Not that this would make a big difference in terms of run-time, but you don't have to keep your own counter for the number of lines in the file. The predefined global variable $. does that for you (cf. the perlvar man page):

print "Num. Line : $. - Occ : $counter2\n";
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A few other observations...

I fetched the "10-million-combos.txt.zip" file you cited in one of the replies above, and noticed that it contains just the one text file. In terms of benchmarking, you might find that a command-line operation like this:

unzip -p 10-million-combos.txt.zip | perlscript
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is likely to be faster than having the perl script read an uncompressed version of the file from disk, because piping output from "unzip -p" involves fetching just 23 MB from disk, as opposed to 112 MB to read the uncompressed version. (Disk access time is always a factor for stuff like this.)

Spoiler alert: your file "10-million-combos.txt" does not contain any lines that match /123456$/. UPDATE: actually, there would be 2 matches on a windows system, and I find those two on my machine if I search for /123456\r\n$/.

I was going to suggest using the gnu/*n*x "grep" command-line utility to get a performance baseline, assuming that this would be the fastest possible way to do your regex search-and-count, but then I tried it out on your actual data and got a surprise (running on a macbook pro, osx 10.10.5, 2.2GHz intel core i7, 4GB ram):

$ unzip -p 10-million-combos.txt.zip | time grep -c 123456$
0
        3.30 real         3.25 user         0.01 sys
$ unzip -p 10-million-combos.txt.zip | time grep -c 123456$
0
        3.23 real         3.22 user         0.01 sys
$ unzip -p 10-million-combos.txt.zip | time grep -c 123456$
0
        3.18 real         3.17 user         0.01 sys

$ unzip -p 10-million-combos.txt.zip | time perl -ne 'BEGIN{$n=0} $n++
+ if /123456$/; END{print "$. lines, $n matches\n"}'
9835513 lines, 0 matches
        1.96 real         1.89 user         0.02 sys
$ unzip -p 10-million-combos.txt.zip | time perl -ne 'BEGIN{$n=0} $n++
+ if /123456$/; END{print "$. lines, $n matches\n"}'
9835513 lines, 0 matches
        1.96 real         1.93 user         0.02 sys
$ unzip -p 10-million-combos.txt.zip | time perl -ne 'BEGIN{$n=0} $n++
+ if /123456$/; END{print "$. lines, $n matches\n"}'
9835513 lines, 0 matches
        1.93 real         1.90 user         0.02 sys
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I ran each command three times in rapid succession, to check for timing differences due to system cache behavior and other unrelated variables. Perl is consistently faster by about 33% (and can report total line count along with match count, which the grep utility cannot do).

(If I remove the "$" from the regex, looking for 123456 anywhere on any line, I find three matches, and the run times are just a few percent longer overall.)