diff --git a/Makefile b/Makefile
index 185e2d38..8ae4261a 100644
--- a/Makefile
+++ b/Makefile
@@ -348,7 +348,7 @@ $(SAUR_CGMLST_DIR)/alleles_rereffed: | $(SAUR_CGMLST_DIR)/alleles/unpacking.done
 	&& echo "WARNING! Prepping cgMLST schema. This takes a looong time. Put on some coffee" \
 	&& singularity exec --bind $(MNT_ROOT) $(CONTAINER_DIR)/chewbbaca.sif \
 		chewie PrepExternalSchema \
-		-i $(SAUR_CGMLST_DIR)/alleles \
+		-g $(SAUR_CGMLST_DIR)/alleles \
 		-o $(SAUR_CGMLST_DIR)/alleles_rereffed \
 		--cpu 2 \
 		--ptf $(PRODIGAL_TRAINING_DIR)/Staphylococcus_aureus.trn |& tee -a $(INSTALL_LOG)
@@ -449,7 +449,7 @@ $(ECOLI_CGMLST_DIR)/alleles_rereffed: | $(ECOLI_CGMLST_DIR)/alleles/unpacking.do
 	cd $(ECOLI_CGMLST_DIR) \
 	&& singularity exec --bind $(MNT_ROOT) $(CONTAINER_DIR)/chewbbaca.sif \
 		chewie PrepExternalSchema \
-		-i $(ECOLI_CGMLST_DIR)/alleles \
+		-g $(ECOLI_CGMLST_DIR)/alleles \
 		-o $(ECOLI_CGMLST_DIR)/alleles_rereffed \
 		--cpu 2 \
 		--ptf $(PRODIGAL_TRAINING_DIR)/Escherichia_coli.trn |& tee -a $(INSTALL_LOG)
@@ -538,7 +538,7 @@ $(KPNEU_CGMLST_DIR)/alleles_rereffed: | $(KPNEU_CGMLST_DIR)/alleles/unpacking.do
 	&& echo "WARNING! Prepping cgMLST schema. This takes a looong time. Put on some coffee" \
 	&& singularity exec --bind $(MNT_ROOT) $(CONTAINER_DIR)/chewbbaca.sif \
 		chewie PrepExternalSchema \
-		-i $(KPNEU_CGMLST_DIR)/alleles \
+		-g $(KPNEU_CGMLST_DIR)/alleles \
 		-o $(KPNEU_CGMLST_DIR)/alleles_rereffed \
 		--cpu 2 \
 		--ptf $(PRODIGAL_TRAINING_DIR)/Klebsiella_pneumoniae.trn |& tee -a $(INSTALL_LOG)