diff --git a/picrust2/pipeline.py b/picrust2/pipeline.py
index 0a22ef8..2a40f63 100755
--- a/picrust2/pipeline.py
+++ b/picrust2/pipeline.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-from os import path
+from os import path, symlink
 import sys
 from picrust2.default import (default_ref_dir_bac, default_ref_dir_arc, default_tables_bac,
                               default_tables_arc, default_pathway_map)
@@ -370,13 +370,15 @@ def full_pipeline_split(study_fasta,
         for pred in predicted_funcs_split:
             if func in pred:
                   combining.append(pred)
-        
+
+        out_file = path.join(output_folder, "combined_" + func + "_predicted.tsv.gz")        
         if len(combining) == 1:
             predicted_funcs[func] = predicted_funcs_split[combining[0]]
             print("Warning: There was only one file for the function: "+ func + "\n"
                   "Maybe that's fine if you used custom traits or there were no sequences "
                   "matching one of the domains.", file=sys.stderr)
-        
+            os.symlink(predicted_funcs[func], out_file)
+
         elif len(combining) > 2:
             sys.exit("More than two files were available for the function: " + func +"\n"
                      "If you are using your own custom trait files, please check that you "
@@ -384,7 +386,6 @@ def full_pipeline_split(study_fasta,
         
         else:
             print(combining, predicted_funcs_split)
-            out_file = path.join(output_folder, "combined_" + func + "_predicted.tsv.gz")
             combine_domain_predictions(predicted_funcs_split[combining[0]], 
                                        predicted_funcs_split[combining[1]], 
                                        out_file,