diff --git a/debian/patches/use_both_hmmsets b/debian/patches/use_both_hmmsets
index 64931c9..7daf6f0 100644
--- a/debian/patches/use_both_hmmsets
+++ b/debian/patches/use_both_hmmsets
@@ -1,45 +1,25 @@
 Description: Use_both_hmmsets
 --- a/bin/barrnap
 +++ b/bin/barrnap
-@@ -4,8 +4,9 @@
- use Time::Piece;
+@@ -3,6 +3,7 @@
+ use warnings;
  use List::Util qw(max);
  use FindBin;
 +use File::Temp qw/ tempfile tempdir /;
+ use File::Temp;
  
--# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 
-+# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
- # global variables
- 
- my $EXE = $FindBin::RealScript;
-@@ -29,13 +30,13 @@
- );
- my $MAXLEN = int( 1.2 * max(values %LENG) );
- 
--# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 
-+# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
- # command line options
- 
- my(@Options, $quiet, $kingdom, $threads, $evalue, $lencutoff, $reject, $incseq);
- setOptions();
- 
--# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 
-+# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
- # check all is well
- 
- msg("This is $EXE $VERSION");
-@@ -64,23 +65,38 @@
+ # . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 
+@@ -64,6 +65,7 @@
  my $hmmdb = "$DBDIR/$kdom.hmm";
  err("Can't find database: $hmmdb") unless -r $hmmdb;
  msg("Using database: $hmmdb");
 +my $nonfreehmmdb = "$DBDIR/nonfree/$kdom.hmm";
  
--# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 
-+# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+ # . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 
+ # check if user is piping to STDIN
+@@ -84,6 +86,20 @@
+ # . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 
  # run the external command
- 
- my $fasta = shift @ARGV;
- $fasta && -r $fasta or err("Usage: $EXE <file.fasta>");
  
 +if (-e $nonfreehmmdb)  {
 +  # prepare full pHMM file (with nonfree if it exists)
@@ -56,21 +36,9 @@
 +}
 +
  msg("Scanning $fasta for $kdom rRNA genes... please wait");
- my $cmd = "$NHMMER --cpu $threads -E $evalue --w_length $MAXLEN  -o /dev/null --tblout /dev/stdout \Q$hmmdb\E \Q$fasta\E";
- msg("Command: $cmd");
- my @hits = qx($cmd 2>&1);
- 
--# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 
-+# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
- # process the output
- 
- my @feat;
--HIT: 
-+HIT:
- foreach (@hits) {
-   chomp;
-   err("nhmmer failed to run - $_") if m/fail|error|core dump|bus error/i;
-@@ -103,7 +119,7 @@
+ my $opts = "--cpu $threads -E $evalue --w_length $MAXLEN -o /dev/null --tblout /dev/stdout";
+ my $cmd = "nhmmer $opts '$hmmdb' '$fasta'";
+@@ -123,7 +139,7 @@
    # check for incomplete alignments
    my $note = '';
    my $len = $end-$begin+1;
@@ -79,7 +47,7 @@
    if ( $len < int($reject * $LENG{$gene}) ) {
      msg("Rejecting short $len nt predicted $gene. Adjust via --reject option.");
      next HIT;
-@@ -121,7 +137,7 @@
+@@ -144,7 +160,7 @@
    ];
  }
  
@@ -88,47 +56,3 @@
  # output a sorted GFF3
  
  sub gff_sort {
-@@ -169,13 +185,13 @@
- 
- sub show_citation {
-   print STDERR << "EOCITE";
--  
-+
- If you use Barrnap in your work, please cite:
- 
-     Seemann T (2013)
-     $EXE $VERSION : $DESC
-     $URL
--    
-+
- Thank you.
- 
- EOCITE
-@@ -194,7 +210,7 @@
-     {OPT=>"help",    VAR=>\&usage,             DESC=>"This help"},
-     {OPT=>"version", VAR=>\&version,           DESC=>"Print version and exit"},
-     {OPT=>"citation",VAR=>\&show_citation,     DESC=>"Print citation for referencing $EXE"},
--    {OPT=>"kingdom=s", VAR=>\$kingdom,  DEFAULT=>'bac', 
-+    {OPT=>"kingdom=s", VAR=>\$kingdom,  DEFAULT=>'bac',
-        DESC=>"Kingdom: ".join(' ', values %KINGDOM) },
-     {OPT=>"quiet!",  VAR=>\$quiet, DEFAULT=>0, DESC=>"No screen output"},
-     {OPT=>"threads=i",  VAR=>\$threads, DEFAULT=>8,  DESC=>"Number of threads/cores/CPUs to use"},
-@@ -227,15 +243,15 @@
-       my $def = defined($_->{DEFAULT}) ? " (default '$_->{DEFAULT}')" : "";
-       $def = ($def ? ' (default OFF)' : '(default ON)') if $_->{OPT} =~ m/!$/;
-       my $opt = $_->{OPT};
--      $opt =~ s/!$//; 
--      $opt =~ s/=s$/ [X]/; 
-+      $opt =~ s/!$//;
-+      $opt =~ s/=s$/ [X]/;
-       $opt =~ s/=i$/ [N]/;
-       $opt =~ s/=f$/ [n.n]/;
-       printf STDERR "  --%-15s %s%s\n", $opt, $_->{DESC}, $def;
-     }
-     else {
-       print STDERR "$_\n";
--    }      
-+    }
-   }
-   exit(1);
- }
diff --git a/debian/patches/use_debian_dirs b/debian/patches/use_debian_dirs
index 914f98e..351364a 100644
--- a/debian/patches/use_debian_dirs
+++ b/debian/patches/use_debian_dirs
@@ -2,7 +2,7 @@
 --- a/bin/barrnap
 +++ b/bin/barrnap
 @@ -14,6 +14,9 @@
- my $AUTHOR = 'Torsten Seemann <torsten.seemann@gmail.com>';
+ my $AUTHOR = 'Torsten Seemann';
  my $URL = 'https://github.com/tseemann/barrnap';
  my $DBDIR = "$FindBin::RealBin/../db";
 +if ( ! -e $DBDIR) {