I tried to make your script a self contained example as follows, but it doesn't like the "data" I gave it. Would you like to improve the sample data?

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

$/ = ''; # Set paragraph mode

my @count;
my %absent;
my $name;

while ( my $para = <DATA> ) {
    # Remove fasta header line
    if ( $para =~ s/^>(.*)//m ){
      $name = $1;
    };
    # Remove comment line(s)
    $para =~ s/^\s*#.*//mg;

    my %prot;
    $para =~ s/([ACDEFGHIKLMNPQRSTVWY])/ ++$prot{ $1 } /eg;
    my $len = length($para);
    my $num = scalar keys %prot;
    push @count,[$num,$name];
    printf "Counted %d for %s ..\n",$num,substr($name,0,50);

    print "$name\n";
    print join( ' ', map "$_=$prot{$_}", sort keys %prot ), "\n";
    printf "Amino acid alphabet = %d\n\n",$num ;
    print "Sequence length = ", $len;

    # count absent
    for ('A'..'Z'){
      ++$absent{$_} unless exists $prot{$_};
    };

};

# sort names by count in ascending order to get lowest
my @sorted = sort { $a->[0] <=> $b->[0] } @count;
my $lowest = $sorted[0]->[0];

# maybe more than 1 lowest
printf "Least number of amino acids is %d in these entries\n",$lowest;
my @lowest = grep { $_->[0] == $lowest } @sorted;
print "$_->[1]\n" for @lowest;

# show all results
print "\nAll results in ascending count\n";
for (@sorted){
  printf "%d  %s\n", @$_;
};

print "\nExclusion of various amino acids is as follows\n";
for (sort keys %absent){
  printf "%s=%d\n",$_,$absent{$_};
};

__DATA__
print 'Please enter protein sequence filename: ';
chomp( my $prot_filename = <STDIN> );

open my $PROTFILE, '<', $prot_filename
  or die "Cannot open '$prot_filename' because: $!";

my $report_name = $prot_filename.'_report';
open my $out_file, '>', $report_name
     or die "Cannot open '$report_name' because: $!";

close $out_file;
print "Results are printed in $report_name\n";

# print absent counts
print "\nExclusion of various amino acids in $prot_filename is as foll
+ows\n";
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