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Published 20 hours ago • verified publisher icon bigdatagenomics

Outdated documantion, lack of real example

Open LeonisX opened this issue 8 years ago • 5 comments

Can't launch Mango. Used Amazon EMR Cluster, all I get - file user/hadoop/... not found.

Could you, please, explain, step-by-step, how to launch application?

I tried project https://github.com/FusionWorks/jbrowse-adam It works fine on Amazon cluster

Thanks

LeonisX avatar Mar 16 '16 14:03 LeonisX

Hi Leonis,

Can you please provide us with a detailed error message or stack trace of the issue? The README should be updated now.

Best,

Alyssa Morrow [email protected] mailto:[email protected] 414-254-6645

On Mar 16, 2016, at 3:44 PM, Leonis [email protected] wrote:

Can't launch Mango. Used Amazon EMR Cluster, all I get - file user/hadoop/... not found.

Could you, please, explain, step-by-step, how to launch application?

I tried project https://github.com/FusionWorks/jbrowse-adam https://github.com/FusionWorks/jbrowse-adam It works fine on Amazon cluster

Thanks

— You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub https://github.com/bigdatagenomics/mango/issues/106

akmorrow13 avatar Mar 16 '16 16:03 akmorrow13

Thanks for docs.

I uploaded genomic files to root of Mango (full path: /home/hadoop/mango/)

First run:

bin/mango-submit human_b37_20.fasta or bin/mango-submit /home/hadoop/mango/human_b37_20.fasta

16/03/17 09:11:04 INFO VizReads: WARNING: No reads file provided
WARNING: No reads file provided
16/03/17 09:11:04 INFO VizReads: WARNING: No variants file provided
WARNING: No variants file provided
16/03/17 09:11:04 INFO VizReads: WARNING: No features file provided
WARNING: No features file provided
16/03/17 09:11:04 INFO BlockManagerMasterEndpoint: Registering block manager ip-172-31-21-181.us-west-1.compute.internal:42715 with 518.1 MB RAM, BlockManagerId(1, ip-172-31-21-181.us-west-1.compute.internal, 42715)
16/03/17 09:11:05 INFO Server: jetty-8.1.17.v20150415
16/03/17 09:11:05 INFO StandardDescriptorProcessor: NO JSP Support for /, did not find org.apache.jasper.servlet.JspServlet
16/03/17 09:11:05 INFO AbstractConnector: Started [email protected]:8080
View the visualization at: 8080
Variant visualization at: /variants
Overall visualization at: /overall
Quit at: /quit

Then we open URL, and get error:

java.lang.NullPointerException
    at org.bdgenomics.mango.cli.VizServlet$$anonfun$7.apply(VizReads.scala:310)
    at org.bdgenomics.mango.cli.VizServlet$$anonfun$7.apply(VizReads.scala:298)
    at org.scalatra.ScalatraKernel$class.org$scalatra$ScalatraKernel$$liftAction(ScalatraKernel.scala:216)
    at org.scalatra.ScalatraKernel$$anonfun$invoke$1.apply(ScalatraKernel.scala:211)
    at org.scalatra.ScalatraKernel$$anonfun$invoke$1.apply(ScalatraKernel.scala:211)
    at org.scalatra.ScalatraKernel$class.withRouteMultiParams(ScalatraKernel.scala:274)
    at org.scalatra.ScalatraServlet.withRouteMultiParams(ScalatraServlet.scala:24)
    at org.scalatra.ScalatraKernel$class.invoke(ScalatraKernel.scala:210)
    at org.scalatra.ScalatraServlet.invoke(ScalatraServlet.scala:24)
    at org.scalatra.ScalatraKernel$$anonfun$runRoutes$1$$anonfun$apply$2.apply(ScalatraKernel.scala:196)
    at org.scalatra.ScalatraKernel$$anonfun$runRoutes$1$$anonfun$apply$2.apply(ScalatraKernel.scala:195)
    at scala.Option.flatMap(Option.scala:170)
    at org.scalatra.ScalatraKernel$$anonfun$runRoutes$1.apply(ScalatraKernel.scala:195)
    at org.scalatra.ScalatraKernel$$anonfun$runRoutes$1.apply(ScalatraKernel.scala:194)
    at scala.collection.immutable.Stream.flatMap(Stream.scala:446)
    at org.scalatra.ScalatraKernel$class.runRoutes(ScalatraKernel.scala:194)
    at org.scalatra.ScalatraServlet.runRoutes(ScalatraServlet.scala:24)
    at org.scalatra.ScalatraKernel$class.executeRoutes(ScalatraKernel.scala:165)
    at org.scalatra.ScalatraServlet.executeRoutes(ScalatraServlet.scala:24)
    at org.scalatra.ScalatraKernel$$anonfun$handle$1$$anonfun$apply$mcV$sp$1.apply$mcV$sp(ScalatraKernel.scala:139)
    at org.scalatra.ScalatraKernel$$anonfun$handle$1$$anonfun$apply$mcV$sp$1.apply(ScalatraKernel.scala:137)
    at org.scalatra.ScalatraKernel$$anonfun$handle$1$$anonfun$apply$mcV$sp$1.apply(ScalatraKernel.scala:137)
    at scala.util.DynamicVariable.withValue(DynamicVariable.scala:57)
    at org.scalatra.ScalatraKernel$$anonfun$handle$1.apply$mcV$sp(ScalatraKernel.scala:137)
    at org.scalatra.ScalatraKernel$$anonfun$handle$1.apply(ScalatraKernel.scala:137)
    at org.scalatra.ScalatraKernel$$anonfun$handle$1.apply(ScalatraKernel.scala:137)
    at scala.util.DynamicVariable.withValue(DynamicVariable.scala:57)
    at org.scalatra.ScalatraKernel$class.handle(ScalatraKernel.scala:136)
    at org.scalatra.ScalatraServlet.handle(ScalatraServlet.scala:24)
    at org.scalatra.ScalatraServlet.service(ScalatraServlet.scala:31)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:848)
    at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:684)
    at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:503)
    at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:137)
    at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:557)
    at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:231)
    at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1086)
    at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:429)
    at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:193)
    at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1020)
    at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:135)
    at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:255)
    at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116)
    at org.eclipse.jetty.server.Server.handle(Server.java:370)
    at org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(AbstractHttpConnection.java:494)
    at org.eclipse.jetty.server.AbstractHttpConnection.headerComplete(AbstractHttpConnection.java:971)
    at org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.headerComplete(AbstractHttpConnection.java:1033)
    at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:644)
    at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:235)
    at org.eclipse.jetty.server.AsyncHttpConnection.handle(AsyncHttpConnection.java:82)
    at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(SelectChannelEndPoint.java:696)
    at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectChannelEndPoint.java:53)
    at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:608)
    at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:543)
    at java.lang.Thread.run(Thread.java:745)

Second run

bin/mango-submit human_b37_20.fasta -read_files dedupped_20.bam

Command body threw exception:
java.io.FileNotFoundException: File does not exist: /user/root/dedupped_20.bam
    at org.apache.hadoop.hdfs.server.namenode.INodeFile.valueOf(INodeFile.java:71)
    at org.apache.hadoop.hdfs.server.namenode.INodeFile.valueOf(INodeFile.java:61)
    at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.getBlockLocationsInt(FSNamesystem.java:1828)
    at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.getBlockLocations(FSNamesystem.java:1799)
    at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.getBlockLocations(FSNamesystem.java:1712)
    at org.apache.hadoop.hdfs.server.namenode.NameNodeRpcServer.getBlockLocations(NameNodeRpcServer.java:587)
    at org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolServerSideTranslatorPB.getBlockLocations(ClientNamenodeProtocolServerSideTranslatorPB.java:365)
    at org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol$2.callBlockingMethod(ClientNamenodeProtocolProtos.java)
    at org.apache.hadoop.ipc.ProtobufRpcEngine$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine.java:632)
    at org.apache.hadoop.ipc.RPC$Server.call(RPC.java:969)
    at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:2049)
    at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:2045)
    at java.security.AccessController.doPrivileged(Native Method)
    at javax.security.auth.Subject.doAs(Subject.java:415)
    at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1657)
    at org.apache.hadoop.ipc.Server$Handler.run(Server.java:2043)

16/03/17 09:18:48 INFO VizReads: Overall Duration: 18,98 secs
Exception in thread "main" java.io.FileNotFoundException: File does not exist: /user/root/dedupped_20.bam
    at org.apache.hadoop.hdfs.server.namenode.INodeFile.valueOf(INodeFile.java:71)
    at org.apache.hadoop.hdfs.server.namenode.INodeFile.valueOf(INodeFile.java:61)
    at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.getBlockLocationsInt(FSNamesystem.java:1828)
    at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.getBlockLocations(FSNamesystem.java:1799)
    at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.getBlockLocations(FSNamesystem.java:1712)
    at org.apache.hadoop.hdfs.server.namenode.NameNodeRpcServer.getBlockLocations(NameNodeRpcServer.java:587)
    at org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolServerSideTranslatorPB.getBlockLocations(ClientNamenodeProtocolServerSideTranslatorPB.java:365)
    at org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol$2.callBlockingMethod(ClientNamenodeProtocolProtos.java)
    at org.apache.hadoop.ipc.ProtobufRpcEngine$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine.java:632)
    at org.apache.hadoop.ipc.RPC$Server.call(RPC.java:969)
    at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:2049)
    at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:2045)
    at java.security.AccessController.doPrivileged(Native Method)
    at javax.security.auth.Subject.doAs(Subject.java:415)
    at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1657)
    at org.apache.hadoop.ipc.Server$Handler.run(Server.java:2043)

    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
    at org.apache.hadoop.ipc.RemoteException.instantiateException(RemoteException.java:106)
    at org.apache.hadoop.ipc.RemoteException.unwrapRemoteException(RemoteException.java:73)
    at org.apache.hadoop.hdfs.DFSClient.callGetBlockLocations(DFSClient.java:1245)
    at org.apache.hadoop.hdfs.DFSClient.getLocatedBlocks(DFSClient.java:1230)
    at org.apache.hadoop.hdfs.DFSClient.getLocatedBlocks(DFSClient.java:1218)
    at org.apache.hadoop.hdfs.DFSInputStream.fetchLocatedBlocksAndGetLastBlockLength(DFSInputStream.java:312)
    at org.apache.hadoop.hdfs.DFSInputStream.openInfo(DFSInputStream.java:278)
    at org.apache.hadoop.hdfs.DFSInputStream.<init>(DFSInputStream.java:270)
    at org.apache.hadoop.hdfs.DFSClient.open(DFSClient.java:1543)
    at org.apache.hadoop.hdfs.DistributedFileSystem$3.doCall(DistributedFileSystem.java:303)
    at org.apache.hadoop.hdfs.DistributedFileSystem$3.doCall(DistributedFileSystem.java:299)
    at org.apache.hadoop.fs.FileSystemLinkResolver.resolve(FileSystemLinkResolver.java:81)
    at org.apache.hadoop.hdfs.DistributedFileSystem.open(DistributedFileSystem.java:299)
    at org.apache.hadoop.fs.FileSystem.open(FileSystem.java:771)
    at org.seqdoop.hadoop_bam.util.SAMHeaderReader.readSAMHeaderFrom(SAMHeaderReader.java:46)
    at org.bdgenomics.adam.rdd.ADAMContext.adamBamDictionaryLoad(ADAMContext.scala:122)
    at org.bdgenomics.adam.rdd.ADAMContext.adamDictionaryLoad(ADAMContext.scala:223)
    at org.bdgenomics.mango.models.LazyMaterialization.setDictionary(LazyMaterialization.scala:67)
    at org.bdgenomics.mango.models.LazyMaterialization.loadSample(LazyMaterialization.scala:85)
    at org.bdgenomics.mango.cli.VizReads.run(VizReads.scala:455)
    at org.bdgenomics.utils.cli.BDGSparkCommand$class.run(BDGCommand.scala:54)
    at org.bdgenomics.mango.cli.VizReads.run(VizReads.scala:427)
    at org.bdgenomics.utils.cli.BDGCommandCompanion$class.main(BDGCommand.scala:32)
    at org.bdgenomics.mango.cli.VizReads$.main(VizReads.scala:70)
    at org.bdgenomics.mango.cli.VizReads.main(VizReads.scala)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:731)
    at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:181)
    at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:206)
    at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:121)
    at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
Caused by: org.apache.hadoop.ipc.RemoteException(java.io.FileNotFoundException): File does not exist: /user/root/dedupped_20.bam
    at org.apache.hadoop.hdfs.server.namenode.INodeFile.valueOf(INodeFile.java:71)
    at org.apache.hadoop.hdfs.server.namenode.INodeFile.valueOf(INodeFile.java:61)
    at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.getBlockLocationsInt(FSNamesystem.java:1828)
    at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.getBlockLocations(FSNamesystem.java:1799)
    at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.getBlockLocations(FSNamesystem.java:1712)
    at org.apache.hadoop.hdfs.server.namenode.NameNodeRpcServer.getBlockLocations(NameNodeRpcServer.java:587)
    at org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolServerSideTranslatorPB.getBlockLocations(ClientNamenodeProtocolServerSideTranslatorPB.java:365)
    at org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol$2.callBlockingMethod(ClientNamenodeProtocolProtos.java)
    at org.apache.hadoop.ipc.ProtobufRpcEngine$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine.java:632)
    at org.apache.hadoop.ipc.RPC$Server.call(RPC.java:969)
    at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:2049)
    at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:2045)
    at java.security.AccessController.doPrivileged(Native Method)
    at javax.security.auth.Subject.doAs(Subject.java:415)
    at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1657)
    at org.apache.hadoop.ipc.Server$Handler.run(Server.java:2043)

    at org.apache.hadoop.ipc.Client.call(Client.java:1476)
    at org.apache.hadoop.ipc.Client.call(Client.java:1407)
    at org.apache.hadoop.ipc.ProtobufRpcEngine$Invoker.invoke(ProtobufRpcEngine.java:238)
    at com.sun.proxy.$Proxy16.getBlockLocations(Unknown Source)
    at org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolTranslatorPB.getBlockLocations(ClientNamenodeProtocolTranslatorPB.java:255)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at org.apache.hadoop.io.retry.RetryInvocationHandler.invokeMethod(RetryInvocationHandler.java:187)
    at org.apache.hadoop.io.retry.RetryInvocationHandler.invoke(RetryInvocationHandler.java:102)
    at com.sun.proxy.$Proxy17.getBlockLocations(Unknown Source)
    at org.apache.hadoop.hdfs.DFSClient.callGetBlockLocations(DFSClient.java:1243)
    ... 31 more

/home/hadoop/mango/ != /user/root/

Explain please, how to decide this problem

LeonisX avatar Mar 17 '16 09:03 LeonisX

Hi Leonis,

I believe this is an issue with loading bams from hdfs, which is why there's a warning provided 16/03/17 09:11:04 INFO VizReads: WARNING: No reads file provided WARNING: No reads file provided . This will be resolved with a downstream change in ADAM. For now, please try converting the bam to an adam file, it should run with that.

My apologies for the inconvenience. Thanks for pointing it out!

erictu avatar Mar 17 '16 17:03 erictu

Hi Eric, thanks for rapid response.

Today I converted files to ADAM format, uploaded to hdfs and tried again:

bin/mango-submit /home/hadoop/adam_adam/human_b37_20.fasta.adam -read_files /home/hadoop/adam_adam/dedupped_20.bam.adam

or

bin/mango-submit /home/hadoop/raw/human_b37_20.fasta -read_files /home/hadoop/raw/dedupped_20.bam

errors when access to http://<my_url>:8080/overall:

16/03/18 12:39:21 WARN ServletHandler: /reference/chr
java.util.NoSuchElementException: None.get
    at scala.None$.get(Option.scala:313)
    at scala.None$.get(Option.scala:311)
    at org.bdgenomics.mango.cli.VizServlet$$anonfun$14.apply(VizReads.scala:417)
    at org.bdgenomics.mango.cli.VizServlet$$anonfun$14.apply(VizReads.scala:415)
    at org.scalatra.ScalatraKernel$class.org$scalatra$ScalatraKernel$$liftAction(ScalatraKernel.scala:216)
    at org.scalatra.ScalatraKernel$$anonfun$invoke$1.apply(ScalatraKernel.scala:211)
    at org.scalatra.ScalatraKernel$$anonfun$invoke$1.apply(ScalatraKernel.scala:211)
    at org.scalatra.ScalatraKernel$class.withRouteMultiParams(ScalatraKernel.scala:274)
    at org.scalatra.ScalatraServlet.withRouteMultiParams(ScalatraServlet.scala:24)
    at org.scalatra.ScalatraKernel$class.invoke(ScalatraKernel.scala:210)
    at org.scalatra.ScalatraServlet.invoke(ScalatraServlet.scala:24)
    at org.scalatra.ScalatraKernel$$anonfun$runRoutes$1$$anonfun$apply$2.apply(ScalatraKernel.scala:196)
    at org.scalatra.ScalatraKernel$$anonfun$runRoutes$1$$anonfun$apply$2.apply(ScalatraKernel.scala:195)
    at scala.Option.flatMap(Option.scala:170)
    at org.scalatra.ScalatraKernel$$anonfun$runRoutes$1.apply(ScalatraKernel.scala:195)
    at org.scalatra.ScalatraKernel$$anonfun$runRoutes$1.apply(ScalatraKernel.scala:194)
    at scala.collection.immutable.Stream.flatMap(Stream.scala:442)
    at org.scalatra.ScalatraKernel$class.runRoutes(ScalatraKernel.scala:194)
    at org.scalatra.ScalatraServlet.runRoutes(ScalatraServlet.scala:24)
    at org.scalatra.ScalatraKernel$class.executeRoutes(ScalatraKernel.scala:165)
    at org.scalatra.ScalatraServlet.executeRoutes(ScalatraServlet.scala:24)
    at org.scalatra.ScalatraKernel$$anonfun$handle$1$$anonfun$apply$mcV$sp$1.apply$mcV$sp(ScalatraKernel.scala:139)
    at org.scalatra.ScalatraKernel$$anonfun$handle$1$$anonfun$apply$mcV$sp$1.apply(ScalatraKernel.scala:137)
    at org.scalatra.ScalatraKernel$$anonfun$handle$1$$anonfun$apply$mcV$sp$1.apply(ScalatraKernel.scala:137)
    at scala.util.DynamicVariable.withValue(DynamicVariable.scala:57)
    at org.scalatra.ScalatraKernel$$anonfun$handle$1.apply$mcV$sp(ScalatraKernel.scala:137)
    at org.scalatra.ScalatraKernel$$anonfun$handle$1.apply(ScalatraKernel.scala:137)
    at org.scalatra.ScalatraKernel$$anonfun$handle$1.apply(ScalatraKernel.scala:137)
    at scala.util.DynamicVariable.withValue(DynamicVariable.scala:57)
    at org.scalatra.ScalatraKernel$class.handle(ScalatraKernel.scala:136)
    at org.scalatra.ScalatraServlet.handle(ScalatraServlet.scala:24)
    at org.scalatra.ScalatraServlet.service(ScalatraServlet.scala:31)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:848)
    at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:684)
    at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:503)
    at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:137)
    at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:557)
    at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:231)
    at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1086)
    at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:429)
    at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:193)
    at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1020)
    at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:135)
    at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:255)
    at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116)
    at org.eclipse.jetty.server.Server.handle(Server.java:370)
    at org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(AbstractHttpConnection.java:494)
    at org.eclipse.jetty.server.AbstractHttpConnection.headerComplete(AbstractHttpConnection.java:971)
    at org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.headerComplete(AbstractHttpConnection.java:1033)
    at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:644)
    at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:235)
    at org.eclipse.jetty.server.AsyncHttpConnection.handle(AsyncHttpConnection.java:82)
    at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(SelectChannelEndPoint.java:696)
    at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectChannelEndPoint.java:53)
    at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:608)
    at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:543)
    at java.lang.Thread.run(Thread.java:745)
16/03/18 12:39:21 WARN ServletHandler: /reads/chr
java.util.NoSuchElementException: None.get
    at scala.None$.get(Option.scala:313)
    at scala.None$.get(Option.scala:311)
    at org.bdgenomics.mango.cli.VizServlet$$anonfun$4$$anonfun$apply$2.apply(VizReads.scala:242)
    at scala.Option.fold(Option.scala:157)
    at org.apache.spark.rdd.Timer.time(Timer.scala:48)
    at org.bdgenomics.mango.cli.VizServlet$$anonfun$4.apply(VizReads.scala:240)
    at org.scalatra.ScalatraKernel$class.org$scalatra$ScalatraKernel$$liftAction(ScalatraKernel.scala:216)
    at org.scalatra.ScalatraKernel$$anonfun$invoke$1.apply(ScalatraKernel.scala:211)
    at org.scalatra.ScalatraKernel$$anonfun$invoke$1.apply(ScalatraKernel.scala:211)
    at org.scalatra.ScalatraKernel$class.withRouteMultiParams(ScalatraKernel.scala:274)
    at org.scalatra.ScalatraServlet.withRouteMultiParams(ScalatraServlet.scala:24)
    at org.scalatra.ScalatraKernel$class.invoke(ScalatraKernel.scala:210)
    at org.scalatra.ScalatraServlet.invoke(ScalatraServlet.scala:24)
    at org.scalatra.ScalatraKernel$$anonfun$runRoutes$1$$anonfun$apply$2.apply(ScalatraKernel.scala:196)
    at org.scalatra.ScalatraKernel$$anonfun$runRoutes$1$$anonfun$apply$2.apply(ScalatraKernel.scala:195)
    at scala.Option.flatMap(Option.scala:170)
    at org.scalatra.ScalatraKernel$$anonfun$runRoutes$1.apply(ScalatraKernel.scala:195)
    at org.scalatra.ScalatraKernel$$anonfun$runRoutes$1.apply(ScalatraKernel.scala:194)
    at scala.collection.immutable.Stream.flatMap(Stream.scala:446)
    at org.scalatra.ScalatraKernel$class.runRoutes(ScalatraKernel.scala:194)
    at org.scalatra.ScalatraServlet.runRoutes(ScalatraServlet.scala:24)
    at org.scalatra.ScalatraKernel$class.executeRoutes(ScalatraKernel.scala:165)
    at org.scalatra.ScalatraServlet.executeRoutes(ScalatraServlet.scala:24)
    at org.scalatra.ScalatraKernel$$anonfun$handle$1$$anonfun$apply$mcV$sp$1.apply$mcV$sp(ScalatraKernel.scala:139)
    at org.scalatra.ScalatraKernel$$anonfun$handle$1$$anonfun$apply$mcV$sp$1.apply(ScalatraKernel.scala:137)
    at org.scalatra.ScalatraKernel$$anonfun$handle$1$$anonfun$apply$mcV$sp$1.apply(ScalatraKernel.scala:137)
    at scala.util.DynamicVariable.withValue(DynamicVariable.scala:57)
    at org.scalatra.ScalatraKernel$$anonfun$handle$1.apply$mcV$sp(ScalatraKernel.scala:137)
    at org.scalatra.ScalatraKernel$$anonfun$handle$1.apply(ScalatraKernel.scala:137)
    at org.scalatra.ScalatraKernel$$anonfun$handle$1.apply(ScalatraKernel.scala:137)
    at scala.util.DynamicVariable.withValue(DynamicVariable.scala:57)
    at org.scalatra.ScalatraKernel$class.handle(ScalatraKernel.scala:136)
    at org.scalatra.ScalatraServlet.handle(ScalatraServlet.scala:24)
    at org.scalatra.ScalatraServlet.service(ScalatraServlet.scala:31)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:848)
    at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:684)
    at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:503)
    at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:137)
    at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:557)
    at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:231)
    at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1086)
    at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:429)
    at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:193)
    at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1020)
    at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:135)
    at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:255)
    at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116)
    at org.eclipse.jetty.server.Server.handle(Server.java:370)
    at org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(AbstractHttpConnection.java:494)
    at org.eclipse.jetty.server.AbstractHttpConnection.headerComplete(AbstractHttpConnection.java:971)
    at org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.headerComplete(AbstractHttpConnection.java:1033)
    at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:644)
    at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:235)
    at org.eclipse.jetty.server.AsyncHttpConnection.handle(AsyncHttpConnection.java:82)
    at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(SelectChannelEndPoint.java:696)
    at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectChannelEndPoint.java:53)
    at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:608)
    at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:543)
    at java.lang.Thread.run(Thread.java:745)
16/03/18 12:39:21 WARN ServletHandler: /viewregion/chr
java.util.NoSuchElementException: None.get
    at scala.None$.get(Option.scala:313)
    at scala.None$.get(Option.scala:311)
    at org.bdgenomics.mango.cli.VizServlet$$anonfun$9.apply(VizReads.scala:333)
    at org.bdgenomics.mango.cli.VizServlet$$anonfun$9.apply(VizReads.scala:329)
    at org.scalatra.ScalatraKernel$class.org$scalatra$ScalatraKernel$$liftAction(ScalatraKernel.scala:216)
    at org.scalatra.ScalatraKernel$$anonfun$invoke$1.apply(ScalatraKernel.scala:211)
    at org.scalatra.ScalatraKernel$$anonfun$invoke$1.apply(ScalatraKernel.scala:211)
    at org.scalatra.ScalatraKernel$class.withRouteMultiParams(ScalatraKernel.scala:274)
    at org.scalatra.ScalatraServlet.withRouteMultiParams(ScalatraServlet.scala:24)
    at org.scalatra.ScalatraKernel$class.invoke(ScalatraKernel.scala:210)
    at org.scalatra.ScalatraServlet.invoke(ScalatraServlet.scala:24)
    at org.scalatra.ScalatraKernel$$anonfun$runRoutes$1$$anonfun$apply$2.apply(ScalatraKernel.scala:196)
    at org.scalatra.ScalatraKernel$$anonfun$runRoutes$1$$anonfun$apply$2.apply(ScalatraKernel.scala:195)
    at scala.Option.flatMap(Option.scala:170)
    at org.scalatra.ScalatraKernel$$anonfun$runRoutes$1.apply(ScalatraKernel.scala:195)
    at org.scalatra.ScalatraKernel$$anonfun$runRoutes$1.apply(ScalatraKernel.scala:194)
    at scala.collection.immutable.Stream.flatMap(Stream.scala:446)
    at org.scalatra.ScalatraKernel$class.runRoutes(ScalatraKernel.scala:194)
    at org.scalatra.ScalatraServlet.runRoutes(ScalatraServlet.scala:24)
    at org.scalatra.ScalatraKernel$class.executeRoutes(ScalatraKernel.scala:165)
    at org.scalatra.ScalatraServlet.executeRoutes(ScalatraServlet.scala:24)
    at org.scalatra.ScalatraKernel$$anonfun$handle$1$$anonfun$apply$mcV$sp$1.apply$mcV$sp(ScalatraKernel.scala:139)
    at org.scalatra.ScalatraKernel$$anonfun$handle$1$$anonfun$apply$mcV$sp$1.apply(ScalatraKernel.scala:137)
    at org.scalatra.ScalatraKernel$$anonfun$handle$1$$anonfun$apply$mcV$sp$1.apply(ScalatraKernel.scala:137)
    at scala.util.DynamicVariable.withValue(DynamicVariable.scala:57)
    at org.scalatra.ScalatraKernel$$anonfun$handle$1.apply$mcV$sp(ScalatraKernel.scala:137)
    at org.scalatra.ScalatraKernel$$anonfun$handle$1.apply(ScalatraKernel.scala:137)
    at org.scalatra.ScalatraKernel$$anonfun$handle$1.apply(ScalatraKernel.scala:137)
    at scala.util.DynamicVariable.withValue(DynamicVariable.scala:57)
    at org.scalatra.ScalatraKernel$class.handle(ScalatraKernel.scala:136)
    at org.scalatra.ScalatraServlet.handle(ScalatraServlet.scala:24)
    at org.scalatra.ScalatraServlet.service(ScalatraServlet.scala:31)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:848)
    at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:684)
    at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:503)
    at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:137)
    at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:557)
    at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:231)
    at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1086)
    at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:429)
    at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:193)
    at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1020)
    at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:135)
    at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:255)
    at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116)
    at org.eclipse.jetty.server.Server.handle(Server.java:370)
    at org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(AbstractHttpConnection.java:494)
    at org.eclipse.jetty.server.AbstractHttpConnection.headerComplete(AbstractHttpConnection.java:971)
    at org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.headerComplete(AbstractHttpConnection.java:1033)
    at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:644)
    at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:235)
    at org.eclipse.jetty.server.AsyncHttpConnection.handle(AsyncHttpConnection.java:82)
    at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(SelectChannelEndPoint.java:696)
    at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectChannelEndPoint.java:53)
    at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:608)
    at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:543)
    at java.lang.Thread.run(Thread.java:745)

I used genomic data from ftp://[email protected] (tutorial_files.zip)

converted with command: bin/adam-submit --executor-memory 10g -- transform s3n://<data_folder>/chr20_dataset/raw/dedupped_20.bam dedupped_20.bam.adam

What am I doing wrong?

LeonisX avatar Mar 18 '16 13:03 LeonisX

This bug should be patched within the next day or so.

Best,

Alyssa Morrow [email protected] mailto:[email protected] 414-254-6645

On Mar 18, 2016, at 6:12 AM, Leonis [email protected] wrote:

Hi Eric, thanks for rapid response.

Today I converted files to ADAM format, uploaded to hdfs and tried again:

bin/mango-submit /home/hadoop/adam_adam/human_b37_20.fasta.adam -read_files /home/hadoop/adam_adam/dedupped_20.bam.adam

or

bin/mango-submit /home/hadoop/raw/human_b37_20.fasta -read_files /home/hadoop/raw/dedupped_20.bam

errors when access to http://:8080/overall:

16/03/18 12:39:21 WARN ServletHandler: /reference/chr java.util.NoSuchElementException: None.get at scala.None$.get(Option.scala:313) at scala.None$.get(Option.scala:311) at org.bdgenomics.mango.cli.VizServlet$$anonfun$14.apply(VizReads.scala:417) at org.bdgenomics.mango.cli.VizServlet$$anonfun$14.apply(VizReads.scala:415) at org.scalatra.ScalatraKernel$class.org$scalatra$ScalatraKernel$$liftAction(ScalatraKernel.scala:216) at org.scalatra.ScalatraKernel$$anonfun$invoke$1.apply(ScalatraKernel.scala:211) at org.scalatra.ScalatraKernel$$anonfun$invoke$1.apply(ScalatraKernel.scala:211) at org.scalatra.ScalatraKernel$class.withRouteMultiParams(ScalatraKernel.scala:274) at org.scalatra.ScalatraServlet.withRouteMultiParams(ScalatraServlet.scala:24) at org.scalatra.ScalatraKernel$class.invoke(ScalatraKernel.scala:210) at org.scalatra.ScalatraServlet.invoke(ScalatraServlet.scala:24) at org.scalatra.ScalatraKernel$$anonfun$runRoutes$1$$anonfun$apply$2.apply(ScalatraKernel.scala:196) at org.scalatra.ScalatraKernel$$anonfun$runRoutes$1$$anonfun$apply$2.apply(ScalatraKernel.scala:195) at scala.Option.flatMap(Option.scala:170) at org.scalatra.ScalatraKernel$$anonfun$runRoutes$1.apply(ScalatraKernel.scala:195) at org.scalatra.ScalatraKernel$$anonfun$runRoutes$1.apply(ScalatraKernel.scala:194) at scala.collection.immutable.Stream.flatMap(Stream.scala:442) at org.scalatra.ScalatraKernel$class.runRoutes(ScalatraKernel.scala:194) at org.scalatra.ScalatraServlet.runRoutes(ScalatraServlet.scala:24) at org.scalatra.ScalatraKernel$class.executeRoutes(ScalatraKernel.scala:165) at org.scalatra.ScalatraServlet.executeRoutes(ScalatraServlet.scala:24) at org.scalatra.ScalatraKernel$$anonfun$handle$1$$anonfun$apply$mcV$sp$1.apply$mcV$sp(ScalatraKernel.scala:139) at org.scalatra.ScalatraKernel$$anonfun$handle$1$$anonfun$apply$mcV$sp$1.apply(ScalatraKernel.scala:137) at org.scalatra.ScalatraKernel$$anonfun$handle$1$$anonfun$apply$mcV$sp$1.apply(ScalatraKernel.scala:137) at scala.util.DynamicVariable.withValue(DynamicVariable.scala:57) at org.scalatra.ScalatraKernel$$anonfun$handle$1.apply$mcV$sp(ScalatraKernel.scala:137) at org.scalatra.ScalatraKernel$$anonfun$handle$1.apply(ScalatraKernel.scala:137) at org.scalatra.ScalatraKernel$$anonfun$handle$1.apply(ScalatraKernel.scala:137) at scala.util.DynamicVariable.withValue(DynamicVariable.scala:57) at org.scalatra.ScalatraKernel$class.handle(ScalatraKernel.scala:136) at org.scalatra.ScalatraServlet.handle(ScalatraServlet.scala:24) at org.scalatra.ScalatraServlet.service(ScalatraServlet.scala:31) at javax.servlet.http.HttpServlet.service(HttpServlet.java:848) at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:684) at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:503) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:137) at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:557) at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:231) at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1086) at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:429) at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:193) at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1020) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:135) at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:255) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116) at org.eclipse.jetty.server.Server.handle(Server.java:370) at org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(AbstractHttpConnection.java:494) at org.eclipse.jetty.server.AbstractHttpConnection.headerComplete(AbstractHttpConnection.java:971) at org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.headerComplete(AbstractHttpConnection.java:1033) at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:644) at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:235) at org.eclipse.jetty.server.AsyncHttpConnection.handle(AsyncHttpConnection.java:82) at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(SelectChannelEndPoint.java:696) at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectChannelEndPoint.java:53) at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:608) at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:543) at java.lang.Thread.run(Thread.java:745) 16/03/18 12:39:21 WARN ServletHandler: /reads/chr java.util.NoSuchElementException: None.get at scala.None$.get(Option.scala:313) at scala.None$.get(Option.scala:311) at org.bdgenomics.mango.cli.VizServlet$$anonfun$4$$anonfun$apply$2.apply(VizReads.scala:242) at scala.Option.fold(Option.scala:157) at org.apache.spark.rdd.Timer.time(Timer.scala:48) at org.bdgenomics.mango.cli.VizServlet$$anonfun$4.apply(VizReads.scala:240) at org.scalatra.ScalatraKernel$class.org$scalatra$ScalatraKernel$$liftAction(ScalatraKernel.scala:216) at org.scalatra.ScalatraKernel$$anonfun$invoke$1.apply(ScalatraKernel.scala:211) at org.scalatra.ScalatraKernel$$anonfun$invoke$1.apply(ScalatraKernel.scala:211) at org.scalatra.ScalatraKernel$class.withRouteMultiParams(ScalatraKernel.scala:274) at org.scalatra.ScalatraServlet.withRouteMultiParams(ScalatraServlet.scala:24) at org.scalatra.ScalatraKernel$class.invoke(ScalatraKernel.scala:210) at org.scalatra.ScalatraServlet.invoke(ScalatraServlet.scala:24) at org.scalatra.ScalatraKernel$$anonfun$runRoutes$1$$anonfun$apply$2.apply(ScalatraKernel.scala:196) at org.scalatra.ScalatraKernel$$anonfun$runRoutes$1$$anonfun$apply$2.apply(ScalatraKernel.scala:195) at scala.Option.flatMap(Option.scala:170) at org.scalatra.ScalatraKernel$$anonfun$runRoutes$1.apply(ScalatraKernel.scala:195) at org.scalatra.ScalatraKernel$$anonfun$runRoutes$1.apply(ScalatraKernel.scala:194) at scala.collection.immutable.Stream.flatMap(Stream.scala:446) at org.scalatra.ScalatraKernel$class.runRoutes(ScalatraKernel.scala:194) at org.scalatra.ScalatraServlet.runRoutes(ScalatraServlet.scala:24) at org.scalatra.ScalatraKernel$class.executeRoutes(ScalatraKernel.scala:165) at org.scalatra.ScalatraServlet.executeRoutes(ScalatraServlet.scala:24) at org.scalatra.ScalatraKernel$$anonfun$handle$1$$anonfun$apply$mcV$sp$1.apply$mcV$sp(ScalatraKernel.scala:139) at org.scalatra.ScalatraKernel$$anonfun$handle$1$$anonfun$apply$mcV$sp$1.apply(ScalatraKernel.scala:137) at org.scalatra.ScalatraKernel$$anonfun$handle$1$$anonfun$apply$mcV$sp$1.apply(ScalatraKernel.scala:137) at scala.util.DynamicVariable.withValue(DynamicVariable.scala:57) at org.scalatra.ScalatraKernel$$anonfun$handle$1.apply$mcV$sp(ScalatraKernel.scala:137) at org.scalatra.ScalatraKernel$$anonfun$handle$1.apply(ScalatraKernel.scala:137) at org.scalatra.ScalatraKernel$$anonfun$handle$1.apply(ScalatraKernel.scala:137) at scala.util.DynamicVariable.withValue(DynamicVariable.scala:57) at org.scalatra.ScalatraKernel$class.handle(ScalatraKernel.scala:136) at org.scalatra.ScalatraServlet.handle(ScalatraServlet.scala:24) at org.scalatra.ScalatraServlet.service(ScalatraServlet.scala:31) at javax.servlet.http.HttpServlet.service(HttpServlet.java:848) at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:684) at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:503) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:137) at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:557) at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:231) at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1086) at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:429) at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:193) at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1020) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:135) at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:255) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116) at org.eclipse.jetty.server.Server.handle(Server.java:370) at org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(AbstractHttpConnection.java:494) at org.eclipse.jetty.server.AbstractHttpConnection.headerComplete(AbstractHttpConnection.java:971) at org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.headerComplete(AbstractHttpConnection.java:1033) at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:644) at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:235) at org.eclipse.jetty.server.AsyncHttpConnection.handle(AsyncHttpConnection.java:82) at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(SelectChannelEndPoint.java:696) at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectChannelEndPoint.java:53) at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:608) at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:543) at java.lang.Thread.run(Thread.java:745) 16/03/18 12:39:21 WARN ServletHandler: /viewregion/chr java.util.NoSuchElementException: None.get at scala.None$.get(Option.scala:313) at scala.None$.get(Option.scala:311) at org.bdgenomics.mango.cli.VizServlet$$anonfun$9.apply(VizReads.scala:333) at org.bdgenomics.mango.cli.VizServlet$$anonfun$9.apply(VizReads.scala:329) at org.scalatra.ScalatraKernel$class.org$scalatra$ScalatraKernel$$liftAction(ScalatraKernel.scala:216) at org.scalatra.ScalatraKernel$$anonfun$invoke$1.apply(ScalatraKernel.scala:211) at org.scalatra.ScalatraKernel$$anonfun$invoke$1.apply(ScalatraKernel.scala:211) at org.scalatra.ScalatraKernel$class.withRouteMultiParams(ScalatraKernel.scala:274) at org.scalatra.ScalatraServlet.withRouteMultiParams(ScalatraServlet.scala:24) at org.scalatra.ScalatraKernel$class.invoke(ScalatraKernel.scala:210) at org.scalatra.ScalatraServlet.invoke(ScalatraServlet.scala:24) at org.scalatra.ScalatraKernel$$anonfun$runRoutes$1$$anonfun$apply$2.apply(ScalatraKernel.scala:196) at org.scalatra.ScalatraKernel$$anonfun$runRoutes$1$$anonfun$apply$2.apply(ScalatraKernel.scala:195) at scala.Option.flatMap(Option.scala:170) at org.scalatra.ScalatraKernel$$anonfun$runRoutes$1.apply(ScalatraKernel.scala:195) at org.scalatra.ScalatraKernel$$anonfun$runRoutes$1.apply(ScalatraKernel.scala:194) at scala.collection.immutable.Stream.flatMap(Stream.scala:446) at org.scalatra.ScalatraKernel$class.runRoutes(ScalatraKernel.scala:194) at org.scalatra.ScalatraServlet.runRoutes(ScalatraServlet.scala:24) at org.scalatra.ScalatraKernel$class.executeRoutes(ScalatraKernel.scala:165) at org.scalatra.ScalatraServlet.executeRoutes(ScalatraServlet.scala:24) at org.scalatra.ScalatraKernel$$anonfun$handle$1$$anonfun$apply$mcV$sp$1.apply$mcV$sp(ScalatraKernel.scala:139) at org.scalatra.ScalatraKernel$$anonfun$handle$1$$anonfun$apply$mcV$sp$1.apply(ScalatraKernel.scala:137) at org.scalatra.ScalatraKernel$$anonfun$handle$1$$anonfun$apply$mcV$sp$1.apply(ScalatraKernel.scala:137) at scala.util.DynamicVariable.withValue(DynamicVariable.scala:57) at org.scalatra.ScalatraKernel$$anonfun$handle$1.apply$mcV$sp(ScalatraKernel.scala:137) at org.scalatra.ScalatraKernel$$anonfun$handle$1.apply(ScalatraKernel.scala:137) at org.scalatra.ScalatraKernel$$anonfun$handle$1.apply(ScalatraKernel.scala:137) at scala.util.DynamicVariable.withValue(DynamicVariable.scala:57) at org.scalatra.ScalatraKernel$class.handle(ScalatraKernel.scala:136) at org.scalatra.ScalatraServlet.handle(ScalatraServlet.scala:24) at org.scalatra.ScalatraServlet.service(ScalatraServlet.scala:31) at javax.servlet.http.HttpServlet.service(HttpServlet.java:848) at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:684) at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:503) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:137) at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:557) at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:231) at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1086) at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:429) at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:193) at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1020) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:135) at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:255) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116) at org.eclipse.jetty.server.Server.handle(Server.java:370) at org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(AbstractHttpConnection.java:494) at org.eclipse.jetty.server.AbstractHttpConnection.headerComplete(AbstractHttpConnection.java:971) at org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.headerComplete(AbstractHttpConnection.java:1033) at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:644) at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:235) at org.eclipse.jetty.server.AsyncHttpConnection.handle(AsyncHttpConnection.java:82) at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(SelectChannelEndPoint.java:696) at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectChannelEndPoint.java:53) at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:608) at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:543) at java.lang.Thread.run(Thread.java:745) I used genomic data from ftp://[email protected] (tutorial_files.zip)

converted with command: bin/adam-submit --executor-memory 10g -- transform s3n:///chr20_dataset/raw/dedupped_20.bam dedupped_20.bam.adam

What am I doing wrong?

— You are receiving this because you commented. Reply to this email directly or view it on GitHub https://github.com/bigdatagenomics/mango/issues/106#issuecomment-198349023

akmorrow13 avatar Mar 21 '16 12:03 akmorrow13