How to fix replica set is already initialized

also I don’t understand the log.
It says that there is a missing directory but it’s not true, the directory is there:

ll /var/lib/
total 0
drwx------. 2 root       root       105 Jan 22 10:41 NetworkManager
drwxr-xr-x. 2 root       root       143 Jan 15 15:40 alternatives
drwxr-xr-x. 2 root       root        35 Jan 15 15:41 authselect
drwxr-x---. 2 chrony     chrony      19 Jan 22 10:40 chrony
drwxr-xr-x. 3 root       root        93 Jan 16 09:31 dnf
drwxr-xr-x. 2 root       root         6 Oct  2 23:00 games
drwxr-xr-x. 2 root       root         6 Oct  1 14:37 initramfs
drwxr-xr-x. 2 root       root         6 Nov 12 15:39 kdump
drwxr-xr-x. 2 root       root        30 Jan 22 00:00 logrotate
drwxr-xr-x. 2 root       root         6 Oct  2 23:00 misc
drwxr-xr-x. 2 mongodb    mongodb      6 Jan 22 10:54 mongo
drwxr-xr-x. 2 mongodb    mongodb      6 Jan 22 10:48 mongodb
drwxr-sr-x. 3 opensearch opensearch 146 Jan 16 09:19 opensearch
drwxr-xr-x. 2 root       root         6 May  9  2023 os-prober
drwx------. 2 root       root         6 Jan 15 15:40 private
drwxr-xr-x. 2 root       root        91 Oct  7 09:47 rpm
drwxr-xr-x. 3 root       root        20 Jan 15 15:40 rpm-state
drwx------. 2 root       root        29 Jan 22 11:23 rsyslog
drwxr-xr-x. 5 root       root        46 Jan 15 15:40 selinux
drwxr-xr-x. 9 root       root       105 Jan 15 15:40 sss
drwxr-xr-x. 7 root       root        98 Jan 15 16:21 systemd
drwxr-xr-x. 3 root       root        20 Jan 15 15:40 tpm2-tss