diff --git a/lib/Bio/PanGenome/Output/GroupsMultifastasNucleotide.pm b/lib/Bio/PanGenome/Output/GroupsMultifastasNucleotide.pm
index ad39f45..beec362 100644
--- a/lib/Bio/PanGenome/Output/GroupsMultifastasNucleotide.pm
+++ b/lib/Bio/PanGenome/Output/GroupsMultifastasNucleotide.pm
@@ -28,6 +28,9 @@ has 'annotate_groups' => ( is => 'ro', isa => 'Bio::PanGenome::AnnotateGroups',
 
 has 'output_directory' => ( is => 'ro', isa => 'Str', lazy => 1, builder => '_build_output_directory');
 
+has '_number_of_groups' => ( is => 'rw', isa => 'Num', lazy_build => 1 );
+has '_group_limit'      => ( is => 'rw', isa => 'Num', default => 8000 );
+
 sub _build_output_directory
 {
   my ($self) = @_;
@@ -35,9 +38,22 @@ sub _build_output_directory
   return $output_directory;
 }
 
+sub _build__number_of_groups {
+  my $self = shift;
+
+  return $self->annotate_groups->_group_counter;
+}
+
 sub create_files {
     my ($self) = @_;
-  
+
+    my $num_groups = $self->_number_of_groups;
+    my $limit      = $self->_group_limit;
+    if ( $num_groups > $limit ){
+      print STDERR "Number of clusters ($num_groups) exceeds limit ($limit). Multifastas not created.\n";
+      return 1;
+    }
+
     make_path($self->output_directory);
     
     for my $gff_file ( @{ $self->gff_files } ) 
diff --git a/lib/Bio/PanGenome/PostAnalysis.pm b/lib/Bio/PanGenome/PostAnalysis.pm
index 13ad5e9..07314af 100644
--- a/lib/Bio/PanGenome/PostAnalysis.pm
+++ b/lib/Bio/PanGenome/PostAnalysis.pm
@@ -181,19 +181,19 @@ sub _delete_intermediate_files
   my ($self) = @_;
   return if($self->dont_delete_files == 1);
   
-  unlink($self->_output_mcl_filename)                      ;
-  unlink($self->_output_inflate_clusters_filename)         ;
-  unlink($self->_output_group_labels_filename)             ;
-  unlink($self->_output_combined_filename)                 ;
+  unlink($self->_output_mcl_filename)              ;
+  unlink($self->_output_inflate_clusters_filename) ;
+  unlink($self->_output_group_labels_filename)     ;
+  unlink($self->_output_combined_filename)         ;
   unlink($self->clusters_filename)                 ;
   unlink($self->clusters_filename . '.clstr' )     ;
   unlink($self->clusters_filename . '.bak.clstr' ) ;
-  unlink('_gff_files')                              ;
-  unlink('_fasta_files')                            ;
-  unlink('_clustered_filtered.fa')                  ;
-  unlink($self->_input_cd_hit_groups_file)                 ;
-  unlink('database_masking.asnb')                   ;
-  unlink('_clustered')                              ;
+  unlink('_gff_files')                             ;
+  unlink('_fasta_files')                           ;
+  unlink('_clustered_filtered.fa')                 ;
+  unlink($self->_input_cd_hit_groups_file)         ;
+  unlink('database_masking.asnb')                  ;
+  unlink('_clustered')                             ;
 }
 
 no Moose;
diff --git a/t/Bio/PanGenome/Output/GroupsMultifastasNucleotide.t b/t/Bio/PanGenome/Output/GroupsMultifastasNucleotide.t
index b59fa82..7584036 100644
--- a/t/Bio/PanGenome/Output/GroupsMultifastasNucleotide.t
+++ b/t/Bio/PanGenome/Output/GroupsMultifastasNucleotide.t
@@ -9,6 +9,7 @@ BEGIN { unshift( @INC, './lib' ) }
 
 BEGIN {
     use Test::Most;
+    use Test::Output;
     use_ok('Bio::PanGenome::Output::GroupsMultifastasNucleotide');
     use Bio::PanGenome::AnnotateGroups;
     use Bio::PanGenome::AnalyseGroups;
@@ -18,6 +19,7 @@ BEGIN {
 remove_tree('pan_genome_sequences');
 my $gff_files = [ 't/data/query_1.gff', 't/data/query_2.gff','t/data/query_3.gff' ];
 
+my $obj;
 
 my $annotate_groups = Bio::PanGenome::AnnotateGroups->new(
   gff_files       => $gff_files,
@@ -26,10 +28,14 @@ my $annotate_groups = Bio::PanGenome::AnnotateGroups->new(
 
 $annotate_groups->reannotate;
 
+#print Dumper $annotate_groups->_genes_to_file;
+#print Dumper $annotate_groups;
+#print $annotate_groups->_group_counter;
+
 ok(
-    my $obj = Bio::PanGenome::Output::GroupsMultifastasNucleotide->new(
-        group_names    => [ 'group_2', 'group_5' ],
-        gff_files      => $gff_files,
+    $obj = Bio::PanGenome::Output::GroupsMultifastasNucleotide->new(
+        group_names     => [ 'group_2', 'group_5' ],
+        gff_files       => $gff_files,
         annotate_groups => $annotate_groups
     ),
     'initialise creating multiple fastas'
@@ -44,4 +50,17 @@ is(read_file('pan_genome_sequences/group_6.fa'), read_file('t/data/pan_genome_se
 is(read_file('pan_genome_sequences/yfnB.fa'),    read_file('t/data/pan_genome_sequences/yfnB.fa' ), 'Check multifasta content is correct for 1-yfnB.fa ');
 remove_tree('pan_genome_sequences');
 
+# test group number limit
+ok(
+    $obj = Bio::PanGenome::Output::GroupsMultifastasNucleotide->new(
+        group_names     => [ 'group_2', 'group_5' ],
+        gff_files       => $gff_files,
+        annotate_groups => $annotate_groups,
+        _group_limit    => 4
+    ),
+    'initialise creating multiple fastas'
+);
+my $exp_stderr = "Number of clusters (8) exceeds limit (4). Multifastas not created.\n";
+stderr_is { $obj->create_files() } $exp_stderr, 'multifasta creation fails when group limit exceeded';
+
 done_testing();