diff --git a/model_angelo/apps/build.py b/model_angelo/apps/build.py
index 26bd042..ece30b4 100644
--- a/model_angelo/apps/build.py
+++ b/model_angelo/apps/build.py
@@ -234,7 +234,15 @@ def main(parsed_args):
             gnn_infer_args.write_hmm_profiles = False
             gnn_infer_args.refine = False
 
-            gnn_infer_args.aggressive_pruning = True
+            if i == total_gnn_rounds - 1:
+                if parsed_args.config_path is None:
+                    gnn_infer_args.aggressive_pruning = True
+                else:
+                    gnn_infer_args.aggressive_pruning = config["gnn_infer_args"][
+                        "aggressive_pruning"
+                    ]
+            else:
+                gnn_infer_args.aggressive_pruning = False
 
             logger.info(
                 f"GNN model refinement round {i + 1} with args: {gnn_infer_args}"
diff --git a/model_angelo/apps/build_no_seq.py b/model_angelo/apps/build_no_seq.py
index ece968e..a43de18 100644
--- a/model_angelo/apps/build_no_seq.py
+++ b/model_angelo/apps/build_no_seq.py
@@ -196,7 +196,14 @@ def main(parsed_args):
             gnn_infer_args.refine = False
 
             if i == total_gnn_rounds - 1:
-                gnn_infer_args.aggressive_pruning = True
+                if parsed_args.config_path is None:
+                    gnn_infer_args.aggressive_pruning = True
+                else:
+                    gnn_infer_args.aggressive_pruning = config["gnn_infer_args"][
+                        "aggressive_pruning"
+                    ]
+            else:
+                gnn_infer_args.aggressive_pruning = False
 
             logger.info(
                 f"GNN model refinement round {i + 1} with args: {gnn_infer_args}"
@@ -225,7 +232,7 @@ def main(parsed_args):
         print(
             f"The HMM profiles are available in the directory: {hmm_profiles_dst}\n"
             f"They are named according to the chains found in {raw_file_dst}\n"
-            f"For example, chain A's profile is in {os.path.join(hmm_profiles_dst, 'A.hmm')}"
+            f"For example, chain A's profile is in {os.path.join(hmm_profiles_dst, 'A_u.hmm')}"
         )
         print(
             f"You can use model_angelo hmm_search to search these HMM profiles against a database"
diff --git a/model_angelo/apps/hmm_search.py b/model_angelo/apps/hmm_search.py
index 6ec3d52..399fd1e 100644
--- a/model_angelo/apps/hmm_search.py
+++ b/model_angelo/apps/hmm_search.py
@@ -150,6 +150,7 @@ def main(parsed_args):
 
     os.makedirs(parsed_args.output_dir, exist_ok=True)
 
+    hmms = [(k.split("_")[0], v) for k, v in hmms]
     pruned_hmms = [k for k in hmms if k[1].alphabet == alphabet]
 
     try:
diff --git a/model_angelo/apps/refine.py b/model_angelo/apps/refine.py
index d4fd2b0..6111ef6 100644
--- a/model_angelo/apps/refine.py
+++ b/model_angelo/apps/refine.py
@@ -186,7 +186,12 @@ def main(parsed_args):
         gnn_infer_args.write_hmm_profiles = parsed_args.write_hmm_profiles
         gnn_infer_args.refine = True
 
-        gnn_infer_args.aggressive_pruning = True
+        if parsed_args.config_path is None:
+            gnn_infer_args.aggressive_pruning = True
+        else:
+            gnn_infer_args.aggressive_pruning = config["gnn_infer_args"][
+                "aggressive_pruning"
+            ]
 
         logger.info(f"GNN model refinement round with args: {gnn_infer_args}")
         gnn_output = gnn_infer(gnn_infer_args)
@@ -217,7 +222,7 @@ def main(parsed_args):
             print(
                 f"The HMM profiles are available in the directory: {hmm_profiles_dst}\n"
                 f"They are named according to the chains found in {file_dst}\n"
-                f"For example, chain A's profile is in {os.path.join(hmm_profiles_dst, 'A.hmm')}"
+                f"For example, chain A's profile is in {os.path.join(hmm_profiles_dst, 'A_u.hmm')}"
             )
             print(
                 f"You can use model_angelo hmm_search to search these HMM profiles against a database"