diff --git a/lib/core_atram.py b/lib/core_atram.py
index c2fa0b1..252bd8f 100644
--- a/lib/core_atram.py
+++ b/lib/core_atram.py
@@ -14,7 +14,6 @@
 
 def assemble(args):
     """Loop thru every blast/query pair and run an assembly for each one."""
-    queries = split_queries(args)
 
     with util.make_temp_dir(
             where=args['temp_dir'],
@@ -22,6 +21,8 @@ def assemble(args):
             keep=args['keep_temp_dir']) as temp_dir:
         util.update_temp_dir(temp_dir, args)
 
+        queries = split_queries(args)
+
         for blast_db in args['blast_db']:
 
             with db.connect(blast_db, check_version=True) as cxn: