diff --git a/backend/src/main/java/cz/cuni/mff/xrg/odcs/backend/execution/pipeline/impl/CleanUp.java b/backend/src/main/java/cz/cuni/mff/xrg/odcs/backend/execution/pipeline/impl/CleanUp.java
index ea382b653f..e28f1e5dd1 100644
--- a/backend/src/main/java/cz/cuni/mff/xrg/odcs/backend/execution/pipeline/impl/CleanUp.java
+++ b/backend/src/main/java/cz/cuni/mff/xrg/odcs/backend/execution/pipeline/impl/CleanUp.java
@@ -61,6 +61,13 @@ public boolean postAction(PipelineExecution execution,
             Map<Node, Context> contexts,
             DependencyGraph graph) {
         LOG.debug("CleanUp start .. ");
+
+        try {
+            this.relationalRepositoryManager.release(execution.getContext().getExecutionId());
+        } catch (Exception e) {
+            LOG.error("Failed to release relational repository", e);
+        }
+
         // first release contexts
         for (Context item : contexts.values()) {
             if (execution.isDebugging()) {
@@ -93,12 +100,6 @@ public boolean postAction(PipelineExecution execution,
             }
         }
 
-        try {
-            this.relationalRepositoryManager.release(execution.getContext().getExecutionId());
-        } catch (Exception e) {
-            LOG.error("Failed to release relational repository", e);
-        }
-
         // prepare execution root
         File rootDir = new File(
                 appConfig.getString(ConfigProperty.GENERAL_WORKINGDIR));
diff --git a/dataunit-relational-impl/src/main/java/eu/unifiedviews/dataunit/relational/repository/FilesRelationalDatabase.java b/dataunit-relational-impl/src/main/java/eu/unifiedviews/dataunit/relational/repository/FilesRelationalDatabase.java
index e344d8efd6..713b6c9c7d 100644
--- a/dataunit-relational-impl/src/main/java/eu/unifiedviews/dataunit/relational/repository/FilesRelationalDatabase.java
+++ b/dataunit-relational-impl/src/main/java/eu/unifiedviews/dataunit/relational/repository/FilesRelationalDatabase.java
@@ -127,12 +127,17 @@ public void release() throws Exception {
 
     private void deleteDatabaseFile() throws IOException {
         Pattern filesPattern = Pattern.compile(this.databaseFileName + ".*");
+        if (this.dataunitDirectory == null || !this.dataunitDirectory.exists()) {
+            return;
+        }
         File[] filesInDataUnitDir = this.dataunitDirectory.listFiles();
+        if (filesInDataUnitDir == null) {
+            return;
+        }
         for (File file : filesInDataUnitDir) {
             if (filesPattern.matcher(file.getName()).matches()) {
                 Files.delete(file.toPath());
             }
-            break;
         }
     }