diff --git a/uk/ac/sanger/artemis/j2ssh/SshPSUClient.java b/uk/ac/sanger/artemis/j2ssh/SshPSUClient.java
index 4126d85c6aaef353990905f78a8fe2863fc79837..e84601606d7e9535596caf18834d70b21cd614e9 100644
--- a/uk/ac/sanger/artemis/j2ssh/SshPSUClient.java
+++ b/uk/ac/sanger/artemis/j2ssh/SshPSUClient.java
@@ -335,6 +335,9 @@ public class SshPSUClient extends Thread
 //    System.out.println(os.toString());
 
       sftp.get(outputfile, filepath+".out");
+      sftp.rm(outputfile);
+      sftp.rm(wdir+filename);
+
       session.close();
     }
     sftp.quit();