diff --git a/Snakefile b/Snakefile
index e7fc493..4066dd1 100644
--- a/Snakefile
+++ b/Snakefile
@@ -326,6 +326,7 @@ rule decompress_cobs:
         cobs_index=f"{decompression_dir}/{{batch}}.cobs_classic",
     input:
         xz=f"{cobs_dir}/{{batch}}.cobs_classic.xz",
+        decompressed_indexes_sizes="data/decompressed_indexes_sizes.txt",
     resources:
         max_io_heavy_threads=1,
     params:
diff --git a/scripts/batch_align.py b/scripts/batch_align.py
index 09d65d3..4330b93 100755
--- a/scripts/batch_align.py
+++ b/scripts/batch_align.py
@@ -162,7 +162,9 @@ def load_qdicts(query_fn, accession_fn):
                     # batch accession filtering on & not in this batch
                     pass
 
-    # STEP 3: Ensure everything get converted to standard dicts
+    # STEP 3: Filter rname_to_qnames to references that have at least one COBS match
+    rname_to_qnames = {k: v for k, v in rname_to_qnames.items() if len(v) > 0}
+
     logging.info(f"Query dictionaries loaded")
     return qname_to_qfa, rname_to_qnames