Magento – Magento 2 cron job not re-indexing products as expected

My problem is Magento 2 doesn’t automatically index as I expect from the cron job. I currently have to SSH in and re-index using php bin/magento indexer:reindex , which is fine for me but not for my customers

The server (WHM cPanel setup, jailed shell) is my own which I am sharing between several of my customers. So I have root login but will need to keep the customers ‘jailed’. The server is almost new with only 1 other WordPress site. I am hoping to put several Magento 2 installs on it.

I suspect the cron job is running but something else is stopping the reindexing from happening.

There are no errors (empty) in magento.cron.log or setup.cron.log

In update.cron.log I'm getting:

Notice: Undefined variable: nonWritablePaths in /home/gabitieartificia/public_html/update/app/code/Magento/Update/CronReadinessCheck.php on line 86
Warning: implode(): Invalid arguments passed in /home/gabitieartificia/public_html/update/app/code/Magento/Update/CronReadinessCheck.php on line 86
update-cron: Please check var/log/update.log for execution summary.

In debug.log I'm getting this error:

[2016-06-12 09:19:07] main.DEBUG: cache_invalidate: {"method":"POST","url":"ht tp://gabitie.artificialart.co.uk/admin_ejiyo5/admin/index/index/key/46b3c13a698e28d113fd7d912659ff6cc5859d09833e8cf81e3448cb01ff357f/","invalidateInfo":{"tags":["BACKEND_MAINMENU"],"mode":"matchingAnyTag"},"is_exception":false} []

In update.log I'm getting this error:

[2016-06-10 11:28:03] update-cron.ERROR: Cron readiness check failure! Found following non-writable paths [] []

And in the cPanel error log I'm getting this error:

[Sun Jun 12 10:19:09.601340 2016] [access_compat:error] [pid 34328] [client 130.185.144.89:50199] AH01797: client denied by server configuration: /home/gabitieartificia/public_html/app/etc/config.php

I don’t know if all these errors relate to my re-indexing problem. I have been Googling permutations of these error messages for the last few days trying to find a solution to no avail.

Im sure my paths to php.ini and the binary are correct.

When I run the commands from a command line as root from the top directory they work fine with no errors at all, but it still doesn’t re-index

Ie this works fine:

sudo –u gabitieartificia /usr/local/bin/php -c /usr/local/lib/php.ini /home/gabitieartificia/public_html/bin/magento cron:run | grep -v "Ran jobs by schedule" >> /home/gabitieartificia/public_html/var/log/magento.cron.log

phpinfo = http://gabitie.artificialart.co.uk/phpinfo.php

crontab contents =

 * * * * /usr/local/bin/php -c /usr/local/lib/php.ini /home/gabitieartificia/public_html/bin/magento cron:run | grep -v "Ran jobs by schedule" >> /home/gabitieartificia/public_html/var/log/magento.cron.log
 * * * * /usr/local/bin/php -c /usr/local/lib/php.ini /home/gabitieartificia/public_html/update/cron.php >> /home/gabitieartificia/public_html/var/log/update.cron.log
 * * * * /usr/local/bin/php -c /usr/local/lib/php.ini /home/gabitieartificia/public_html/bin/magento setup:cron:run >> /home/gabitieartificia/public_html/var/log/setup.cron.log

I have even tried setting up a second copy of Magento 2 on the same server and putting all folders to chmod 777 to prove if it is permissions related, but that didn’t work either. It still wasn’t re-indexing.

Any help/insight anyone can provide will be hugely appreciated.