diff --git a/barcodeforge/cli.py b/barcodeforge/cli.py
index 49bc033..bbe542a 100644
--- a/barcodeforge/cli.py
+++ b/barcodeforge/cli.py
@@ -295,9 +295,9 @@ def barcode(
 @click.option(
     "--output_metadata_path",
     type=click.Path(),
-    default="metadata.csv",
+    default="metadata.tsv",
     show_default=True,
-    help="Path to save the metadata table (CSV format).",
+    help="Path to save the metadata table (TSV format).",
 )
 @click.option(
     "--output_tree_path",
diff --git a/barcodeforge/ref_muts.py b/barcodeforge/ref_muts.py
index ad8912a..3f24aae 100755
--- a/barcodeforge/ref_muts.py
+++ b/barcodeforge/ref_muts.py
@@ -174,7 +174,7 @@ def process_and_reroot_lineages(
                 console.print(
                     f"[{STYLES['warning']}]Warning: Sample {sample_id} not found in FASTA file. Skipping.[/{STYLES['warning']}]"
                 )
-                break
+                continue
             root_seqs.append(_construct_root_sequence(root_muts, seq))
 
         if not root_seqs: