diff --git a/src/scripts/get_layout_from_mbg.py b/src/scripts/get_layout_from_mbg.py
index 3842822..897c1bf 100755
--- a/src/scripts/get_layout_from_mbg.py
+++ b/src/scripts/get_layout_from_mbg.py
@@ -263,9 +263,11 @@ def get_exact_match_length(clusters):
 			pieceid = pieceid + 1
 			pathname = f"piece{pieceid:06d}"
 
-			contig_pieces[fullname].append(pathname)
-
 			(path, overlaps) = get_leafs(re.findall(r"[<>][^<>]+", pp), node_mapping, edge_overlaps, raw_node_lens)
+			# skip a path if the only thing in it is a gapfill
+			if len(path) == 1 and path[0][0][1:4] == "gap":
+				continue
+			contig_pieces[fullname].append(pathname)
 
 			contig_nodeseqs[pathname] = path
 			contig_nodeoverlaps[pathname] = overlaps