Certs created but not accesible or readable by nginx

Hello, just like many times before, I ran this command on my ubuntu server:

sudo certbot certonly --webroot -w /var/www/rgarza/mywebsite.mx -d www.mywebsite -d mywebsite.mx

Which gave me the usual congratulations output text stating that the certs was successfully generated.

So that part is fine, but then, if i run the usual sudo nginx -t command to check if there are any errors before i reload nginx i get this unusual error:

  [emerg] BIO_new_file("/etc/letsencrypt/live/mywebsite.mx/fullchain.pem")
 failed (SSL: error:02001002:system library:fopen:No such file or directory:fopen('/etc/letsencrypt/live/mywebsite.mx/fullchain.pem','r')
 error:2006D080:BIO routines:BIO_new_file:no such file)
 nginx: configuration file /etc/nginx/nginx.conf test failed

This sound to me like a permission problem. Now i don’t know why i get this error now cause this is the exact procedure that i do everytime i need to generate a cert for any given website on my server.

The first three lines of my nginx.conf are these:

user www-data;
worker_processes auto;
pid /run/nginx.pid;

And the relevant server block of this particular website which is stored within the sites-available folder is this:

server {
    listen 80;
    server_name mywebsite.mx www.mywebsite.mx;
    rewrite ^/(.*) https://mywebsite.mx/$1 permanent;

server {
listen 443 ssl http2;
    server_name www.mywebsite.mx;
    ssl_certificate /etc/letsencrypt/live/mywebsite.mx/fullchain.pem;
    ssl_certificate_key /etc/letsencrypt/live/mywebsite.mx/privkey.pem;
    ssl_prefer_server_ciphers on;
    return 301 https://mywebsite.mx$request_uri;

server {
    listen 443 ssl http2;
    server_name mywebsite.mx;
    ssl_certificate /etc/letsencrypt/live/mywebsite.mx/fullchain.pem;
    ssl_certificate_key /etc/letsencrypt/live/mywebsite.mx/privkey.pem;
    ssl_prefer_server_ciphers on;

    root /var/www/rgarza/mywebsite**strong text**.mx;
    index index.php index.html index.htm;

location / {
        try_files $uri $uri/ /index.php?q=$request_uri;

    # deny running scripts inside writable directories
        location ~* /(images|cache|media|logs|tmp)/.*\.(php|pl|py|jsp|asp|sh|cgi)$ {
                return 403;
                error_page 403 /403_error.html;

location ~ \.php$ {
                try_files $uri =404;
                fastcgi_split_path_info ^(.+\.php)(/.+)$;
                fastcgi_pass unix:/run/php/php7.0-fpm.sock;
                fastcgi_param  SCRIPT_FILENAME  $document_root$fastcgi_script_name;
                fastcgi_index index.php;
                include fastcgi_params;

        location ~*  \.(jpg|jpeg|svg|png|gif|ico|css|js|woff)$ {
                expires 20d;

        location ~*  \.(pdf)$ {
                expires 30d;

location ~ /\.ht {
        deny all;


I have many certs generated like this and already working, this is the first time i get this problem. I guess it had somenthing to do that i did an apt update and apt upgrade last week. Maybe something changed because of that upgrade. Anyway nginx does not complain about the old certs from other sites, just this one, and it looks like a permission problem like i said before.

I have no experience chaning permission, can someone point me in the right direction here? By the way I AM NOT USING DOCKER

Thanks in advanced.

If i run: certbot --nginx

I get this output:

The following error was encountered:
[Errno 13] Permission denied: '/var/log/letsencrypt/.certbot.lock'
If running as non-root, set --config-dir, --work-dir, and --logs-dir to writeable paths.

Ok I found the solution.

Turns out that i have a habit of usually running the command issuing the non-www site before the www-version just like this example below:

sudo certbot certonly --webroot -w /var/www/rgarza/mywebsite.mx -d mywebsite -d www.mywebsite.mx

but this time i wrote the command with the www version first:

sudo certbot certonly --webroot -w /var/www/rgarza/mywebsite.mx -d www.mywebsite -d mywebsite.mx

Turns out lets encrypt stores the certs on a folder that matches the name of the first website name version you are trying to issue. So this means the cert was stored on a folder called /etc/letsencrypt/live/www.mywebsite.mx/fullchain.pem. (with www)
whereas i was expecting to be stored in the non www version like this: /etc/letsencrypt/live/mywebsite.mx/fullchain.pem.

Long story short, the order you use to issue the non www and www versions matters.

I’m glad you were able to get the problem resolved. Another way of viewing this would be to say that you shouldn’t make an assumption about where a new certificate will be stored on disk, but instead look at the output of Certbot, which will tell you at the end where your certificate can be found (or use an installer via --apache or --nginx to have it configure those web servers for you with the appropriate certificate location).

This topic was automatically closed 30 days after the last reply. New replies are no longer allowed.