One thing to improve your code:
The construct:

  open ONE,"<","Filename"  || die  "Cannot open the file ";
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Will not DIE as you expect, due to operator precedence (The 'die' will NEVER get executed).

The preferred, and correct usage is:

open my $one ,"<","/var/www/html/piRNA_html/UNAFold/output_folder_1.tx
+t" or die "Cannot open the file (ONE): $!";
  # Note the use of a block-scoped variable $one, 
  #   and "||" replaced by the low-precedence "or"
  #   and "$!" added to provide the OS error message corresponding to 
+the failure
 @folder = <$one>;
close $one;
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