diff --git a/include/valik/split/metadata.hpp b/include/valik/split/metadata.hpp
index 3ea3cd2f..19204035 100644
--- a/include/valik/split/metadata.hpp
+++ b/include/valik/split/metadata.hpp
@@ -457,6 +457,10 @@ struct metadata
                 else
                     arguments.seg_count = std::max(arguments.seg_count, (uint32_t) sequences.size() * 2);
             }
+            else
+            {
+                arguments.seg_count = arguments.seg_count_in;
+            }
 
             scan_database_sequences(arguments);
             if (arguments.manual_parameters && (segments.size() != arguments.seg_count))