diff --git a/babs/babs.py b/babs/babs.py
index f9719fe1..5912308c 100644
--- a/babs/babs.py
+++ b/babs/babs.py
@@ -379,7 +379,8 @@ def babs_bootstrap(self, input_ds,
             proc_git_commit_amend = subprocess.run(
                 ["git", "commit", "--amend", "-m",
                     "Register input data dataset '" + input_ds.df["name"][i_ds]
-                    + "' as a subdataset"],
+                    + "' as a subdataset",
+                    "--allow-empty"],
                 cwd=self.analysis_path,
                 stdout=subprocess.PIPE
             )