Perhaps your code will run better like this:

#!/usr/bin/perl
#network_coco.plx

use warnings;
use strict;


open DATAOUT2, '>>', 'cococount.txt' or die "$!\n";

for my $count ( 90 .. 95 ) {

    open DATAIN, '<', $ARGV[ 0 ] or die "cannot open \"ARGV[0]\":$!";
    open DATAOUT, '>', 'variable' or die "$!\n";

    while ( <DATAIN> ) {
        my $field = ( split /\t/ )[ 2 ];
        if ( $field >= "0.$count" ) {
            print DATAOUT;
        }
    }

    close DATAOUT;
    close DATAIN;

    #clm close reads file variable, and gives back an integer

    open VAR2, '-|, 'clm', 'close', '-abc', 'variable', '--is-undirect
+ed', '--write-count', '-cc-bound', '5' or die "$!\n";

    while ( <VAR2> ) {
        chomp;
        print DATAOUT2 "0.$count\t$_\n";
    }

    close VAR2 or warn $! ? "Error closing pipe: $!"
                          : "Exit status $? from clm";

}

close DATAOUT2;
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