diff --git a/checkm2/diamond.py b/checkm2/diamond.py
index e38bd37..4f82570 100644
--- a/checkm2/diamond.py
+++ b/checkm2/diamond.py
@@ -43,7 +43,7 @@ def check_for_diamond(self):
         # else returns something non-zero
 
         try:
-            subprocess.call(['diamond', 'help'], stdout=open(os.devnull, 'w'), stderr=subprocess.STDOUT)
+            subprocess.check_call(['diamond', 'help'], stdout=open(os.devnull, 'w'), stderr=subprocess.STDOUT)
         except:
             logging.error("Make sure diamond is on your system path.")
             sys.exit(1)
@@ -98,7 +98,7 @@ def __call_diamond(self, seq_object, diamond_output):
                             diamond_working_dir.name)
 
                 logging.debug(cmd)
-                subprocess.call(cmd, shell=True)
+                subprocess.check_call(cmd, shell=True)
                 logging.debug('Finished Running DIAMOND')
             except Exception as e:
                 logging.error('An error occured while running DIAMOND: {}'.format(e))
diff --git a/checkm2/prodigal.py b/checkm2/prodigal.py
index 97d8c77..a7d8624 100644
--- a/checkm2/prodigal.py
+++ b/checkm2/prodigal.py
@@ -196,10 +196,8 @@ def areORFsCalled(self, bNucORFs):
     def checkForProdigal(self):
         """Check to see if Prodigal is on the system before we try to run it."""
 
-        # Assume that a successful prodigal -h returns 0 and anything
-        # else returns something non-zero
         try:
-            subprocess.call(['prodigal', '-h'], stdout=open(os.devnull, 'w'), stderr=subprocess.STDOUT)
+            subprocess.check_call(['prodigal', '-h'], stdout=open(os.devnull, 'w'), stderr=subprocess.STDOUT)
         except:
             logging.error("Make sure prodigal is on your system path.")
             sys.exit(1)