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
@@ -255,7 +255,11 @@
 
     for node in all_nodes:
         if node.otype == CONTENT and not node.known:
-            all_nodes_copy.remove(node)
+            remove_parents(node, all_nodes_copy)
+
+    all_nodes.reverse()
+    for node in all_nodes:
+        if node.otype == DIRECTORY and not node.known:
             remove_parents(node, all_nodes_copy)
 
     for node in all_nodes_copy: