diff --git a/workflow/scripts/pool_and_psuedoreplicate.py b/workflow/scripts/pool_and_psuedoreplicate.py
index f8334d058082b38af8afbacc37b76086d7325cd4..9d8a82f6b43623088dfc600404e4d33633903fb6 100644
--- a/workflow/scripts/pool_and_psuedoreplicate.py
+++ b/workflow/scripts/pool_and_psuedoreplicate.py
@@ -242,7 +242,7 @@ def main():
         # Check controls against cutoff_ratio
         # if so replace with pool_control
         path_to_pool_control = cwd + '/' + pool_control
-        if control_df.values.max() > 1.2:
+        if control_df.values.max() > 1.2 and not single_control:
             logger.info("Number of reads in controls differ by " +
                 " > factor of %f. Using pooled controls." % (cutoff_ratio))
             design_new_df['control_tag_align'] = path_to_pool_control