Thanks for your reply! Well, it's only the  my $prot3 = $seq->translate(2); part that does not work, which makes me think the input is fine since it works for the $prot and $prot2.

However, here is sample input if it helps! The file contains 194,503 of these sequences, but here are a couple for an idea:

>3HSAA000001 CA000001
tgcagccgcgggcccagggtgctgttggtgtcctcagaagtgccggggattctggactgg
ctccctcccctcctgttgcagcacaaggccggggtctctggggggctggagaagcctccc
tcattcctcccaggaattaataaatgtgaagagaggctctgtttaaaatgtctttggact
cccagggctgagtgggctgggatctcgtgtcctcaa
>3HSAA000002 CA000002
tgcagccgcgggcccagggtgctgttggtgtcctcagaagtgccggggattctggactgg
ctccctcccctcctgttgcagcacaaggccggggtctctggggggctggagaagcctccc
tcattcctcccaggaattaataaatgtgaagagaggctctgtttaaaatgtctttggact
cccagggctgagtgggctgggatctcgtgtcctcaaagtggatgggttctggggtggctc
ctgaggtagaggagtggagaactggctcttaagagcacagttttcttttcttttttcttt
tttgagacagggtctcacactgtcacccaggctggagtgcagtgttgcagtccggctcac
tgcagttttgacctcccaggctcaagcgatcctcctgcctcagcctcccaagtagctggg
agcctgggcatgcatcgccacgtctggctaattattattttttgtagacagggtctcact
gtgttgcccaagcttgtcttgaactcctggccttaagtgatcctcccacctcagcctcct
gagtagctgggactacaggcatgagccaccatgcctggccaactcacatttttctttcta
ttatttattttttgtagagatgagtctcactatgttgcccaggctggtcttgaactcttg
ggctcaagtgatcctcccgcctcagcctcccaaagtgttgggattacaggtgtgagccac
agcacctggccaaccaacacttctcagggcctctttcatctgtgctcttccaggatgctg
cctcttactccctgggcacctcggcctggtcccagcaggtatgggcagttgcttgaggct
ccagacatactcacctctacctcgaccacatcaaccccatcaccaagaggaggttcaggg
aagctgcattttgtggtcttgtcctcccagtccagggtggtagtgctgggctgttcccag
cctcccacagcagagctggacgctgtggaaatggctggattcctctgtgttctttcccat
tatccctcagctctgagtcctcttgtgccatctgacatctgatgccttcccaaccactgc
cgagtttctgcctggagcagggcctcaaggccctggcacacagaagatgcgtatcagtat
tatcaaccaatagttgatgaattgtgtttttcaacgaatttgctagtgatctggtttact
gccttagtaatatctagttcctaatatgcctatgccttttaatgtctgcacagtctatga
tgatgtcacttctctcaagcctgatgtgtcctctctctctttcttgctagtggtttatca
atttttaaaaccttttcttgtttatttgtttttgagacagaattttgctcttgttgccca
ggctggagtgcaatggcgtgatcttggctcacagcaacctctacctcctgggttcaagtg
attctcgtgcctcagcctcctgagtagctgggctgacaggcacccaccaccacacccagc
taatttttatgtttttagtagagatggggtttcaccttgttgggtggccaggctggtctc
caactcctgagctcaagtgatccacccgcctcagcctcccaaagtgctgggattacaggg
gtgagccaccacgcccagccccagcttagttttttaaaaagtttattttagccattctaa
taggtatgtagacatatctaatagtggttttccttgcgtttccttaatgtctgatgatgt
taagcattttttccccaagtgcttagttgccatctatatagcatctttgatgaaatgtct
gtttatatattttgcacactttaaaatattgggttgttttcttt
>3HSAA000003 CA000003
tgcagccgcgggcccagggtgctgttggtgtcctcagaagtgccggggattctggactgg
ctccctcccctcctgttgcagcacaaggccggggtctctggggggctggagaagcctccc
tcattcctcccaggaattaataaatgtgaagagaggctctgtttaaaatgtc
[download]

You're welcome. And what is the goal of the script? To convert the DNA to ribose nucleic acid (RNA) ?
UPDATED CODE TO REFLECT TRANSLATING TO RNA
For starters, here is code I made (with acknowledgements to the Perl Monks for help) to parse a fasta file:

use strict;
use warnings;
use Data::Dumper;

my $file = '/path/to/your/file/here.fasta';
open (my $fh, '<', $file) or die "Could not open file '$file' $!";

my (%sequence_hash, $header);

while ( my $line = <$fh> ) {
    chomp($line);
    if ( $line =~ m/^>(.*)/ ) {
        $header = $1;
    }
    else {
        $sequence_hash{$header} .= $line;
    }
}

# look at the header and sequence
print Dumper(\%sequence_hash);

my @translated_sequences;

foreach my $seq ( keys %sequence_hash ) {
      $sequence_hash{$seq} =~ s/t/u/ig;
      push @translated_sequences, $sequence_hash{$seq};
}

print Dumper(\@translated_sequences);
[download]

My overall goal is converting DNA to AMINO ACIDS (protein). (DNA to RNA is transcription, not translation).

Here is information from BioPerl for using this function:

http://search.cpan.org/~cjfields/BioPerl-1.6.924/Bio/PrimarySeqI.pm#translate

"Function: Provides the translation of the DNA sequence using full IUPAC ambiguities in DNA/RNA and amino acid codes."

Here is the code example from the Beginner's guidelines:

$prot_obj = $my_seq_object->translate(-frame => 1);

And here is an example code I found online in which they call using Bio::SeqIO

 #!/usr/bin/perl -w
use strict;
use Bio::Seq;
use Bio::SeqIO;

my $input = $ARGV[0];

my $seqio_obj = Bio::SeqIO->new(-file => $input, -format => "fasta" );

my $line_count;

# process multi-fasta sequences
while(my $seq_obj = $seqio_obj->next_seq){
  $line_count++;

#  print "===========================================================\
+n";
  # obtain id of the nt sequence
  my $id = $seq_obj->display_id;
  # print id of nt sequence
#  print "SEQ ID\t>\t", $id, "\n";
#  print "===========================================================\
+n";

  # use translate to convert amino acid squence to protein sequence fr
+om frame 0 (default)
  # 'complete' - do some checks for ORF
#  print ">>>>>>>> Frame 0 <<<<<<<\n";
  print ">", $id, "-0", "\n";
  my $prot_obj = $seq_obj->translate();
  # print the protein sequence
  print $prot_obj->seq,"\n";
#  print "\n";
 
#  print ">>>>>>>> Frame 1 <<<<<<<\n";
  # translation starting from the second nucleotide (frame 1)
  print ">", $id, "-1", "\n";
  $prot_obj = $seq_obj->translate(-frame => 1);
  # print the protein sequence
  print $prot_obj->seq,"\n";
#  print "\n";
[download]

My script is working fine for the default frame, for the 1st frame, and until line 5401 for the 2nd frame. The part that messes up is when it gets to the (-frame => 2) file, but even that file works until line 5401. So I don't think it is an input issue.

And thank you for the above code, but I am translating to amino acids.