Are the log files updated precisely every 5 minutes according to a clock that you have access to (system time for example) or is the update period stochastic?

If the update time is predictable you can arrange your work to fit in between updates based on the same clock that the update process is using.

If the update process is stochastic, but there is a usable minimum time between updates, you may be able to look at the last modified time of the log files and base your work on that.