everything is fine in config, no /root/.my.cnf exist.
I run the command.
Same error 
i-MSCP backup script - Cannot dump mysql databases - Percona DB
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everything is fine in config, no /root/.my.cnf exist.
I run the command.
Same error
Re;
Problem fixed on your server.
The /etc/mysql/my.cnf file which include files from /etc/mysql/conf.d was missing. This is because Percona DB doesn't create that file by default. I'll fix the issue by creating it if needed during i-MSCP installation if missing.
Thank you for your report.