diff --git a/strategoutil.py b/strategoutil.py
index f220c63..d11fa1b 100644
--- a/strategoutil.py
+++ b/strategoutil.py
@@ -192,7 +192,7 @@ def run_stratego(model_file, query_file="", learning_args=None, verifyta_command
         "query": f'"{query_file}"',
         "config": merge_verifyta_args(learning_args)
     }
-    args_list = [v for v in args.values() if v != ""]
+    args_list = [v for v in args.values() if v != "" and v != "\"\""]
     task = " ".join(args_list)
 
     process = subprocess.Popen(task, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
diff --git a/test/test_strategoutil.py b/test/test_strategoutil.py
index a5346a1..97bee95 100644
--- a/test/test_strategoutil.py
+++ b/test/test_strategoutil.py
@@ -93,7 +93,7 @@ def test_run_stratego_model_only(self):
         with mock.patch("strategoutil.subprocess.Popen") as mock_Popen:
             sutil.run_stratego("model.xml", verifyta_command="$HOME/verifyta")
             # Below is the expected result with Popen default shell.
-            expected = "$HOME/verifyta model.xml"
+            expected = "$HOME/verifyta \"model.xml\""
 
             mock_Popen.assert_called_with(expected, **self.POPEN_KWARGS)
 
@@ -101,7 +101,7 @@ def test_run_stratego_model_and_query(self):
         with mock.patch("strategoutil.subprocess.Popen") as mock_Popen:
             sutil.run_stratego("model.xml", "query.q")
             # Below is the expected result with Popen default shell.
-            expected = "verifyta model.xml query.q"
+            expected = "verifyta \"model.xml\" \"query.q\""
             mock_Popen.assert_called_with(expected, **self.POPEN_KWARGS)
 
     def test_run_stratego_all_variables(self):
@@ -117,7 +117,7 @@ def test_run_stratego_all_variables(self):
             }
             sutil.run_stratego("model.xml", "query.q", learning_args, "verifyta")
             # Below is the expected result with Popen default shell.
-            expected = ("verifyta model.xml query.q --learning-method 4 "
+            expected = ("verifyta \"model.xml\" \"query.q\" --learning-method 4 "
                         "--good-runs 100 --total-runs 100 --runs-pr-state 100 "
                         "--eval-runs 100 --max-iterations 30 --filter 0")
             mock_Popen.assert_called_with(expected, **self.POPEN_KWARGS)