diff --git a/pgge b/pgge
index cb09554..4d3627d 100755
--- a/pgge
+++ b/pgge
@@ -399,19 +399,19 @@ then
     (echo sample.name cons.jump aln.id qsc uniq multi nonaln; ls "$output_dir" | grep gaf | grep pgge$ | while read f; \
     do
     echo "$(echo "$f" | cut -f 2 -d .)" "$(echo "$f" | cut -f 2 -d @ | cut -f 1 -d.)" "$(cat "$output_dir"/"$f")"; \
-    done) | tr ' ' '\t' > "$prefix_pgge".tsv
+    done) | tr ' ' '\t' > "$prefix_pgge"."$(basename $output_dir)".tsv
     "$timer" -f "$fmt" Rscript \
-        "$beehave_R" "$prefix_pgge".tsv \
-        "$prefix_pgge".tsv.png \
+        "$beehave_R" "$prefix_pgge"."$(basename $output_dir)".tsv \
+        "$prefix_pgge"."$(basename $output_dir)".tsv.png \
         2> >(tee -a "$log_file")
 else 
     (echo sample.name cons.jump aln.id qsc uniq multi nonaln; ls "$output_dir" | grep gaf | grep pgge$ | while read f; \
     do
     echo "$(echo "$f" | cut -f 2 -d .)" "$(basename $(echo "$output_dir"/"$f"))" "$(cat "$output_dir"/"$f")"; \
-    done) | tr ' ' '\t' > "$prefix_pgge".tsv
+    done) | tr ' ' '\t' > "$prefix_pgge"."$(basename $output_dir)".tsv
     "$timer" -f "$fmt" Rscript \
-        "$beehave_R" "$prefix_pgge".tsv \
-        "$prefix_pgge".tsv.png \
+        "$beehave_R" "$prefix_pgge"."$(basename $output_dir)".tsv \
+        "$prefix_pgge"."$(basename $output_dir)".tsv.png \
         "$input_graph_names" \
         2> >(tee -a "$log_file")
 fi
\ No newline at end of file