$sth->finish() is *only* needed when you have not fetched all available rows in the statement handle.

Since your "results.100.out" file and your "marker.list.txt" file appear to be "tab delimited" files, you may want to consider using DBD::CSV which can easily handle files with tabs as field separators and anything as a record separator. That way, you'd be able to use DBI and SQL to search those files, eliminate the parsing parts of your code, gain the benefits of file locking (if relevant), and gain some speed (if relevant).