Tolerate failure of the midas genes step

Closes #2, albeit in a slightly different way than described
FredHutch · Feb 8, 2018 · c1e5860 · c1e5860
1 parent a5541db
commit c1e5860
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Showing 2 changed files with 6 additions and 4 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1 +1,2 @@
-temp/
+temp/
+*pyc
diff --git 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")