Following are the Steps to delete logs:

1. Go to path C:\Program Files\MongoDB\Server\4.2\bin\ 
2. Run the deleteLogMessagesLogs.js file.
    
3. Add the Batch file in Task Scheduler for auto cleanup: Run Removelogmessagescollection.bat
    
4. From the Task Scheduler, run the following job:
   

Files required: ( * change the extension from jsp to js and batt to bat )

• deleteLogMessagesLog
• Removelogmessagescollection