diff --git a/bin/1.2_filter_motifs/compareBed.sh b/bin/1.2_filter_motifs/compareBed.sh
index 2c4c9ba..8534f1b 100644
--- a/bin/1.2_filter_motifs/compareBed.sh
+++ b/bin/1.2_filter_motifs/compareBed.sh
@@ -279,7 +279,7 @@ then
 	# add some final values to the log file
 	fp_initial=`cat $data | wc -l`
 	fp_initial=`expr $fp_initial - 1`
-	fp_final=`cat "$workdir"/filtered.bed | wc -l`
+	fp_final=`cat "$workdir"/filtered_flagged.bed | wc -l`
 	fp_final=`expr $fp_final - 1`
 	echo $fp_initial | sed 's/^/initial number of footprints: /g' >> "$workdir"/compareBed.stats
 	echo $fp_final | sed 's/^/number of footprints after subtract: /g' >> "$workdir"/compareBed.stats
@@ -288,7 +288,7 @@ else
 	rm -f $output
 	# add some final values to the log file
 	cat $data | wc -l | sed 's/^/initial number of footprints: /g' >> "$workdir"/compareBed.stats
-	cat "$workdir"/filtered.bed | wc -l | sed 's/^/number of footprints after subtract: /g' >> "$workdir"/compareBed.stats
+	cat "$workdir"/filtered_flagged.bed | wc -l | sed 's/^/number of footprints after subtract: /g' >> "$workdir"/compareBed.stats
 fi
 
 # add fasta sequences to bed and create fasta file