use strict;
use warnings;                                       # Already mentioned.
print "\n Enter The file name :>";
chomp(my $filename1 = <STDIN>);
open(FILE,"<",$filename1)
    or die "\n...Cannot find the file: $filename1"; # Missing 1 at the end of the message.
open (W, "> Result.txt");
my @line;
my $count;                                          # To be declared outside the loop to survive.
while (<FILE>)
{
    push (@line, $_);
    $count++;                                       # Using 'my' here means $count is initialized
}                                                   # to 0 in each iteration of the loop.
print W $line [0];
for (my $i = 0; $i < $count; $i++)                  # $i was not declared
{
    my @st = split (' ', $line [$i]);               # @st was not declared
    if (($st [4] eq /chr1/) && ($st [10] eq /chr1/))
    {
        print W $line [$i];
    }
}