diff --git a/test/test_unit/test_annotate/test_annotation_functions-prodigal.py b/test/test_unit/test_annotate/test_annotation_functions-prodigal.py
index 1bc41c406a5adb89062fcf934077854c13af7f6c..5efd57fc152e0081b685cce3124bfaaca1c79ec9 100644
--- a/test/test_unit/test_annotate/test_annotation_functions-prodigal.py
+++ b/test/test_unit/test_annotate/test_annotation_functions-prodigal.py
@@ -39,7 +39,11 @@ def setup_teardown_module():
     - remove all log files
     - remove directory with generated results
     """
-    if not os.path.exists(GENEPATH):
+    if os.path.isdir(GENEPATH):
+        content = os.listdir(GENEPATH)
+        for f in content:
+            assert f.startswith(".fuse")
+    else:
         os.mkdir(GENEPATH)
     print("setup")
 
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 375ff94113b7585a04235773f41155052c159a93..5195543b398f69809f14f3524d2bc940f1c34a84 100644
--- a/test/test_unit/test_annotate/test_annotation_functions-prokka.py
+++ b/test/test_unit/test_annotate/test_annotation_functions-prokka.py
@@ -40,7 +40,11 @@ def setup_teardown_module():
     - remove all log files
     - remove directory with generated results
     """
-    if not os.path.exists(GENEPATH):
+    if os.path.isdir(GENEPATH):
+        content = os.listdir(GENEPATH)
+        for f in content:
+            assert f.startswith(".fuse")
+    else:
         os.mkdir(GENEPATH)
     print("setup")
 
diff --git a/test/test_unit/test_annotate/test_annotation_general.py b/test/test_unit/test_annotate/test_annotation_general.py
index 02244e95bc9c078f1d55f6e9594dd21343615ade..9fc5612945b0dd56f44c8ac0e0a5593e81294dfb 100644
--- a/test/test_unit/test_annotate/test_annotation_general.py
+++ b/test/test_unit/test_annotate/test_annotation_general.py
@@ -37,7 +37,11 @@ def setup_teardown_module():
     - remove all log files
     - remove directory with generated results
     """
-    if not os.path.exists(GENEPATH):
+    if os.path.isdir(GENEPATH):
+        content = os.listdir(GENEPATH)
+        for f in content:
+            assert f.startswith(".fuse")
+    else:
         os.mkdir(GENEPATH)
     print("setup")