Removed unused arguments

scripts/kraken

@@ -55,9 +55,7 @@ my $paired = 0;
 my $check_names = 0;
 my $only_classified_output = 0;
 my $unclassified_out;
-my $unclassified_out_prefix;
 my $classified_out;
-my $classified_out_prefix;
 my $output_format = "legacy";
 my $outfile;
 
@@ -72,9 +70,7 @@ GetOptions(
   "quick" => \$quick,
   "min-hits=i" => \$min_hits,
   "unclassified-out=s" => \$unclassified_out,
-  "unclassified-out-prefix=s" => \$unclassified_out_prefix,
   "classified-out=s" => \$classified_out,
-  "classified-out-prefix=s" => \$classified_out_prefix,
   "out-fmt=s" => \$output_format,
   "output=s" => \$outfile,
   "preload" => \$preload,
@@ -150,9 +146,7 @@ push @flags, "-m", $min_hits if $min_hits > 1;
 push @flags, "-f", if $fastq_input;
 push @flags, "-F", if $fastq_output;
 push @flags, "-U", $unclassified_out if defined $unclassified_out;
-push @flags, "-r", $unclassified_out_prefix if defined $unclassified_out_prefix;
 push @flags, "-C", $classified_out if defined $classified_out;
-push @flags, "-p", $classified_out_prefix if defined $classified_out_prefix;
 push @flags, "-O", $output_format if defined $output_format;
 push @flags, "-o", $outfile if defined $outfile;
 push @flags, "-c", if $only_classified_output;