I am getting the following error. Are you getting the same one?

Can't locate warning.pm in @INC (...
[download]

OK, so change warning to warnings only to get the rest of the errors:

Global symbol "$filename" requires explicit package name at 2.pl line 
+7.
Global symbol "$i" requires explicit package name at 2.pl line 16.
Global symbol "$i" requires explicit package name at 2.pl line 16.
Global symbol "$count" requires explicit package name at 2.pl line 16.
Global symbol "$i" requires explicit package name at 2.pl line 16.
Global symbol "@st" requires explicit package name at 2.pl line 18.
Global symbol "$i" requires explicit package name at 2.pl line 18.
Global symbol "@st" requires explicit package name at 2.pl line 19.
Global symbol "@st" requires explicit package name at 2.pl line 19.
Global symbol "$i" requires explicit package name at 2.pl line 21.
[download]

Seems like scoping problems. Here is the code fixed with explanation:

use strict;
use warnings;                                       # Already mentione
+d.
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 o
+utside the loop to survive.
while (<FILE>)
{
    push (@line, $_);
    $count++;                                       # Using 'my' here 
+means $count is initialized
}                                                   # to 0 in each ite
+ration of the loop.
print W $line [0];
for (my $i = 0; $i < $count; $i++)                  # $i was not decla
+red
{
    my @st = split (' ', $line [$i]);               # @st was not decl
+ared
    if (($st [4] eq /chr1/) && ($st [10] eq /chr1/))
    {
        print W $line [$i];
    }
}
[download]

Now the code has no compilation errors. It probably still does not work, though. Happy debugging!