Use a timer to schedule the execution of your deletion code every 5 minutes. Note that if matlab is too busy to process events, the timer may not be called until matlab is less busy. There's no way around that since matlab is single threaded.
There is actually no way in matlab to simply truncate a file. You have two options:
1. Read the entire content of the file and rewrite bar the last line. That's probably not going to be fast.
fcontent = fileread('somefile.txt');
fid = fopen('somefile.txt', 'wt');
fwrite(fid, regexp(fcontent, '.*(?=\n.*?)', 'match', 'once'));
fclose(fid);
2. Figure out the length the file should be without the last line (possibly using fopen, fgetl and ftell), and use this submission from the FEX to truncate the file to that length.
