refunnel rfd3 cli output to stdout

utils/pipelines.py

@@ -142,7 +142,7 @@ def generation_with_input_config(input_file, pdb_file, num_batches, num_designs_
             command += f" {extra_args}"
         print(f"Running command: {command}")
         start = perf_counter()
-        subprocess.run(command, shell=True, check=True, capture_output=True, text=True)
+        subprocess.run(command, shell=True, check=True, text=True)
         print("Command took", perf_counter() - start, "seconds to run.")