Fix alignment batch tagging (#375)

lib/idseq_utils/idseq_utils/batch_run_helpers.py

@@ -306,9 +306,9 @@ def run_alignment(
     aligner_wdl_version: str,
     queries: List[str],
 ):
-    bucket, prefix = _bucket_and_key(db_path)
+    db_bucket, db_prefix = _bucket_and_key(db_path)
     chunk_dir = os.path.join(input_dir, f"{aligner}-chunks")
-    _, chunk_prefix = _bucket_and_key(chunk_dir)
+    chunk_bucket, chunk_prefix = _bucket_and_key(chunk_dir)
     chunks = (
         [
             input_dir,
@@ -318,9 +318,9 @@ def run_alignment(
             aligner_wdl_version,
             queries,
             chunk_id,
-            f"s3://{bucket}/{db_chunk}",
+            f"s3://{db_bucket}/{db_chunk}",
         ]
-        for chunk_id, db_chunk in enumerate(_db_chunks(bucket, prefix))
+        for chunk_id, db_chunk in enumerate(_db_chunks(db_bucket, db_prefix))
     )
     with Pool(MAX_CHUNKS_IN_FLIGHT) as p:
         p.starmap(_run_chunk, chunks)
@@ -332,11 +332,15 @@ def run_alignment(
     for fn in listdir("chunks"):
         if fn.endswith("json"):
             os.remove(os.path.join("chunks", fn))
-            _s3_client.put_object_tagging(
-                Bucket=bucket,
-                Key=os.path.join(chunk_prefix, fn),
-                Tagging={"TagSet": [{"Key": "AlignmentCoordination", "Value": "True"}]},
-            )
+            try:
+                _s3_client.put_object_tagging(
+                    Bucket=chunk_bucket,
+                    Key=os.path.join(chunk_prefix, fn),
+                    Tagging={"TagSet": [{"Key": "AlignmentCoordination", "Value": "True"}]},
+                )
+            except ClientError as e:
+                log.error(f"failed to tag 's3://{chunk_bucket}/{os.path.join(chunk_prefix, fn)}'")
+                raise e
     if aligner == "diamond":
         blastx_join("chunks", result_path, aligner_args, *queries)
     else: