There are some big errors in there...

I see where you have tried to adopt some of what I have done but there are some points that you are missing.

Let's start here:

Code:

my $outputfile = "COUNTBASE";
unless (open(COUNTBASE, ">$outputfile")) {print "cant open file\n\n";
exit;}
print COUNTBASE "$dataline[7]";
close (COUNTBASE);
my $dnafile = <COUNTBASE>;
#Remove the newline from the dna file name
chomp $dnafile;
#Open this file or exit 
unless (open(COUNTBASE, $dnafile)){
         print  "can't open file \"$dnafile\"\n\n";
        exit;
}
#store dna information
my @dna = <COUNTBASE>;
#close now read file
close COUNTBASE;

At the top you are trying to open a file, and you appear to want to "READ" it because you try to set $dnafile with the filehandle. However your method is a slightly off, to read is "<", if writing (">") you would not try to GET content from the file into a variable (unless using read & write ("+<" or "+>").

Code:

my $outputfile = "COUNTBASE";
unless (open(COUNTBASE, ">$outputfile")) {print "cant open file\n\n";
exit;}
print COUNTBASE "$dataline[7]";
close (COUNTBASE);

should be something more like (if reading the file):

Code:

open(COUNTBASE, "<", "countbase.log") or die $!;
@data = <COUNTBASE>; 
close (COUNTBASE);

The open function is easiest to use when you stick to the 3 argument form. Also, when using a variable, you should escape the "$" symbol in the open function...
Taken from perldoc.org:
While that is not to say "only" takes 3 arguments, it is most often used that way. You can read more on that function at:
Perl Doc - Open Function

The "or die $!" says if we couldn't open the file, exit with the error that was returned while trying to open it. The "$!" variable contains the actual error that was returned to perl from the OS. You will want to see that error not "Could't open file". A generic error message is confusing and makes debugging very hard. The actual error will be more helpful in tracking down errors.

I suggest changing to this style for the rest of your file operations as well.

The errors you see are are actually correct because you try to use "COUNTBASE" which is the file handle (not the file name or even the file itself) AFTER you have closed it.

Code:

unless (open(COUNTBASE, ">$outputfile")) {print "cant open file\n\n"; exit;}
print COUNTBASE "$dataline[7]";
close (COUNTBASE); # CLOSE FILEHANDLE HERE
my $dnafile = <COUNTBASE>; # ERROR GENERATED HERE

Given that as a start, I am not sure exactly what you are trying to do with that section of code.

Consider this code:

Code:

#!/usr/bin/perl
use strict;
use warnings;

open(FILE1,"<","file1.txt") or die $!; 
while (<FILE1>) {
	print $_;
}
close(FILE1);

RESULTS:

Code:

blah blah one
blah blah two
blah blah three

Now consider this code (more like yours):

Code:

#!/usr/bin/perl
use strict;
use warnings;

my $data;
open(FILE1,"<","file1.txt") or die $!; 
$data = <FILE1>;
close(FILE1);
chomp $data;
print $data . "\n";

RESULTS:

Code:

blah blah one

That code is not what you want, you have type cast "data" as a string not an array!
Because of this you only managed to get the first line into the string variable.
What I think you wanted was something more like this though...

Code:

#!/usr/bin/perl

use strict;
use warnings;

my (@data, $row, @dataline);
open(FILE1,"<","file1.txt") or die $!; 
@data = <FILE1>; 
close(FILE1);
foreach $row (@data) {
	@dataline = split('\s',$row);
	print $dataline[2] . "\n";
}

RESULTS:

Code:

one
two
three