Others beat me to the punch, in that you were making the assumption that every line in your input file would consist of the three arguments separated by a tab character. This brings up a matter of good programming practice - never assume that the data you are being fed meets the rules. So you need to allow for two situations; the first which you have already found, where there are less than the required number of fields; and the case where there may be more than 3.

A quick scan through the split documentation says that when called in the scalar context, it will return the count of the substrings. You may want to put a test in first - something like:

if ( (scalar (split /\t/)) == 3 ) {
    # Do our stuff
}
else {
    print "Bad data", $_;
}
[download]

Updated I should not try to program before my first cup of coffee. Yes, fastolfe and runrig picked up the error - the single "=" has been replaced with the "==". (slaps himself silly)