java.lang.AssertionError

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    • java.lang.AssertionError: assertion failed: Timer name from on top of stack [/GET variants(19,false)] did not match passed-in timer name [GET reads] at scala.Predef$.assert(Predef.scala:179) at org.bdgenomics.utils.instrumentation.MetricsRecorder.finishPhase(MetricsRecorder.scala:55) at org.apache.spark.rdd.Timer$$anonfun$time$1.apply(Timer.scala:54) at org.apache.spark.rdd.Timer$$anonfun$time$1.apply(Timer.scala:48) at scala.Option.fold(Option.scala:157) at org.apache.spark.rdd.Timer.time(Timer.scala:48) at org.bdgenomics.mango.cli.VizServlet$$anonfun$12.apply(VizReads.scala:308) at org.bdgenomics.mango.cli.VizServlet$$anonfun$12.apply(VizReads.scala:308) at org.scalatra.ScalatraBase$class.org$scalatra$ScalatraBase$$liftAction(ScalatraBase.scala:285) at org.scalatra.ScalatraBase$$anonfun$invoke$1.apply(ScalatraBase.scala:279) at org.scalatra.ScalatraBase$$anonfun$invoke$1.apply(ScalatraBase.scala:279) at org.scalatra.ScalatraBase$class.withRouteMultiParams(ScalatraBase.scala:356) at org.bdgenomics.mango.cli.VizServlet.withRouteMultiParams(VizReads.scala:211) at org.scalatra.ScalatraBase$class.invoke(ScalatraBase.scala:278) at org.bdgenomics.mango.cli.VizServlet.invoke(VizReads.scala:211) at org.scalatra.ScalatraBase$$anonfun$runRoutes$1$$anonfun$apply$8.apply(ScalatraBase.scala:253) at org.scalatra.ScalatraBase$$anonfun$runRoutes$1$$anonfun$apply$8.apply(ScalatraBase.scala:251) at scala.Option.flatMap(Option.scala:170) at org.scalatra.ScalatraBase$$anonfun$runRoutes$1.apply(ScalatraBase.scala:251) at org.scalatra.ScalatraBase$$anonfun$runRoutes$1.apply(ScalatraBase.scala:250) at scala.collection.immutable.Stream.flatMap(Stream.scala:446) at org.scalatra.ScalatraBase$class.runRoutes(ScalatraBase.scala:250) at org.bdgenomics.mango.cli.VizServlet.runRoutes(VizReads.scala:211) at org.scalatra.ScalatraBase$class.runActions$1(ScalatraBase.scala:175) at org.scalatra.ScalatraBase$$anonfun$executeRoutes$1.apply$mcV$sp(ScalatraBase.scala:187) at org.scalatra.ScalatraBase$$anonfun$executeRoutes$1.apply(ScalatraBase.scala:187) at org.scalatra.ScalatraBase$$anonfun$executeRoutes$1.apply(ScalatraBase.scala:187) at org.scalatra.ScalatraBase$class.org$scalatra$ScalatraBase$$cradleHalt(ScalatraBase.scala:205) at org.scalatra.ScalatraBase$class.executeRoutes(ScalatraBase.scala:187) at org.bdgenomics.mango.cli.VizServlet.executeRoutes(VizReads.scala:211) at org.scalatra.ScalatraBase$$anonfun$handle$1.apply$mcV$sp(ScalatraBase.scala:126) at org.scalatra.ScalatraBase$$anonfun$handle$1.apply(ScalatraBase.scala:126) at org.scalatra.ScalatraBase$$anonfun$handle$1.apply(ScalatraBase.scala:126) at scala.util.DynamicVariable.withValue(DynamicVariable.scala:57) at org.scalatra.DynamicScope$class.withResponse(DynamicScope.scala:78) at org.bdgenomics.mango.cli.VizServlet.withResponse(VizReads.scala:211) at org.scalatra.DynamicScope$$anonfun$withRequestResponse$1.apply(DynamicScope.scala:58) at scala.util.DynamicVariable.withValue(DynamicVariable.scala:57) at org.scalatra.DynamicScope$class.withRequest(DynamicScope.scala:69) at org.bdgenomics.mango.cli.VizServlet.withRequest(VizReads.scala:211) at org.scalatra.DynamicScope$class.withRequestResponse(DynamicScope.scala:57) at org.bdgenomics.mango.cli.VizServlet.withRequestResponse(VizReads.scala:211) at org.scalatra.ScalatraBase$class.handle(ScalatraBase.scala:125) at org.bdgenomics.mango.cli.VizServlet.org$scalatra$servlet$ServletBase$$super$handle(VizReads.scala:211) at org.scalatra.servlet.ServletBase$class.handle(ServletBase.scala:53) at org.bdgenomics.mango.cli.VizServlet.handle(VizReads.scala:211) at org.scalatra.ScalatraServlet$class.service(ScalatraServlet.scala:60) at org.bdgenomics.mango.cli.VizServlet.service(VizReads.scala:211) at javax.servlet.http.HttpServlet.service(HttpServlet.java:848) at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:565) at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:479) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:119) at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:521) at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:227) at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1031) at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:406) at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:186) at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:965) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:117) at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:250) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:111) at org.eclipse.jetty.server.Server.handle(Server.java:349) at org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(AbstractHttpConnection.java:449) at org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.headerComplete(AbstractHttpConnection.java:910) at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:634) at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:230) at org.eclipse.jetty.server.AsyncHttpConnection.handle(AsyncHttpConnection.java:76) at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(SelectChannelEndPoint.java:609) at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectChannelEndPoint.java:45) at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:599) at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:534) at java.lang.Thread.run(Thread.java:745)

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