diff --git a/test/test_functional/test_annote.py b/test/test_functional/test_annote.py
index f56e520e78cd453d99c2334421068a7f96300fef..814866994af16e4d44a942bdc4ead7b33df1b1b0 100755
--- a/test/test_functional/test_annote.py
+++ b/test/test_functional/test_annote.py
@@ -621,7 +621,7 @@ def test_main_prodigal_ok(capsys):
     os.makedirs(res_folder)
 
     # Function arguments
-    list_file = os.path.join(TEST_DIR, "list_genomes.txt")
+    list_file = os.path.join(GENEPATH, "list_genomes.txt")
     with open(list_file, "w") as lf:
         lf.write("A_H738.fasta \n")
         lf.write("H299_H561.fasta::TOTO")
diff --git a/test/test_functional/test_prepare.py b/test/test_functional/test_prepare.py
index d04ee928aa32d3c15eb3665c196db13125fb4d88..8128dc4e07c5420b0ec90c204695eccf04700271 100644
--- a/test/test_functional/test_prepare.py
+++ b/test/test_functional/test_prepare.py
@@ -55,15 +55,15 @@ def test_main_from_parse():
     """
     args = argparse.Namespace()
     args.argv = ["prepare", "test_func_prepare"]
-    args.NCBI_species = "Acetobacter orleanensis"
-    args.NCBI_species_taxid = "104099"
+    args.ncbi_species = "Acetobacter orleanensis"
+    args.ncbi_species_taxid = "104099"
     args.outdir = GENEPATH
     args.tmp_dir = ""
     args.parallel = 1
     args.no_refseq = False
     args.db_dir = ""
     args.only_mash = False
-    args.from_info = ""
+    args.info_file = ""
     args.l90 = 100
     args.nbcont = 999
     args.cutn = 0
diff --git a/test/test_unit/test_annotate/test_annotation_functions-prokka.py b/test/test_unit/test_annotate/test_annotation_functions-prokka.py
index 19eb2ea5f435ba1c00ce2b6e7f0a9dd9a7e7de6f..aab5d7299e5a74f6009ddfc3c05b51a156d55f5a 100644
--- a/test/test_unit/test_annotate/test_annotation_functions-prokka.py
+++ b/test/test_unit/test_annotate/test_annotation_functions-prokka.py
@@ -77,7 +77,7 @@ def test_check_prokka_no_outdir():
     Test that prokka returns the right error message when output directory does not exist
     """
     logger = my_logger("test_check_prokka_no_outdir")
-    outdir = "outdir"
+    outdir = os.path.join(GENEPATH, "outdir")
     name = "prokka_out_for_test"
     logf = "prokka.log"
     gpath = os.path.join(GENEPATH, "toto.fna")