improved error handling

AmpliconSuite · Apr 19, 2024 · dbaf0d1 · dbaf0d1
1 parent d34c954
commit dbaf0d1
Showing 1 changed file with 5 additions and 1 deletion.
diff --git a/src/AmpliconSuiteAggregatorFunctions.py b/src/AmpliconSuiteAggregatorFunctions.py
@@ -80,6 +80,7 @@ def unzip_file(fp, dest_root):
 
     except Exception as e:
         print(e)
+        sys.exit(1)
 
 
 def clean_dirs(dlist):
@@ -259,7 +260,10 @@ def run_amp_classifier(self):
             sys.exit(1)
 
         print(f"AC_SRC is set to {AC_SRC}")
-        os.system(f"{AC_SRC}/make_input.sh {OUTPUT_PATH} {OUTPUT_PATH}/{self.output_name}" )
+        input_ec = os.system(f"{AC_SRC}/make_input.sh {OUTPUT_PATH} {OUTPUT_PATH}/{self.output_name}")
+        if input_ec != 0:
+            print("Failed to make input for AC!")
+            sys.exit(1)
 
         ## if reference isn't downloaded already, then download appropriate reference genome
         try: