diff --git a/PanACoTA/annotate_module/format_prodigal.py b/PanACoTA/annotate_module/format_prodigal.py
index 30679831ce87064a8216cb72a7f5d8c5a9f96514..76d6b124be68b5e9b59a7ad42b13a024b80d571f 100644
--- a/PanACoTA/annotate_module/format_prodigal.py
+++ b/PanACoTA/annotate_module/format_prodigal.py
@@ -358,7 +358,7 @@ def create_gff(gpath, gff_file, res_gff_file, res_lst_file, contigs, sizes):
     # open lst file to read all information saved from prodigal results
     with open(gff_file, 'r') as gf, open(res_gff_file, "w") as rgf, open(res_lst_file, "r") as rlf:
         # Write headers of gff3 file
-        rgf.write("##gff-version  3\n")
+        rgf.write("##gff-version 3\n")
         for ori_name, new_name in contigs.items():
             # Write the list of contigs, with their size
             end = sizes[new_name]
diff --git a/PanACoTA/annotate_module/format_prokka.py b/PanACoTA/annotate_module/format_prokka.py
index ec9e4fd4363f44436f61e8e45b3aa2ff2b11f260..ba299738c1bbc8f5f9fb5c6f6c811c45edbf4225 100644
--- a/PanACoTA/annotate_module/format_prokka.py
+++ b/PanACoTA/annotate_module/format_prokka.py
@@ -411,7 +411,7 @@ def generate_gff(gpath, prokka_gff_file, res_gff_file, res_lst_file, sizes, cont
     with open(prokka_gff_file, "r") as prokf, open(res_lst_file, "r") as lstf, \
             open(res_gff_file, "w") as gfff:
         # Write headers of gff3 file
-        gfff.write("##gff-version  3\n")
+        gfff.write("##gff-version 3\n")
         # Write all sequences with their size. Order by name in gembase format
         for old, new in sorted(contigs.items(), key=lambda items:items[1]):
             end = sizes[new]