diff --git a/src/agat/agat_sp_compare_two_annotations/script.sh b/src/agat/agat_sp_compare_two_annotations/script.sh
index 8c6d09a4..31f7f33d 100644
--- a/src/agat/agat_sp_compare_two_annotations/script.sh
+++ b/src/agat/agat_sp_compare_two_annotations/script.sh
@@ -7,11 +7,20 @@
 [[ "$par_debug" == "false" ]] && unset par_debug
 [[ "$par_verbose" == "false" ]] && unset par_verbose
 
+# Debug statement to check if par_output_dir is set
+echo "par_output_dir is set to: ${par_output_dir}"
+
+# Ensure par_output_dir is set
+if [ -z "$par_output_dir" ]; then
+  echo "Error: par_output_dir is not set."
+  exit 1
+fi
+
 # run agat_sp_compare_two_annotations.pl
 agat_sp_compare_two_annotations.pl \
   -gff1 "$par_gff1" \
   -gff2 "$par_gff2" \
-  -output "$par_output" \
+  ${par_output_dir:+-o "${par_output_dir}"} \
   ${par_debug:+--debug} \
   ${par_verbose:+--verbose} \
   ${par_config:+--config "${par_config}"}