What does "not working fine" mean? (For that matter, what does "working fine" mean?)

When you do this part:

while(<FILE>){
    $_=~s/\s+//g;
    push(@array1,$_);
}
my %s = ();
$s{$_}++ for @array1;
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Is it really your intention to create a hash whose keys look like this:

N01A0000.fBG1_c22
N01A000X.fBG1_c5
N01A000X.rBG1_c5
...
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The list you showed us has 15 lines. When the lines are converted to hash keys using your method, they are all unique. What were you expecting to get as a result?

Update: By the way, why do you use an array and a hash? You could have just done this:

my %s;
while(<FILE>) {
    s/\s+//g;
    $s{$_}++;
}
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(Of course, for the data you've shown, that will still end up with all lines being unique. So, what is it about the data that makes two or more lines duplicates?)