moved the 3 files from conf.robb to sites-enabled and commented out the corresponding line (conf.robb) in apache2.conf, then executed the following commands:

sudo /home/dellfalconer/certbot-auto delete

sudo /home/dellfalconer/certbot-auto --apache

Everything seems to be working fine now. Thanks much!


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