diff --git a/pygmt/clib/session.py b/pygmt/clib/session.py
index a2b8ef1e355..201e96cf26f 100644
--- a/pygmt/clib/session.py
+++ b/pygmt/clib/session.py
@@ -970,7 +970,7 @@ def open_virtual_file(self, family, geometry, direction, data):
         ...     lib.put_vector(dataset, column=0, vector=x)
         ...     lib.put_vector(dataset, column=1, vector=y)
         ...     # Add the dataset to a virtual file
-        ...     vfargs = (family, geometry, 'GMT_IN|GMT_IS_REFERENCE', dataset)
+        ...     vfargs = (family, geometry, 'GMT_IN', dataset)
         ...     with lib.open_virtual_file(*vfargs) as vfile:
         ...         # Send the output to a temp file so that we can read it
         ...         with GMTTempFile() as ofile:
@@ -1102,7 +1102,7 @@ def virtualfile_from_vectors(self, *vectors):
             self.put_vector(dataset, column=col, vector=array)
 
         with self.open_virtual_file(
-            family, geometry, "GMT_IN|GMT_IS_REFERENCE", dataset
+            family, geometry, "GMT_IN", dataset
         ) as vfile:
             yield vfile
 
@@ -1185,7 +1185,7 @@ def virtualfile_from_matrix(self, matrix):
         self.put_matrix(dataset, matrix)
 
         with self.open_virtual_file(
-            family, geometry, "GMT_IN|GMT_IS_REFERENCE", dataset
+            family, geometry, "GMT_IN", dataset
         ) as vfile:
             yield vfile
 
@@ -1271,7 +1271,7 @@ def virtualfile_from_grid(self, grid):
             registration=_reg,
         )
         self.put_matrix(gmt_grid, matrix)
-        args = (family, geometry, "GMT_IN|GMT_IS_REFERENCE", gmt_grid)
+        args = (family, geometry, "GMT_IN", gmt_grid)
         with self.open_virtual_file(*args) as vfile:
             yield vfile
 
diff --git a/pygmt/tests/test_clib.py b/pygmt/tests/test_clib.py
index a90be7c338e..628c2bd0d37 100644
--- a/pygmt/tests/test_clib.py
+++ b/pygmt/tests/test_clib.py
@@ -474,7 +474,7 @@ def test_virtual_file():
             data = np.arange(shape[0] * shape[1], dtype=dtype).reshape(shape)
             lib.put_matrix(dataset, matrix=data)
             # Add the dataset to a virtual file and pass it along to gmt info
-            vfargs = (family, geometry, "GMT_IN|GMT_IS_REFERENCE", dataset)
+            vfargs = (family, geometry, "GMT_IN", dataset)
             with lib.open_virtual_file(*vfargs) as vfile:
                 with GMTTempFile() as outfile:
                     lib.call_module("info", "{} ->{}".format(vfile, outfile.name))
@@ -494,7 +494,7 @@ def test_virtual_file_fails():
     vfargs = (
         "GMT_IS_DATASET|GMT_VIA_MATRIX",
         "GMT_IS_POINT",
-        "GMT_IN|GMT_IS_REFERENCE",
+        "GMT_IN",
         None,
     )