diff --git a/gff3toembl/EMBLContig.py b/gff3toembl/EMBLContig.py
index f662b4d..74d856c 100644
--- a/gff3toembl/EMBLContig.py
+++ b/gff3toembl/EMBLContig.py
@@ -58,7 +58,7 @@ def compare_features(feature_1, feature_2):
       elif feature_1.start > feature_2.start:
         return 1
       else:
-        return feature_2.end - feature_1.end
+        return int(feature_2.end - feature_1.end)
     return sorted(self.features.values(), cmp=compare_features)
 
 class EMBLFeature(object):
diff --git a/gff3toembl/EMBLWriter.py b/gff3toembl/EMBLWriter.py
index b215907..2d87680 100644
--- a/gff3toembl/EMBLWriter.py
+++ b/gff3toembl/EMBLWriter.py
@@ -71,7 +71,7 @@ def create_chromosome_list(self, chromosome_list_filename, embl_filename):
 
     def sort_and_tidy_gff_file(self):
         try:
-          subprocess.check_call("gt gff3 -sort -retainids -tidy -o "+str(self.fixed_gff_file)+" "+str(self.gff3_file), shell=True)
+          subprocess.check_call("gt gff3 -force -sort -retainids -tidy -o "+str(self.fixed_gff_file)+" "+str(self.gff3_file), shell=True)
         except:
           sys.exit("Failed to sort and tidy gff file with GT")