diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/LocalDataSetFileOperationsExcecutor.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/LocalDataSetFileOperationsExcecutor.java
index 9ebfe9c9f51d87db57d59da18ae9cef5432cf929..c4f7db70e33b0ddf853843fd28aadda977d9224f 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/LocalDataSetFileOperationsExcecutor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/LocalDataSetFileOperationsExcecutor.java
@@ -17,6 +17,7 @@
 package ch.systemsx.cisd.openbis.dss.generic.server;
 
 import java.io.File;
+import java.io.FileFilter;
 import java.io.IOException;
 import java.util.LinkedHashMap;
 import java.util.List;
@@ -61,15 +62,14 @@ public final class LocalDataSetFileOperationsExcecutor implements IDataSetFileOp
         {
             if (destination.isDirectory())
             {
-                List<File> dataSetFiles = FileUtilities.listFilesAndDirectories(dataSet, true);
-                List<File> destinationFiles =
-                        FileUtilities.listFilesAndDirectories(destination, true);
+                FileFilter nullFilter = null;
+                List<File> storeFiles = FileUtilities.listFiles(dataSet, nullFilter, true);
+                List<File> destFiles = FileUtilities.listFiles(destination, nullFilter, true);
 
                 Map<String, Long> dataSetFileSizesByPaths =
-                        FolderFileSizesReportGenerator.extractSizesByPaths(dataSetFiles, dataSet);
+                        FolderFileSizesReportGenerator.extractSizesByPaths(storeFiles, dataSet);
                 Map<String, Long> destinationFileSizesByPaths =
-                        FolderFileSizesReportGenerator.extractSizesByPaths(destinationFiles,
-                                destination);
+                        FolderFileSizesReportGenerator.extractSizesByPaths(destFiles, destination);
                 String inconsistenciesReport =
                         FolderFileSizesReportGenerator.findInconsistencies(dataSetFileSizesByPaths,
                                 destinationFileSizesByPaths);
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/DataSetFileOperationsManagerTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/DataSetFileOperationsManagerTest.java
index ac72a88af4295a453180ea7f6a87b88e5cae0ba1..b4ec9acb1d33d2bda782099a8f565736fa7b6541 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/DataSetFileOperationsManagerTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/DataSetFileOperationsManagerTest.java
@@ -414,9 +414,7 @@ public class DataSetFileOperationsManagerTest extends AbstractFileSystemTestCase
         // delete second file from destination
         FileUtilities.delete(ds1ArchivedDataFile2);
         boolStatus = dataSetCopier.isPresentInDestination(ds1Location, ds1);
-        // TODO ignore dirs
         assertFalse(boolStatus, "Inconsistencies:\n"
-                + "'original' - different file sizes; store: 136, destination: 102\n"
                 + "'original/data1_1.txt' - different file sizes; store: 14, destination: 28\n"
                 + "'original/data1_2.txt' - exists in store but is missing in destination\n");
 
@@ -609,7 +607,8 @@ public class DataSetFileOperationsManagerTest extends AbstractFileSystemTestCase
         context.assertIsSatisfied();
     }
 
-    @Test(groups="broken") // FIXME
+    @Test(groups = "broken")
+    // FIXME
     public void testRemoteViaSshIsPresentInDestination()
     {
         Properties properties = createRemoteViaSshDestinationProperties();