diff --git a/.gitignore b/.gitignore
index cd78447..28ecab6 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1 +1,2 @@
-temp/
\ No newline at end of file
+temp/
+*pyc
\ No newline at end of file
diff --git a/lib/midas_helpers.py b/lib/midas_helpers.py
index d2bd44c..e983067 100644
--- a/lib/midas_helpers.py
+++ b/lib/midas_helpers.py
@@ -117,9 +117,10 @@ def run_midas(
         "-t", str(threads),
         "--remove_temp",
         "-d", db_fp
-    ])
-    assert os.path.exists(
-        os.path.join(output_folder, "genes")
+    ],
+        # Tolerate failure of this command because it may fail if
+        # there are no species meeting the indicated depth threshold
+        catchExcept=True
     )
 
     logging.info("Done running MIDAS")