diff --git a/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala b/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala
index 07c03d289..ed71b586c 100755
--- a/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala
+++ b/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala
@@ -484,7 +484,7 @@ class QGraph extends Logging {
   }
 
   private def failedDescription(failed: FunctionEdge) = {
-    var description = new StringBuilder
+    val description = new StringBuilder
     if (settings.retries > 0)
       description.append("Attempt %d of %d.%n".format(failed.retries + 1, settings.retries + 1))
     description.append(failed.function.description)
@@ -749,7 +749,7 @@ class QGraph extends Logging {
     if (running && !settings.keepIntermediates && success) {
       logger.info("Deleting intermediate files.")
       traverseFunctions(edge => {
-        if (edge.function.isIntermediate) {
+        if (edge.function.isIntermediate && edge.function.deleteIntermediateOutputs) {
           logger.debug("Deleting intermediates:" + edge.function.description)
           edge.function.deleteOutputs()
         }
diff --git a/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala b/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala
index 5c77f53bb..707ae8f13 100644
--- a/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala
+++ b/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala
@@ -55,6 +55,12 @@ trait QFunction extends Logging {
    */
   var isIntermediate = false
 
+  /**
+   * If true and isIntermediate is true, the files listed
+   * via outputs will deleted after the command completes.
+   */
+  var deleteIntermediateOutputs = true
+
   /**
    * Copies settings from this function to another function.
    * @param function QFunction to copy values to.
@@ -70,6 +76,7 @@ trait QFunction extends Logging {
     function.jobRestartable = this.jobRestartable
     function.updateJobRun = this.updateJobRun
     function.isIntermediate = this.isIntermediate
+    function.deleteIntermediateOutputs = this.deleteIntermediateOutputs
   }
 
   /** File to redirect any output.  Defaults to <jobName>.out */
diff --git a/scala/src/org/broadinstitute/sting/queue/function/scattergather/GatherFunction.scala b/scala/src/org/broadinstitute/sting/queue/function/scattergather/GatherFunction.scala
index 3d09c6061..28c3e89a2 100644
--- a/scala/src/org/broadinstitute/sting/queue/function/scattergather/GatherFunction.scala
+++ b/scala/src/org/broadinstitute/sting/queue/function/scattergather/GatherFunction.scala
@@ -13,6 +13,9 @@ trait GatherFunction extends QFunction {
   @Input(doc="Parts to gather back into the original output")
   var gatherParts: List[File] = Nil
 
+  @Input(doc="Other log files that will be gathered before this output", required=false)
+  var originalLogFiles: List[File] = Nil
+
   @Output(doc="The original output of the scattered function")
   var originalOutput: File = _
 
diff --git a/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala b/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala
index 18f60a28f..91561609b 100644
--- a/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala
+++ b/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala
@@ -82,6 +82,11 @@ trait ScatterGatherableFunction extends CommandLineFunction {
     // Ask the scatter function how many clones to create.
     val numClones = scatterFunction.scatterCount
 
+    // List of the log files that are output by this function.
+    var logFiles = List(this.jobOutputFile)
+    if (this.jobErrorFile != null)
+      logFiles :+= this.jobErrorFile
+
     // Create the gather functions for each output field
     var gatherFunctions = Map.empty[ArgumentSource, GatherFunction]
     var gatherOutputs = Map.empty[ArgumentSource, File]
@@ -92,12 +97,23 @@ trait ScatterGatherableFunction extends CommandLineFunction {
       this.copySettingsTo(gatherFunction)
       gatherFunction.addOrder = this.addOrder :+ gatherAddOrder
       gatherFunction.commandDirectory = this.scatterGatherTempDir("gather-" + gatherField.field.getName)
-      gatherFunction.originalOutput = this.getFieldFile(gatherField)
+      gatherFunction.originalOutput = gatherOutput
       initGatherFunction(gatherFunction, gatherField)
       functions :+= gatherFunction
       gatherFunctions += gatherField -> gatherFunction
       gatherOutputs += gatherField -> gatherOutput
       gatherAddOrder += 1
+
+      // If this is a gather for a log file, make the gather intermediate just in case the log file name changes
+      // Otherwise have the regular output function wait on the log files to gather
+      if (isLogFile(gatherOutput)) {
+        gatherFunction.isIntermediate = true
+        // Only delete the log files if the original function is an intermediate
+        // and the intermediate files are supposed to be deleted
+        gatherFunction.deleteIntermediateOutputs = this.isIntermediate && this.deleteIntermediateOutputs
+      } else {
+        gatherFunction.originalLogFiles = logFiles
+      }
     }
 
     // Create the clone functions for running the parallel jobs
@@ -122,7 +138,6 @@ trait ScatterGatherableFunction extends CommandLineFunction {
       // Allow the script writer to change the paths to the files.
       initCloneFunction(cloneFunction, i)
 
-
       // If the command directory is relative, insert the run directory ahead of it.
       cloneFunction.absoluteCommandDirectory()