diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/FlowLineFeeder.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/FlowLineFeeder.java
index a9be637dad6488279f6fe1d4e48c39159793eb5a..144306f2bb868ad3b2f26d20cac0840915e581ee 100644
--- a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/FlowLineFeeder.java
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/FlowLineFeeder.java
@@ -24,6 +24,7 @@ import java.util.List;
 import java.util.Map;
 import java.util.Properties;
 
+import ch.systemsx.cisd.common.Constants;
 import ch.systemsx.cisd.common.TimingParameters;
 import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
 import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
@@ -82,7 +83,8 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler
         {
             String flowLine = extractFlowLine(file);
             File dropBox = createDropBoxFile(flowLine);
-            File flowLineDataSet = new File(dropBox, flowcellID + "_" + flowLine);
+            String fileName = flowcellID + "_" + flowLine;
+            File flowLineDataSet = new File(dropBox, fileName);
             if (flowLineDataSet.exists())
             {
                 throw new EnvironmentFailureException("There is already a data set for flow line "
@@ -103,6 +105,9 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler
                         + file.getAbsolutePath() + "' in folder '"
                         + flowLineDataSet.getAbsolutePath() + "'.");
             }
+            File markerFile = new File(dropBox, Constants.IS_FINISHED_PREFIX + fileName);
+            flowLineDataSets.add(markerFile);
+            FileUtilities.writeToFile(markerFile, "");
         }
 
     }
@@ -198,7 +203,10 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler
     {
         for (File file : flowLineDataSets)
         {
-            fileOperations.deleteRecursively(file);
+            if (file.exists())
+            {
+                fileOperations.deleteRecursively(file);
+            }
         }
     }
 
diff --git a/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/FlowLineFeederTest.java b/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/FlowLineFeederTest.java
index 20698af13e3059cb52d34226c8e4539e034d3a48..b91f946efd50575487485cc63d4f22dc3ed45f2b 100644
--- a/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/FlowLineFeederTest.java
+++ b/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/FlowLineFeederTest.java
@@ -31,6 +31,7 @@ import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
 import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
+import ch.systemsx.cisd.common.Constants;
 import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
 import ch.systemsx.cisd.common.filesystem.FileUtilities;
 import ch.systemsx.cisd.common.test.AssertionUtil;
@@ -186,8 +187,8 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase
     public void testUndoLastOperation()
     {
         testHappyCase();
-        assertEquals(1, new File(workingDirectory, DROP_BOX_PREFIX + "1").list().length);
-        assertEquals(1, new File(workingDirectory, DROP_BOX_PREFIX + "2").list().length);
+        assertEquals(2, new File(workingDirectory, DROP_BOX_PREFIX + "1").list().length);
+        assertEquals(2, new File(workingDirectory, DROP_BOX_PREFIX + "2").list().length);
         
         flowLineFeeder.undoLastOperation();
         
@@ -245,7 +246,8 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase
     private void checkFlowLineDataSet(File originalFlowLine, String flowLineNumber)
     {
         File dropBox = new File(workingDirectory, DROP_BOX_PREFIX + flowLineNumber);
-        File ds = new File(dropBox, "abc_" + flowLineNumber);
+        String fileName = "abc_" + flowLineNumber;
+        File ds = new File(dropBox, fileName);
         assertEquals(true, ds.isDirectory());
 
         File flowLine = new File(ds, originalFlowLine.getName());
@@ -257,6 +259,7 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase
         originalFlowLine.setLastModified(4711000);
         assertEquals(4711000, flowLine.lastModified());
         assertEquals(true, new File(ds, FlowLineFeeder.META_DATA_FILE_NAME).exists());
+        assertEquals(true, new File(dropBox, Constants.IS_FINISHED_PREFIX + fileName).exists());
     }
     
     private Sample createFlowLineSample(int flowLineNumber)