one answer for exonerate

Snakefile

@@ -416,7 +416,7 @@ rule alignment_consensus_ref :
         "env_conda/exonerate.yaml"
     shell :
         'if [ `cat {input.consensus}|grep ">"|wc -l` -ne 0 ]; then'
-        '   ORDER="exonerate -Q dna -E -m a:g {input.consensus} {input.region}";'
+        '   ORDER="exonerate --bestn 1 -Q dna -E -m a:g {input.consensus} {input.region}";'
         '   echo "ORDER: $ORDER" >{log};'
         '   $ORDER >{output} 2>>{log};'
         'else'
@@ -557,7 +557,7 @@ rule alignment_meta_consensus_ref :
         "env_conda/exonerate.yaml"
     shell :
         'if [ `cat {input.consensus}|grep ">"|wc -l` -ne 0 ]; then'
-        '   ORDER="exonerate -Q dna -E -m a:g {input.consensus} {input.region}";'
+        '   ORDER="exonerate --bestn 1 -Q dna -E -m a:g {input.consensus} {input.region}";'
         '   echo "ORDER: $ORDER" >{log};'
         '   $ORDER >{output} 2>>{log};'
         'else'