diff --git a/swh/scanner/benchmark_algos.py b/swh/scanner/benchmark_algos.py
--- a/swh/scanner/benchmark_algos.py
+++ b/swh/scanner/benchmark_algos.py
@@ -70,10 +70,6 @@
 
 
 def stopngo(source_tree: Tree, api_url: str, counter: collections.Counter):
-    def set_children_known(node):
-        for child_node in node.iterate():
-            child_node.known = True
-
     nodes = []
     nodes.append(source_tree)
 
@@ -87,7 +83,7 @@
                 if not node.known:
                     nodes.extend(list(node.children.values()))
                 else:
-                    set_children_known(node)
+                    set_children_status(node, [CONTENT, DIRECTORY], True)
 
 
 def set_father_status(node, known):
@@ -105,12 +101,14 @@
     set_father_status(parent, known)
 
 
-def set_children_status(node, node_type, known, status: Status = Status.unset):
+def set_children_status(
+    node: Tree, node_types: Iterable[str], known: bool, status: Status = Status.unset
+):
     """
-    Recursively change father known and visited status of a given node
+    Recursively change the status of the children of the provided node
     """
     for child_node in node.iterate():
-        if child_node.otype == node_type and child_node.status == status:
+        if child_node.otype in node_types and child_node.status == status:
             child_node.known = known
 
 
@@ -149,7 +147,8 @@
             # update directory status
             dir_.known = query_swhids([dir_], api_url, counter)[dir_.swhid]["known"]
             dir_.status = Status.queried
-            set_children_status(dir_, DIRECTORY, dir_.known)
+            if dir_.known:
+                set_children_status(dir_, [DIRECTORY], True)
 
 
 def directory_priority(source_tree: Tree, api_url: str, counter: collections.Counter):
@@ -161,9 +160,6 @@
         )
     )
     unset_dirs.reverse()
-    # insert root if it has no contents
-    if source_tree.has_contents:
-        unset_dirs.append(source_tree)
 
     for dir_ in unset_dirs:
         # if the directory is known set all the downstream file contents to known
@@ -171,7 +167,7 @@
             dir_.known = query_swhids([dir_], api_url, counter)[dir_.swhid]["known"]
             dir_.status = Status.queried
             if dir_.known:
-                set_children_status(dir_, CONTENT, True)
+                set_children_status(dir_, [CONTENT], True)
             else:
                 set_father_status(dir_, False)
 
@@ -249,8 +245,7 @@
         for child_node in node.iterate():
             nodes.remove(child_node)
 
-    all_nodes = [node for node in source_tree.iterate()]
-    all_nodes.insert(0, source_tree)
+    all_nodes = [node for node in source_tree.iterate_bfs()]
 
     parsed_nodes = query_swhids(all_nodes, api_url)
     for node in all_nodes:
diff --git a/swh/scanner/model.py b/swh/scanner/model.py
--- a/swh/scanner/model.py
+++ b/swh/scanner/model.py
@@ -185,12 +185,15 @@
     def iterate_bfs(self) -> Iterator[Tree]:
         """Get nodes in BFS order
         """
-        nodes = set(node for node in self.children.values())
-        for node in nodes:
-            yield node
-        for node in nodes:
-            if node.otype == DIRECTORY:
-                yield from node.iterate_bfs()
+        nodes = []
+        nodes.append(self)
+
+        while len(nodes) > 0:
+            for node in nodes.copy():
+                yield node
+                nodes.remove(node)
+                if node.otype == DIRECTORY:
+                    nodes.extend(list(node.children.values()))
 
     def get_files_from_dir(self, dir_path: Path) -> List:
         """