diff --git a/bactopia/utils.py b/bactopia/utils.py
index 66daa53..ba6646f 100644
--- a/bactopia/utils.py
+++ b/bactopia/utils.py
@@ -1,4 +1,5 @@
 import logging
+import shlex
 import subprocess
 import sys
 from pathlib import Path
@@ -33,7 +34,7 @@ def execute(
     logging.debug(f"Working directory: {directory}")
     try:
         command = subprocess.run(
-            cmd.split(" "),  # Replace with your command and arguments
+            shlex.split(cmd),  # Replace with your command and arguments
             cwd=directory,
             capture_output=True,
             text=True,  # Decodes stdout/stderr as strings using default encoding
@@ -49,15 +50,18 @@ def execute(
             return command.returncode
     except subprocess.CalledProcessError as e:
         if allow_fail:
-            logging.debug(f'"{cmd}" return exit code {e.returncode}')
-            logging.debug(e)
+            logger = logging.debug
+        else:
+            logger = logging.error
+        logger(f"STDOUT: \n{e.stdout}")
+        logger(f"STDERR:\n{e.stderr}")        
+        logger(f'"{cmd}" return exit code {e.returncode}')
+        logger(e)
+        if allow_fail:
             return None
         else:
-            logging.error(f'"{cmd}" return exit code {e.returncode}')
-            logging.error(e)
             sys.exit(e.returncode)
 
-
 def pgzip(files: list, cpus: int) -> list:
     """
     Parallel gzip a list of files