diff --git a/oak-run/src/main/java/org/apache/jackrabbit/oak/run/DataStoreCheckCommand.java b/oak-run/src/main/java/org/apache/jackrabbit/oak/run/DataStoreCheckCommand.java
index 5ce6a700d00..389b9bb3516 100644
--- a/oak-run/src/main/java/org/apache/jackrabbit/oak/run/DataStoreCheckCommand.java
+++ b/oak-run/src/main/java/org/apache/jackrabbit/oak/run/DataStoreCheckCommand.java
@@ -459,6 +459,7 @@ public void addReference(String blobId, String nodeId) {
                 }
             );
             writer.flush();
+            writer.close();
             sort(marked, idComparator);
 
             System.out.println(count.get() + " blob references found");
@@ -564,6 +565,7 @@ public void traverse(String ... paths) throws IOException {
                 }
 
                 writer.flush();
+                writer.close();
                 sort(references, idComparator);
 
                 System.out.println(count.get() + " blob references found");