I had created cron.php file in my project and added the script.This is the code inside the file and setup cron job once per 5 minutes successfully even I got mail notifications too.
/usr/local/bin/php /usr/local/php56/bin/php-cli /home/username/public_html/bin/magento indexer:reindex
/usr/local/bin/php /usr/local/php56/bin/php-cli /home/username/public_html/bin/magento cron:run
/usr/local/bin/php /usr/local/php56/bin/php-cli /home/username/public_html/update/cron.php
/usr/local/bin/php /usr/local/php56/bin/php-cli /home/username/public_html/bin/magento setup:cron:run
/usr/local/bin/php /usr/local/php56/bin/php-cli /home/username/public_html/bin/magento cache:clean
/usr/local/bin/php /usr/local/php56/bin/php-cli /home/username/public_html/bin/magento cache:flush
Whenever the cron file is running there should be a change in cron_shedule table,unfortunately I found that there is no change in the table.But when I run the command through ssh (magento cron:run) values are generated in table and showing status as pending .