Error from Updater Application Cron Script Found non-writable path(s): /home/USERNAME/public_html/.htaccess.sample
I guess it's just a permission problem.
Just make this
.htaccess.sample writeable for the user that runs the script
You can find the permissions documentation on the official website: http://devdocs.magento.com/guides/v2.0/install-gde/prereq/file-system-perms.html
I had the same problem with that .htaccess.sample.
And I thought it was a permission problem but it was not so what I did is I created that .htaccess.sample file and I run my cron using this commands "bin/magento cron:run" then "bin/magento indexer:reindex" and it solves my problem.
I hope this would help