diff --git a/scala/src/org/broadinstitute/sting/queue/engine/QFile.scala b/scala/src/org/broadinstitute/sting/queue/engine/QFile.scala
index 7f443ceb9..27c11b545 100755
--- a/scala/src/org/broadinstitute/sting/queue/engine/QFile.scala
+++ b/scala/src/org/broadinstitute/sting/queue/engine/QFile.scala
@@ -16,7 +16,7 @@ class QFile(val fileType: String, val parts: String*) {
   override def hashCode = HashCodeBuilder.reflectionHashCode(this)
 
   def matchesFile(path: String): Boolean = matchesFile(new File(path))
-  def matchesFile(file: File): Boolean = file.getCanonicalPath.endsWith(extension)
+  def matchesFile(file: File): Boolean = file.getAbsolutePath.endsWith(extension)
   def baseName(path: String): String = baseName(new File(path))
   def baseName(file: File): String = StringUtils.removeEnd(file.getAbsolutePath, extension)
   def fullName(baseName: String) = baseName + extension
diff --git a/scala/src/org/broadinstitute/sting/queue/engine/graphing/TreeJobGrapher.scala b/scala/src/org/broadinstitute/sting/queue/engine/graphing/TreeJobGrapher.scala
index ed8e2d05c..149cef2ed 100644
--- a/scala/src/org/broadinstitute/sting/queue/engine/graphing/TreeJobGrapher.scala
+++ b/scala/src/org/broadinstitute/sting/queue/engine/graphing/TreeJobGrapher.scala
@@ -56,7 +56,7 @@ class TreeJobGrapher extends JobGrapher {
   }
 
   private def addPaths(shortestPath: java.util.List[QCommand], qArgs: QArguments) {
-    for (inputFile <- qArgs.inputPaths.map(_.getCanonicalPath))
+    for (inputFile <- qArgs.inputPaths.map(_.getAbsolutePath))
       if (modelGraph.getEdgeSource(shortestPath.head).matchesFile(inputFile))
         addPath(shortestPath, inputFile)
   }