diff --git a/src/workflow/CommandExecutor.py b/src/workflow/CommandExecutor.py
index 6cc493014..646bea8cf 100644
--- a/src/workflow/CommandExecutor.py
+++ b/src/workflow/CommandExecutor.py
@@ -9,6 +9,7 @@
 import sys
 import importlib.util
 import json
+import queue
 
 class CommandExecutor:
     """
@@ -43,12 +44,21 @@ def run_multiple_commands(
         self.logger.log(f"Running {len(commands)} commands in parallel...", 1)
         start_time = time.time()
 
+        # Queue to capture exceptions from threads
+        exceptions_queue = queue.Queue()
+
+        def run_command_thread_target(cmd):
+            try:
+                self.run_command(cmd)
+            except Exception as e:
+                exceptions_queue.put(e)
+
         # Initialize a list to keep track of threads
         threads = []
 
         # Start a new thread for each command
         for cmd in commands:
-            thread = threading.Thread(target=self.run_command, args=(cmd,))
+            thread = threading.Thread(target=run_command_thread_target, args=(cmd,))
             thread.start()
             threads.append(thread)
 
@@ -60,6 +70,11 @@ def run_multiple_commands(
         end_time = time.time()
         self.logger.log(f"Total time to run {len(commands)} commands: {end_time - start_time:.2f} seconds", 1)
 
+        # Exceptions are logged once all threads have completed execution
+        # The first exception amongst all is logged and raised
+        if not exceptions_queue.empty():
+            raise RuntimeError(exceptions_queue.get())
+
     def run_command(self, command: list[str]) -> None:
         """
         Executes a specified shell command and logs its execution details.
@@ -105,6 +120,7 @@ def run_command(self, command: list[str]) -> None:
         if stderr or process.returncode != 0:
             error_message = stderr.decode().strip()
             self.logger.log(f"ERRORS OCCURRED:\n{error_message}", 2)
+            raise RuntimeError(error_message)
 
     def run_topp(self, tool: str, input_output: dict, custom_params: dict = {}) -> None:
         """