As I reread your initial post, I suspect you want to split nt into smaller chunks and write those to file. Here is a script I've been using to do that

### USAGE
# perl -w splitter.pl <filename> <seq-per-file>
# e.g. perl -w splitter.pl nt 20000

### INCLUDES
use strict;
use Bio::SeqIO;

### LOCALS
my $infile    = $ARGV[0];
my $size    = $ARGV[1];
my $i        = 0;
my $j        = 1;

### OBJECT INSTANTIATION
my $in    = Bio::SeqIO->new(
            -file    => $infile,
            -format    => 'Fasta',
            );
my $out    = Bio::SeqIO->new(
            -file    => ">$infile"."_$j.fasta",
            -format    => 'Fasta',
            );

### PROCESS FILES
while ( my $seq = $in->next_seq() ) {

    $i++;

    if ($i == $size) {
        $j++;
        $out = Bio::SeqIO->new(
                    -file    => ">$infile"."_$j.fasta",
                    -format    => 'Fasta');
        $i = 0;
        }

    $out->write_seq($seq);

    }
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