diff --git a/run_gubbins.pl b/run_gubbins.pl
index 23bcec37..adfcc6d5 100755
--- a/run_gubbins.pl
+++ b/run_gubbins.pl
@@ -48,7 +48,7 @@ =head1 METHODS
     $previous_tree = "-t $previous_tree_name";
     $base_filename = $previous_tree_name;
    }
-  system("$tree_builder_exec -s $starting_base_filename.phylip -n $filename.$current_time.iteration_$i $previous_tree");
+  system("$tree_builder_exec -s $previous_tree_name.phylip -n $filename.$current_time.iteration_$i $previous_tree");
   system("$gubbins_exec -r $input_multi_fasta_alignment_file $starting_base_filename.vcf $current_tree $starting_base_filename.phylip");
 }