--addprofile added, doesn't break even if one seq

cov-lineages · May 3, 2020 · a6bce9f · a6bce9f
1 parent d1d0e6e
commit a6bce9f
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/pangolin/scripts/assign_query_lineage.smk b/pangolin/scripts/assign_query_lineage.smk
@@ -39,7 +39,7 @@ rule profile_align_query:
     output:
         temp(config["tempdir"] + "/{query}.aln.fasta")
     shell:
-        "mafft --add {input.query:q} {input.aln:q} > {output:q}"
+        "mafft --addprofile {input.query:q} {input.aln:q} > {output:q}"
 
 rule iqtree_with_guide_tree:
     input: