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#!/usr/bin/perl
use warnings; use strict;
...
close $output;

print "Done\n";

cat output.txt

3162    0    0    501093    0    0
3163    0    0    2958    0    0
3164    0    0    1895    0    0
3165    0    0    1382    0    0
3166    0    0    2869    0    0