diff --git a/dist.ini b/dist.ini
index 0762d92..5309b93 100644
--- a/dist.ini
+++ b/dist.ini
@@ -1,5 +1,5 @@
 name    = Bio-Roary
-version = 2.2.2
+version = 2.2.3
 author  = Andrew J. Page <ap13@sanger.ac.uk>
 license = GPL_3
 copyright_holder = Wellcome Trust Sanger Institute
diff --git a/lib/Bio/Roary/External/Mcl.pm b/lib/Bio/Roary/External/Mcl.pm
index f3aa353..265d469 100644
--- a/lib/Bio/Roary/External/Mcl.pm
+++ b/lib/Bio/Roary/External/Mcl.pm
@@ -64,7 +64,7 @@ sub _command_to_run {
         " ",
         (
             $self->mcxdeblast_exec, '-m9', '--score='.$self->_score,
-            '--line-mode=abc', $self->blast_results, 
+            '--line-mode=abc', $self->blast_results, '2> /dev/null',
             '|', $self->mcl_exec, '-', '--abc',
             '-I', $self->_inflation_value, '-o', $self->output_file, 
             $self->_logging
diff --git a/lib/Bio/Roary/PostAnalysis.pm b/lib/Bio/Roary/PostAnalysis.pm
index efcc868..f3b829e 100644
--- a/lib/Bio/Roary/PostAnalysis.pm
+++ b/lib/Bio/Roary/PostAnalysis.pm
@@ -218,6 +218,11 @@ sub _delete_intermediate_files
   my ($self) = @_;
   return if($self->dont_delete_files == 1);
   
+  for my $fasta_file (@{$self->fasta_files})
+  {
+      unlink($fasta_file) if(-e $fasta_file);
+  }
+  
   unlink($self->_output_mcl_filename)              ;
   unlink($self->_output_inflate_clusters_filename) ;
   unlink($self->_output_group_labels_filename)     ;
diff --git a/lib/Bio/Roary/SplitGroups.pm b/lib/Bio/Roary/SplitGroups.pm
index de56cec..d039c18 100644
--- a/lib/Bio/Roary/SplitGroups.pm
+++ b/lib/Bio/Roary/SplitGroups.pm
@@ -24,11 +24,11 @@ has 'outfile'     => ( is => 'ro', isa => 'Str',      required => 1 );
 has 'iterations'  => ( is => 'ro', isa => 'Int',      default  => 5 );
 has 'dont_delete' => ( is => 'ro', isa => 'Bool',     default  => 0 );
 
-has '_outfile_handle'     => ( is => 'ro', lazy_build => 1 );
 has '_neighbourhood_size' => ( is => 'ro', isa => 'Int', default => 5 );
 
 has '_group_filelist'  => ( is => 'rw', isa => 'ArrayRef', lazy_build => 1 );
-has '_tmp_dir'         => ( is => 'ro', isa => 'Str',      default => 'split_groups' );
+has '_tmp_dir_object' => ( is => 'ro', isa => 'File::Temp::Dir', default => sub { File::Temp->newdir( DIR => getcwd, CLEANUP => 1 ); } );
+has '_tmp_dir'        => ( is => 'ro', isa => 'Str', lazy => 1, builder => '_build__tmp_dir' );
 
 has '_analyse_groups_obj' => ( is => 'ro', lazy_build => 1 );
 has '_genes_to_files'     => ( is => 'ro', lazy_build => 1 );
@@ -45,11 +45,9 @@ has '_gene_files_temp_dir_obj' =>
 
 has '_do_sorting' => ( is => 'rw', isa => 'Bool', default => 0 ); # set to 1 for testing only
 
-sub _build__outfile_handle {
-	my ( $self ) = @_;
-
-	open( my $fh, '>', $self->outfile );
-	return $fh;
+sub _build__tmp_dir {
+    my ($self) = @_;
+    return $self->_tmp_dir_object->dirname();
 }
 
 sub _build__analyse_groups_obj {
@@ -79,14 +77,6 @@ sub _build__group_filelist {
 	return \@filelist;
 }
 
-sub _make_tmp_dir {
-	my ( $self ) = @_;
-	my $dir = $self->_tmp_dir;
-	unless ( -e $dir ) {
-		make_path($dir) or die "Cannot make dir: $dir\n" ;
-	}
-}
-
 sub _build__genes_to_neighbourhood
 {
   my ( $self ) = @_;
@@ -119,8 +109,6 @@ sub _build__genes_to_neighbourhood
 sub split_groups {
 	my ( $self ) = @_;
 
-	$self->_make_tmp_dir;
-
 	# iteratively
 	for my $x ( 0..($self->iterations - 1) ){
 		my ( $in_groups, $out_groups ) = $self->_get_files_for_iteration( $x ); 
@@ -168,8 +156,6 @@ sub split_groups {
 		}
 		close( $outfile_handle );
 	}
-
-	remove_tree( $self->_tmp_dir ) unless ( $self->dont_delete );
 }
 
 sub _set_genes_to_groups {
@@ -177,8 +163,8 @@ sub _set_genes_to_groups {
 
 	my %genes2groups;
 	my $c = 0;
-	open( GFH, '<', $groupfile );
-	while( my $line = <GFH> ){
+	open( my $gfh, '<', $groupfile );
+	while( my $line = <$gfh> ){
 		chomp $line;
 		my @genes = split( /\s+/, $line );
 		for my $g ( @genes ){
@@ -186,6 +172,7 @@ sub _set_genes_to_groups {
 		}
 		$c++;
 	}
+    close($gfh);
 	$self->_genes_to_groups( \%genes2groups );
 }
 
diff --git a/t/Bio/Roary/CommandLine/Roary.t b/t/Bio/Roary/CommandLine/Roary.t
index ef4dd10..88d0570 100755
--- a/t/Bio/Roary/CommandLine/Roary.t
+++ b/t/Bio/Roary/CommandLine/Roary.t
@@ -53,8 +53,24 @@ cleanup_files();
   );
 
 mock_execute_script_and_check_output_sorted_groups( $script_name, \%scripts_and_expected_files, [0,6,7,8,9] );
+
+# Make sure faa files are cleaned up automatically
+ok(!(-e 'query_1.gff.proteome.faa'),'Check protein query_1.gff.proteome.faa is cleaned up');
+ok(!(-e 'query_2.gff.proteome.faa'),'Check protein query_2.gff.proteome.faa is cleaned up');
+ok(!(-e 'query_5.gff.proteome.faa'),'Check protein query_5.gff.proteome.faa is cleaned up');
+
+
+%scripts_and_expected_files = (
+'-j Local --dont_delete_files t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff ' =>
+  [  'empty_file', 't/data/empty_file'  ],
+  );
+mock_execute_script_and_check_output_sorted_groups( $script_name, \%scripts_and_expected_files, [0,6,7,8,9] );
+ok((-e 'query_1.gff.proteome.faa'),'Check protein query_1.gff.proteome.faa is not cleaned up');
+ok((-e 'query_2.gff.proteome.faa'),'Check protein query_2.gff.proteome.faa is not cleaned up');
+ok((-e 'query_5.gff.proteome.faa'),'Check protein query_5.gff.proteome.faa is not cleaned up'); 
+
 cleanup_files();
-  
+ 
 SKIP: 
 {
 
@@ -89,32 +105,42 @@ done_testing();
 sub cleanup_files
 {
   remove_tree('pan_genome_sequences');
+  unlink('_blast_results');
+  unlink('_clustered');
+  unlink('_clustered.bak.clstr');
+  unlink('_clustered.clstr');
+  unlink('_combined_files');
+  unlink('_combined_files.groups');
+  unlink('_fasta_files');
+  unlink('_gff_files');
+  unlink('_inflated_mcl_groups');
+  unlink('_inflated_unsplit_mcl_groups');
+  unlink('_labeled_mcl_groups');
+  unlink('_uninflated_mcl_groups');
+  unlink('accessory.header.embl');
+  unlink('accessory.header.tab');
+  unlink('accessory.tab');
+  unlink('blast_identity_frequency.Rtab');
   unlink('clustered_proteins');
+  unlink('core_accessory.header.embl');
+  unlink('core_accessory.header.tab');
+  unlink('core_accessory.tab');
+  unlink('core_gene_alignment.aln');  
   unlink('database_masking.asnb');
   unlink('example_1.faa.tmp.filtered.fa');
   unlink('example_2.faa.tmp.filtered.fa');
   unlink('example_3.faa.tmp.filtered.fa');
   unlink('gene_presence_absence.csv');
-  unlink('query_1.gff.proteome.faa');
-  unlink('query_2.gff.proteome.faa');
-  unlink('query_3.gff.proteome.faa');
-  unlink('_clustered');
-  unlink('_clustered.bak.clstr');
-  unlink('pan_genome.fa');
-  unlink('core_accessory.header.tab');
-  unlink('accessory.header.tab');
-  unlink('accessory.tab');
-  unlink('core_accessory.tab');
   unlink('number_of_conserved_genes.Rtab');
   unlink('number_of_genes_in_pan_genome.Rtab');
   unlink('number_of_new_genes.Rtab');
   unlink('number_of_unique_genes.Rtab');
+  unlink('pan_genome.fa');
+  unlink('query_1.gff.proteome.faa');
+  unlink('query_2.gff.proteome.faa');
+  unlink('query_3.gff.proteome.faa');
   unlink('query_5.gff.proteome.faa');
-  unlink('core_gene_alignment.aln');  
-  unlink('blast_identity_frequency.Rtab');
   unlink('real_data_1.gff.proteome.faa');
   unlink('real_data_2.gff.proteome.faa');
-  unlink('accessory.header.embl');
-  unlink('core_accessory.header.embl');
 
 }
\ No newline at end of file
diff --git a/t/Bio/Roary/External/Mcl.t b/t/Bio/Roary/External/Mcl.t
index 58af5f5..b8f1a9c 100644
--- a/t/Bio/Roary/External/Mcl.t
+++ b/t/Bio/Roary/External/Mcl.t
@@ -28,7 +28,7 @@ ok(
 is(
     $obj->_command_to_run,
     $cwd
-      . '/t/bin/dummy_mcxdeblast -m9 --score=r --line-mode=abc some_blast_results | '
+      . '/t/bin/dummy_mcxdeblast -m9 --score=r --line-mode=abc some_blast_results 2> /dev/null | '
       . $cwd
       . '/t/bin/dummy_mcl - --abc -I 1.5 -o output.groups > /dev/null 2>&1',
     'Command constructed as expected'