I'm clearing all the caches etc as the very last step of my deployment script like this:

php please clear:cache && php please clear:glide && php please clear:stache && php please clear:static

Now I'm wondering is this the reason why I see error "no input file specified" for 30-60s immediately after the deployment job has finished, or is it caused by something else?

Other than that the deployment script literally just moves the files onto the server and switches the server's webroot symlink pointing to the folder with the latest files in it.