diff --git a/exercises/Pangenome_analysis/panaroo.sh b/exercises/Pangenome_analysis/panaroo.sh
index b8a788f44a15c58d426d46ed9c8ab748134850d3..d73272fd10bbed779fc57f686e15bd21a0a6f769 100644
--- a/exercises/Pangenome_analysis/panaroo.sh
+++ b/exercises/Pangenome_analysis/panaroo.sh
@@ -35,5 +35,5 @@ done
 # Runs singularity on the annotations and send the output to the output folder
 echo Starting panaroo $(date +"%T")
 cd panaroo
-$singpath/panaroo_1.3.0--pyhdfd78af_0.sif panaroo -i $wd/panaroo/annotation_files/*.gff -o ./panaroo_output/ --clean-mode strict --remove-invalid-genes
+$singpath/panaroo_1.3.0--pyhdfd78af_0.sif panaroo -i $wd/panaroo/annotation_files/*.gff -o ./panaroo_output/ --clean-mode strict --remove-invalid-genes --core_threshold
 echo Done $(date +"%T")
\ No newline at end of file