diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/QJobReport.scala b/public/scala/src/org/broadinstitute/sting/queue/util/QJobReport.scala
index 093741b5d..73ab7c366 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/util/QJobReport.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/util/QJobReport.scala
@@ -40,6 +40,7 @@ trait QJobReport extends Logging {
   self: QFunction =>
 
   protected var reportGroup: String = null
+  protected var userReportFeatures: Map[String, String] = Map()
   protected var reportFeatures: Map[String, String] = Map()
   protected var reportEnabled: Boolean = true
 
@@ -49,7 +50,7 @@ trait QJobReport extends Logging {
 
   def setRunInfo(info: JobRunInfo) {
     //logger.info("info " + info)
-    reportFeatures = Map(
+    val runtimeFeatures = Map(
       "iteration" -> 1,
       "analysisName" -> getReportGroup,
       "jobName" -> QJobReport.workAroundSameJobNames(this),
@@ -59,36 +60,39 @@ trait QJobReport extends Logging {
       "doneTime" -> info.getDoneTime.getTime,
       "formattedStartTime" -> info.getFormattedStartTime,
       "formattedDoneTime" -> info.getFormattedDoneTime,
-      "runtime" -> info.getRuntimeInMs).mapValues((x:Any) => if (x != null) x.toString else "null") ++ reportFeatures
+      "runtime" -> info.getRuntimeInMs).mapValues((x:Any) => if (x != null) x.toString else "null")
+    reportFeatures = runtimeFeatures ++ userReportFeatures
     // note -- by adding reportFeatures second we override iteration
     // (or any other binding) with the user provided value
   }
 
   /** The report Group is the analysis name transform to only contain valid GATKReportTable characters */
   def getReportGroup = self.analysisName.replaceAll(GATKReportTable.INVALID_TABLE_NAME_REGEX, "_")
-  def getReportFeatures = reportFeatures
 
-  def getReportFeatureNames: Seq[String] = getReportFeatures.keys.toSeq
+  def getReportFeatureNames: Seq[String] = reportFeatures.keys.toSeq
   def getReportFeature(key: String): String = {
-    getReportFeatures.get(key) match {
+    reportFeatures.get(key) match {
       case Some(x) => x
-      case None => throw new RuntimeException("Get called with key %s but no value was found".format(key))
+      case None =>
+        logger.warn("getReportFeature called with key %s but no value was found for group %s.  This can be caused by adding user-defined job features to a job with a generic name used elsewhere in the Queue script.  To fix the problem make sure that each group of commands with user-specific features has a unique analysisName".format(key, reportGroup))
+        "NA"
     }
   }
 
   def getReportName: String = getReportFeature("jobName")
 
   def configureJobReport(features: Map[String, Any]) {
-    this.reportFeatures = features.mapValues(_.toString)
+    this.userReportFeatures = features.mapValues(_.toString)
   }
 
   def addJobReportBinding(key: String, value: Any) {
-    this.reportFeatures += (key -> value.toString)
+    this.userReportFeatures += (key -> value.toString)
   }
 
   // copy the QJobReport information -- todo : what's the best way to do this?
   override def copySettingsTo(function: QFunction) {
     self.copySettingsTo(function)
+    function.userReportFeatures = this.userReportFeatures
     function.reportFeatures = this.reportFeatures
   }
 }