MongoDB deleted logs
Looks like somebody deleted the log file while it was used by the mongodb process. Deleting log files is such a manner is not a good idea as the process will keep it locked and that means the file will keep occupying space on the disk. Such deleted files entry in the lsof will disappear once the process that is locking it is restarted.

The best way to handle logs files is by using proper log rotation by utilities like logrotate which is available on almost all linux systems.

If you ever face a situation where the log file has grown too big and you want to free up space without restarting the service, the best way would be to truncate the file using - cat /dev/null &gt; /var/log/my_big_log_file.log or just echo "" &gt; /var/log/my_big_log_file.log. Just remember that, this is not a proper solution for handling log files and should be used as a temporary fix.