OK,I've checked the exit values of all of the components of the script and they all exit with a status of 0. However, when trying to make my script smaller, I realized that it works fine if I simply have the first subroutine print a txt file. So it seems to me that the issue has to due with this subroutine:

sub rep_set{

    open(FILE, "Superior_seqs2.txt")
        ||die;
    $/=">";

    my%hash=();
    my$hashref=\%hash;

    while(<FILE>){
        if($_ =~ /^(.+?)\((\d+)\)(.+)\n(.+)/){
            my$site=$1;my$count=$2;my$qiime=$3;my$seq=$4;
            $hashref -> {$seq}{$site}=$count;
        }else{
            print "ERROR!\n"
        }
    }
    open (TABLE, ">>OTU_TABLE.txt")||die; 
    open (REP,">>rep_set.txt")||die;

    my$seq_label=0;

    for my$seq_key(keys %hash){
        $seq_label++;
        print REP ">$seq_label\n$seq_key\n";
        print TABLE ">$seq_label\t";
        for my$site_key(keys %{$hash{$seq_key}}){
                my$counts="$hash{$seq_key}{$site_key}";
                #print "$counts\n";
            
                for(my$i=0;$i<=$counts;$i++){
                    print TABLE "$site_key\t";
                }        
        }
        print TABLE "\n";
    }
    close FILE;close TABLE;close REP;
}
[download]

The file that is being opened has the following format:

>ZZ2(12)orig_bc=GTAGCAACGTC new_bc=GTAGCAACGTC bc_diffs=0
TACGAAGGGACCTAGCGTAGTTCGGAATTACTGGGCGTAAAGCGCGCGTAGGCCGTTGAGTTAGTTAATT
+GTGAAATCCCAAAGCTTAACTTTGGAACTGCAATTAAAACTGCTCGACTAGAGTTTGATAGAGGAAAGC
+GGAATACATAGTGTAGAGGTGAAATTCGTAGATATTATGTAGAGCACCAGTTGCGAAGGCGGCTTTCTG
+GATCAACACTGACGCTGAGGCGCGAAAGTATGGGTAGCAAAGAGG

>ZZ2(6)orig_bc=GTAGCAACGTC new_bc=GTAGCAACGTC bc_diffs=0
TACGAAGGGACCTAGCGTAGTTCGGAATTACTGGGCGTAAAGCGCGCGTAGGCCGTTGAGTTAGTTAATT
+GTGAAATCCCAAAGCTTAACTTTGGAACTGCAATTAAAACTGCTCGACTAGAGTTTGATAGAGGAAAGC
+GGAATACATAGTGTAGAGGTGAAATTCGTAGATATTATGTAGAACACCAGTTGCGAAGGCGGCTTTCTG
+GATCAACACTGACGCCGAGGCGCGAAAGTATGGGTAGCAAAGAGG

>ZZ2(15)orig_bc=GTAGCAACGTC new_bc=GTAGCAACGTC bc_diffs=0
TACGTAGGGACCTAGCGTAGTTCGGAATTACTGGGCGTAAAGCGCGCGTAGGCCGTTGAGTTAGTTAATT
+GTGAAATCCCAAAGCTTAACTTTGGAACTGCAATTAAAACTGCTCGACTAGAGTTTGATAGAGGAAAGC
+GGAATACATAGTGTAGAGGTGAAATTCGTAGATATTATGTAGAACACCAGTTGCGAAGGCGGCTTTCTG
+GATCAACACTGACGCTGAGGCGCGAAAGTATGGGTAGCAAAGAGG
[download]

it has ~39,000 entries

To avoid potential headaches, always localize assignments to global variables like $/.

local $/ = '>';

That way, the value of $/ will be automatically restored after the sub exits. Later parts of your program might not like having a weird line terminator dropped on them.

Also good practice to localize $_ if you're using it for that type of while loop.

local $_;
while (<FILE>) {
[download]

Thanks, that solved my problem. I had to localize the $/ value. :)

Also, if you have any suggestions to make my code more readable, I would appreciate it. Not being from a computer background, I don't have much experience making it readable by others. :)