Apply rule at local take very long time

I have 50k email in different accounts(around 5).

Since I didn’t do any filter before, and it is so chaos.

I made some local rule in eM Client and apply it in all mail and including sub-folder. But it is running so slow.

Running an hour, only 2500 mails got apply the rule. ;_;

How can I make the progress to apply rule quickly?