is there a parameter similar to MEB "apply-incremental-backup" in Percona Xtrabackup

  1. Take a full (base) backup with Percona Xtrabackup.

What you see from the logs is not your database getting shutdown, rather it is xtrabackup’s way of simulating crash recovery on the backup.
You will need to review the manual and understand how Xtrabackup works - https://www.percona.com/doc/percona-xtrabackup/2.3/how_xtrabackup_works.html

Thank you jrivera for your reply, i think the document you gave helps.