From af9c8c70b81942d8c5f03f598dea81152281dd12 Mon Sep 17 00:00:00 2001
From: Harrison Deng <yunyangdeng@outlook.com>
Date: Wed, 19 Feb 2025 15:50:18 +0000
Subject: [PATCH] Stop on fail argument now works

---
 src/autobigs/cli/st.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/autobigs/cli/st.py b/src/autobigs/cli/st.py
index 9edec5a..c085ab6 100644
--- a/src/autobigs/cli/st.py
+++ b/src/autobigs/cli/st.py
@@ -50,7 +50,7 @@ async def run(args: Namespace):
     async with BIGSdbIndex() as bigsdb_index:
         gen_strings = read_multiple_fastas(args.fastas)
         async with await bigsdb_index.build_profiler_from_seqdefdb(False, args.seqdefdb, args.schema) as mlst_profiler:
-            mlst_profiles = mlst_profiler.profile_multiple_strings(gen_strings)
+            mlst_profiles = mlst_profiler.profile_multiple_strings(gen_strings, args.stop_on_fail)
             failed = await write_mlst_profiles_as_csv(mlst_profiles, args.out)
             if len(failed) > 0:
                 print(f"A total of {len(failed)} IDs failed (no profile found):\n{"\n".join(failed)}")