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while (<FILE> ) {

AB00001 N120001
BB00002 N200023
CB00003 N300011
DB00004 N400022

# replace the while(<FILE>) { with the following two lines

for(my $i = 1; $i <= 2; $i++) {
        $_ = <FILE>;

        # ftp directories
my @ftp_locations = ("FTP/A1", "FTP/B2");
...
        # Sleep for 20 minutes before processing next file.
        sleep (20 * 60)
}