--- a/scripts/upgrade/upgrade_4.4_5.0.sh
+++ a/scripts/upgrade/upgrade_4.4_5.0.sh
@@ -206,6 +206,7 @@
         $seafile_data_dir/seafile.conf
         $seahub_settings_py
     )
+    mkdir -p $default_conf_dir
     for conffile in ${confs[*]}; do
         if grep -q "This file has been moved" $conffile; then
             continue