linux - The SSL CA cert (path? access rights) on Ubuntu 16?

Problem with the SSL CA cert (path? access rights?). I got a SSL cert from Commodo and it installed ok. Everything seems to be working correctly and I have restarted my server and Apache2.

Service apache2 status shows no errors.

This was used:

sudo apt-get update && sudo apt-get upgrade -fy && sudo apt-get dist-upgrade -fy

The issues I see online either deal with Amazons Linux (using yum) or CentOS. They said to restart the server. I am using Ubuntu 16.04 and not sure what to do next?

This affects packages being downloaded such as this example:

I tried to do a command such as:

I made a composer.json file

{
  "require": {
      "aws/aws-sdk-php": "3.*"
  }
}

composer install

[RuntimeException]
  Failed to clone https://github.com/jmespath/jmespath.php.git via https, ssh
   protocols, aborting.
  - https://github.com/jmespath/jmespath.php.git
    Cloning into '/var/www/ssl/s3/test/vendor/mtdowling/jmespath.php'...
    fatal: unable to access 'https://github.com/jmespath/jmespath.php.git/':
  Problem with the SSL CA cert (path? access rights?)
  - git@github.com:jmespath/jmespath.php.git
    Cloning into '/var/www/ssl/s3/test/vendor/mtdowling/jmespath.php'...
    Permission denied (publickey).
    fatal: Could not read from remote repository.

    Please make sure you have the correct access rights
    and the repository exists.