diff --git a/Examples/commands/1-Annotate.sh b/Examples/commands/1-Annotate.sh
index 5be2fef69375c895e29881f1572fa844b771f268..0cbf1f761f09afee7b9582ff6aa89024d743f211 100644
--- a/Examples/commands/1-Annotate.sh
+++ b/Examples/commands/1-Annotate.sh
@@ -3,4 +3,4 @@ PanACoTA annotate -d Examples/genomes_init -r Examples/1-res-prokka -l Examples/
 
 
 # With prodigal
-PanACoTA annotate -d Examples/genomes_init -l Examples/input_files/list_genomes.lst -n EXAM -r Examples/1-res-Annotate-prodigal --prodigal --small
+PanACoTA annotate -d Examples/genomes_init -r Examples/1-res-prodigal -l Examples/input_files/list_genomes.lst -n EXAM  --l90 3 --prodigal --small 
diff --git a/README.md b/README.md
index ffafd17953224c745ec7e287b4a3cb90cb6cd9b0..a0315398556129e26273498747a9d522ca2b538c 100755
--- a/README.md
+++ b/README.md
@@ -111,6 +111,7 @@ If you installed the dependencies (such as prokka) via our installation script,
 ## Quick run
 
 `PanACoTA` contains 5 different subcommands:
+
 - `annotate` (annotate all genomes of the dataset, after a quality control)
 - `pangenome` (generate pan-genome)
 - `corepers` (generate core-genome or persistent-genome)
diff --git a/test/test_unit/test_annotate/test_format_prodigal.py b/test/test_unit/test_annotate/test_format_prodigal.py
index 61c291cfc31aba717eacf23334218dc0272d92b3..31806890bed100320c4aa227008f481f9ac2039f 100644
--- a/test/test_unit/test_annotate/test_format_prodigal.py
+++ b/test/test_unit/test_annotate/test_format_prodigal.py
@@ -271,6 +271,12 @@ def test_create_prt_not_moreprots_lst(caplog):
     assert ("Protein test.0417.00002.0007b_00015 is in .lst file but its sequence is not "
             "in the protein file generated by prodigal.") in caplog.text
 
+
+def test_format_1genome(caplog):
+    """
+    Test that when prodigal results are ok, all files are
+    generated as expected.
+    """
 # # def test_tbl_to_lst_not_changed_names(caplog):
 #     """
 #     Check that generated lstinfo file is as expected, when the genome name is the same as