diff --git a/pangolin/scripts/pangolearn.smk b/pangolin/scripts/pangolearn.smk
index d0f547e..ca6a2dd 100644
--- a/pangolin/scripts/pangolearn.smk
+++ b/pangolin/scripts/pangolearn.smk
@@ -50,6 +50,7 @@ rule align_to_reference:
             --reference {input.reference:q} \
             --trimstart {params.trim_start} \
             --trimend {params.trim_end} \
+            --trim \
             --pad > {output.fasta:q}
         """