diff --git a/src/main/java/nl/wur/bif/pantools/construction/grouping/Grouping.java b/src/main/java/nl/wur/bif/pantools/construction/grouping/Grouping.java
index 0d0f3b144a8472d50310b40491a6e75dedf08eb6..a3ceb880700606191e4e954b8ca2b86453f8b6e2 100644
--- a/src/main/java/nl/wur/bif/pantools/construction/grouping/Grouping.java
+++ b/src/main/java/nl/wur/bif/pantools/construction/grouping/Grouping.java
@@ -1858,25 +1858,19 @@ public class Grouping {
      * Transactions must be committed frequently to prevent the program from running out of memory
      */
     public void delete_is_similar_to_relations() {
-        boolean present = false;
+        Pantools.logger.debug("Deleting existing similarity links between mRNA nodes.");
         for (int i = 1; i <= total_genomes; ++i) {
             int trsc = 0;
             Transaction tx = GRAPH_DB.beginTx();
             try {
                 ResourceIterator<Node> mrna_nodes = GRAPH_DB.findNodes(MRNA_LABEL, "genome", i);
-                int rel_count = 0;
-                System.out.print("\rDeleting 'is_similar_to' relationships between mRNA nodes. Genome " + i + "                          ");
+                Pantools.logger.debug("Deleting 'is_similar_to' relationships between mRNA nodes. Genome {}", i);
                 while (mrna_nodes.hasNext()) {
                     Node mrna_node = mrna_nodes.next();
-                    if (rel_count % 100 == 0 && rel_count > 0) {
-                        System.out.print("\rDeleting 'is_similar_to' relationships between mRNA nodes. "
-                                + "Genome " + i + ": " + rel_count + " relations           ");
-                    }
                     Iterable<Relationship> similar_rels = mrna_node.getRelationships(RelTypes.is_similar_to);
                     for (Relationship sim_rel : similar_rels) {
                         sim_rel.delete();
                         ++trsc;
-                        rel_count ++;
                     }
                     if (trsc >= 10000) { // Commit changes every 10K relations
                         tx.success();
@@ -1890,7 +1884,6 @@ public class Grouping {
             } finally {
                 tx.close();
             }
-            System.out.println("");
         }
     }
 
@@ -2875,6 +2868,8 @@ public class Grouping {
             System.exit(1);
         }
 
+        delete_is_similar_to_relations(); // just before we start the grouping, we will remove any is_similar_to links that are present
+
         if (THREADS < 3) {
             THREADS = 3;
         }