diff --git a/CHANGELOG.md b/CHANGELOG.md
index cd3ac4ff26828c9262cd1f71a3a1e84f341a7f27..6fe704988327703f19432b301ca19c8023ec4c48 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -20,7 +20,7 @@ All notable changes to Pantools will be documented in this file.
 - Fixed `pantools add_functions` when protein names have special characters (!242).
 - Fixed the KMC command needed for `pantools add_genomes` (!243).
 - Fixed CI/CD pipeline by setting specific dependency version (!247).
-- Fixed long MCL runtime by properly capturing the output (!246).
+- Fixed long MCL runtime by properly capturing the output (!246, !248).
 
 ## [4.3.1] - 08-12-2023
 
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 ff643f6eb2edc121829d130ae6a0d1d1d517b17f..e36ce847a8eb79ccfeffd7a26f12296821c4a946 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
@@ -732,8 +732,8 @@ public class Grouping {
             // Run MCL
             command = "mcl " + graph_path + " --abc -I " + MCL_INFLATION + " -o " + clusters_path + " -overlap keep -V all";
             Pantools.logger.debug(command);
-            if (!executeCommand_for(command, 10 + (int) Math.round(group_size / 100000000.0 * group_size))) { // estimated time for MCL + 10 seconds for I/O
-                Pantools.logger.warn("Failed to split group ID = {}", component.getFirst().getId());
+            if (!executeCommand_for(command, 3600 + (int) Math.round(group_size / 100000000.0 * group_size))) { // estimated time for MCL + 3600 seconds to ensure it doesn't crash because of I/O
+                Pantools.logger.warn("Failed to split group ID = {} (size = {}) because MCL ran out of time.", component.getFirst().getId(), group_size);
                 homology_groups_list.put(component);
                 if ((tmp_file = new File(clusters_path)).exists()) {
                     tmp_file.delete();