Drush not connecting to site's settings.php

Question

When I run drush --debug status in the docroot of my Drupal site, I get the following message:

[user@computer]$ drush --debug status
Phar detected. Proceeding to drush_main().
Loading drushrc "/home/user/.drush/drushrc.php" into "home.drush"[bootstrap]
scope. [0.02 sec, 3.54 MB]
Cache HIT cid: 8.1.14-commandfiles-removed    [debug]
[0.03 sec, 3.59 MB]
Bootstrap to phase 0. [0.28 sec, 9.55 MB]                            [bootstrap]
Trying to bootstrap as far as we can. [0.28 sec, 9.56 MB]                [debug]
Found command: core-status (commandfile=core) [0.28 sec, 9.56 MB]    [bootstrap]
Loading outputformat engine. [0.28 sec, 9.56 MB]                        [notice]
Calling hook drush_core_status [0.29 sec, 9.85 MB]                       [debug]
Returned from hook drush_core_status [0.38 sec, 9.86 MB]        
         [debug]
 PHP configuration      :  /etc/php.ini /home/user/.drush/drush.ini
 PHP OS                 :  Linux
 Drush script           :  /usr/local/bin/drush
 Drush version          :  8.1.14
 Drush temp directory   :  /tmp
 Drush configuration    :
 Drush alias files      :  /home/user/.drush/aliases.drushrc.php
Command dispatch complete [x.xx sec, x.xx MB]                           [notice]

As you may see in that output, "PHP Configuration" has two entries where as "Drush configuration" has none. And that one of the entries for "PHP Configuration" looks like the entry that should be in "Drush configuration".

I did run it within the docroot of Drupal. And I have even tried in sites/default. Plus, I have even tried my aliases and none of them are working. This all worked before though with another Drupal site. It just stopped working after I transferred the Drupal files from one server to another. I thought my permissions were correct but they don't look correct. Plus I have even tried adding --uri and --root to Drush and that didn't work either. For the transfer I used rsync options avzp.

drush -d pm-info give's the following:

[user@computer]$ drush -d pm-info
Phar detected. Proceeding to drush_main().
Loading drushrc "/home/user/.drush/drushrc.php" into "home.drush"[bootstrap]
scope. [0.02 sec, 3.54 MB]
Cache HIT cid: 8.1.14-commandfiles-removed    [debug] [0.03 sec, 3.59 MB]
Bootstrap to phase 0. [0.27 sec, 9.55 MB]                                              [bootstrap]
Bootstrap to phase 6. [0.28 sec, 9.56 MB]                              [bootstrap]
Command pm-info needs a higher bootstrap level to run - you will need[error]
to invoke drush from a more functional Drupal environment to run this
command. [0.28 sec, 9.56 MB]
The drush command 'pm-info' could not be executed. [0.28 sec, 9.56   [error]
MB]

Answer 1

Changing the ownership of the some of the files in the sites directory seems to have fixed the issue.