use strict;
use warnings;    #<<-- warnings

print "\n Enter The file name :>";
chomp( my $filename1 = <STDIN> );
open( FILE, "<", $filename1 )
  or die "\n...Cannot find the file: $filename1";    #<<-- $filename1"
open( W, "> Result.txt" );
my @line;
while (<FILE>) {
    push( @line, $_ );
    my $count++;
}
print W $line[0];
for ( my $i = 0 ;$i < $count ;$i++ ) #<<-- my $i; $count, from above, has dropped outside of scope and is now undefined. Update: use $i < $#line+1
{
    my @st = split( ' ', $line[$i] );    #<<-- my @st
    if ( ( $st[4] eq /chr1/ ) && ( $st[10] eq /chr1/ ) ) {
        print W $line[$i];
    }
}