Unless otherwise specified (usually happens on admin side, and image access), all requests to wordpress pass and are processed by the index.php
file, therefor it is not very interesting to look at which file is being “run”, you should look more at the request log and how much time it takes to complete each request.
So if it is not any kind of attack, you probably have a traffic spike which might be worth investigating it source, but whether it is a DDOS attempt or just normal traffic, it sounds like either your theme code can be optimized or there is some thing that can be improved in your server setup.
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