You need to provide a value to printf for example

printf $out_file "string length = %d\n",length($num) ;
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but that gives you the length of the count value not the sequence. You need to calculate the sequence length before the value is changed by this counting regex $para =~ s/([A-Z])/ ++$prot{ $1 } /eg;

Try making these changes

    # Remove comment line(s) and white space
    $para =~ s/^\s*#.*//mg;
    $para =~ s/\s//g; # add
    my $seq_length = length($para); # add
    print "[$para]\n"; # optional
    .
    .
    printf $out_file "Number of proteins = %d\n",$num ;
    printf $out_file "String length = %d\n\n",$seq_length; # add
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poj