diff --git a/scala/src/org/broadinstitute/sting/queue/QSettings.scala b/scala/src/org/broadinstitute/sting/queue/QSettings.scala
index 3b420bf93..b3dd6fb3c 100644
--- a/scala/src/org/broadinstitute/sting/queue/QSettings.scala
+++ b/scala/src/org/broadinstitute/sting/queue/QSettings.scala
@@ -29,9 +29,6 @@ class QSettings {
   @Argument(fullName="temp_directory", shortName="tempDir", doc="Temp directory to pass to functions.", required=false)
   var tempDirectory = new File(System.getProperty("java.io.tmpdir"))
 
-  @Argument(fullName="mount_directory", shortName="mountDir", doc="Extra directory to automount via 'cd <dir>' before running functions.", required=false)
-  var mountDirectories: Set[File] = Set.empty[File]
-
   @ArgumentCollection
   val emailSettings = new EmailSettings
 }
diff --git a/scala/src/org/broadinstitute/sting/queue/engine/CommandLineJobRunner.scala b/scala/src/org/broadinstitute/sting/queue/engine/CommandLineJobRunner.scala
index eda4ed92a..39c47291d 100755
--- a/scala/src/org/broadinstitute/sting/queue/engine/CommandLineJobRunner.scala
+++ b/scala/src/org/broadinstitute/sting/queue/engine/CommandLineJobRunner.scala
@@ -29,7 +29,7 @@ trait CommandLineJobRunner extends JobRunner[CommandLineFunction] with Logging {
   protected def writeExec() {
     var exec = new StringBuilder
     
-    var dirs = function.mountDirectories
+    var dirs = Set.empty[File]
     for (dir <- function.jobDirectories)
       dirs += IOUtils.dirLevel(dir, 2)
     if (dirs.size > 0) {
diff --git a/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala b/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala
index b177353ab..da6a5e0c8 100644
--- a/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala
+++ b/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala
@@ -34,9 +34,6 @@ trait QFunction extends Logging {
   /** Temporary directory to write any files */
   var jobTempDir: File = null
 
-  /** Directories to mount via 'cd <dir>' before running the command. */
-  var mountDirectories: Set[File] = Set.empty[File]
-
   /** Order the function was added to the graph. */
   var addOrder: List[Int] = Nil
 
@@ -308,8 +305,6 @@ trait QFunction extends Logging {
     // Do not set the temp dir relative to the command directory
     jobTempDir = IOUtils.absolute(jobTempDir)
 
-    mountDirectories ++= qSettings.mountDirectories
-
     absoluteCommandDirectory()
   }
 
diff --git a/scala/test/org/broadinstitute/sting/queue/pipeline/FullCallingPipelineTest.scala b/scala/test/org/broadinstitute/sting/queue/pipeline/FullCallingPipelineTest.scala
index fffb5cfa8..d7d44bd96 100644
--- a/scala/test/org/broadinstitute/sting/queue/pipeline/FullCallingPipelineTest.scala
+++ b/scala/test/org/broadinstitute/sting/queue/pipeline/FullCallingPipelineTest.scala
@@ -14,9 +14,6 @@ class FullCallingPipelineTest extends BaseTest {
 
   private final val validationReportsDataLocation = "/humgen/gsa-hpprojects/GATK/validationreports/submitted/"
 
-  // Explicit directories known to cause problems due to automount failures, and not detected by @Input / @Outputs
-  private final val mountDirectories = Set("/broad/software")
-
   // In fullCallingPipeline.q VariantEval is always compared against 129.
   // Until the newvarianteval is finalized which will allow java import of the prior results,
   // we re-run VariantEval to validate the run, and replicate that behavior here.
@@ -111,11 +108,6 @@ class FullCallingPipelineTest extends BaseTest {
     if (dataset.jobQueue != null)
       pipelineCommand += " -jobQueue " + dataset.jobQueue
 
-    //for (dir <- mountDirectories)
-    //  pipelineCommand += " -mountDir " + dir
-    if (PipelineTest.run)
-      System.getenv.foreach{case (name, value) => println("DEBUG_ENVIRONMENT: %s=%s".format(name, value))}
-
     // Run the test, at least checking if the command compiles
     PipelineTest.executeTest(testName, pipelineCommand, null)
 
diff --git a/shell/queue.sh b/shell/queue.sh
index c34b920bb..d95b55425 100755
--- a/shell/queue.sh
+++ b/shell/queue.sh
@@ -14,4 +14,4 @@ use R-2.10
 use Oracle-full-client
 use .cx-oracle-5.0.2-python-2.6.5-oracle-full-client-11.1
 
-java -Djava.io.tmpdir="$TMP_DIR" -jar "$STING_HOME"/dist/Queue.jar -jobQueue "$JOB_QUEUE" -shortJobQueue "$SHORT_QUEUE" -jobProject "$SAMPLE_SET" -jobPrefix "$SAMPLE_SET" -tearScript ~/Sting/R/DataProcessingReport/GetTearsheetStats.R -S ~/Sting/scala/qscript/fullCallingPipeline.q -Y "$SAMPLE_SET".yaml -refseqTable "$REFSEQ_TABLE" --gatkjar "$STING_HOME"/dist/GenomeAnalysisTK.jar -mountDir /broad/software -log queue_log.txt -statusTo corin -bsub $2
+java -Djava.io.tmpdir="$TMP_DIR" -jar "$STING_HOME"/dist/Queue.jar -jobQueue "$JOB_QUEUE" -shortJobQueue "$SHORT_QUEUE" -jobProject "$SAMPLE_SET" -jobPrefix "$SAMPLE_SET" -tearScript ~/Sting/R/DataProcessingReport/GetTearsheetStats.R -S ~/Sting/scala/qscript/fullCallingPipeline.q -Y "$SAMPLE_SET".yaml -refseqTable "$REFSEQ_TABLE" --gatkjar "$STING_HOME"/dist/GenomeAnalysisTK.jar -log queue_log.txt -statusTo corin -bsub $2