Please help: Failed to load parser

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Manuel Jesús Gil López

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Oct 7, 2016, 10:16:29 AM10/7/16
to beast-users
Hi there! I would like to run BEAST with some chloroplast sequences but I got this message and I have no idea about what is the problem: 


Failed to load parser: dr.inferencexml.trace.GeneralizedHarmonicMeanAnalysisParser
line = dr.inferencexml.trace.GeneralizedHarmonicMeanAnalysisParser



Loading additional development parsers from development_parsers.properties, which is additional set of parsers only available for development version ...

WARNING: parser - dr.inferencexml.model.DifferenceParameterParser in development_parsers.properties is duplicated, which is REPLACING the same parser loaded previously.

WARNING: parser - dr.inferencexml.model.SumParameterParser in development_parsers.properties is duplicated, which is REPLACING the same parser loaded previously.

WARNING: parser - dr.evomodelxml.operators.SubtreeJumpOperatorParser in development_parsers.properties is duplicated, which is REPLACING the same parser loaded previously.


Failed to load parser: dr.evomodel.treelikelihood.RootDiscreteStateStatistic
line = dr.evomodel.treelikelihood.RootDiscreteStateStatistic


Failed to load parser: dr.evomodel.epidemiology.casetocase.operators.InfectionBranchGibbsOperator
line = dr.evomodel.epidemiology.casetocase.operators.InfectionBranchGibbsOperator

WARNING: parser - dr.app.beagle.multidimensionalscaling.MultiDimensionalScalingLikelihood in development_parsers.properties is duplicated, which is REPLACING the same parser loaded previously.

Parsing XML file: result7oct.xml
  File encoding: Cp1252
Looking for plugins in C:\Users\Gil-Lo\Desktop\BEAST oct 2016\BEAST v1.8.3\plugins
Read alignment: alignment
  Sequences = 31
      Sites = 2196
   Datatype = nucleotide
Site patterns 'patterns' created from positions 1-2196 of alignment 'alignment'
  unique pattern count = 134
Tree is assumed to be ultrametric
  Changing height of leaf node Etrimera_1 from 0.015613999999999996 to 0.0
  Changing height of leaf node Etrimera_3 from 0.016693999999999997 to 0.0
  Changing height of leaf node Etrimera_4 from 0.016475999999999998 to 0.0
  Changing height of leaf node Etrimera_2 from 0.015565999999999997 to 0.0
  Changing height of leaf node Hap_4 from 5.289999999999982E-4 to 0.0
  Changing height of leaf node Hap_6 from 1.559999999999999E-4 to 0.0
  Changing height of leaf node Hap_13 from 1.2999999999999817E-4 to 0.0
  Changing height of leaf node Hap_15 from 0.0015969999999999977 to 0.0
  Changing height of leaf node Hap_18 from 0.0013859999999999983 to 0.0
  Changing height of leaf node Hap_17 from 0.0014159999999999971 to 0.0
  Changing height of leaf node Hap_2 from 0.0018359999999999974 to 0.0
  Changing height of leaf node Hap_1 from 0.0014109999999999956 to 0.0
  Changing height of leaf node Hap_9 from 0.0024059999999999984 to 0.0
  Changing height of leaf node Hap_10 from 0.0019699999999999995 to 0.0
  Changing height of leaf node Hap_5 from 4.139999999999977E-4 to 0.0
  Changing height of leaf node Hap_3 from 6.599999999999974E-4 to 0.0
  Changing height of leaf node Hap_7 from 2.0299999999999832E-4 to 0.0
  Changing height of leaf node Hap_19 from 2.3699999999999763E-4 to 0.0
  Changing height of leaf node Hap_12 from 4.2999999999999636E-4 to 0.0
  Changing height of leaf node Hap_14 from 4.359999999999989E-4 to 0.0
  Changing height of leaf node Hap_16 from 8.829999999999984E-4 to 0.0
  Changing height of leaf node Hap_11 from 0.001637999999999997 to 0.0
  Changing height of leaf node aus_Hap_7 from 0.007427 to 0.0
  Changing height of leaf node aus_Hap_1 from 0.007882999999999996 to 0.0
  Changing height of leaf node aus_Hap_4 from 0.007887999999999997 to 0.0
  Changing height of leaf node aus_Hap_6 from 0.006485999999999995 to 0.0
  Changing height of leaf node aus_Hap_5 from 0.007056999999999997 to 0.0
  Changing height of leaf node aus_Hap_2 from 0.007042999999999997 to 0.0
  Changing height of leaf node aus_Hap_3 from 0.006477999999999994 to 0.0
  Changing height of leaf node LU1 from 0.012003999999999996 to 0.0
dr.xml.XMLParseException: Error parsing '<rescaledTree>' element with id, 'startingTree':
Clade defined by taxon Set, untitled1, is not found in the guide tree
at dr.xml.AbstractXMLObjectParser.parseXMLObject(Unknown Source)
at dr.xml.XMLParser.convert(Unknown Source)
at dr.xml.XMLParser.convert(Unknown Source)
at dr.xml.XMLParser.parse(Unknown Source)
at dr.app.beast.BeastMain.<init>(Unknown Source)
at dr.app.beast.BeastMain.main(Unknown Source)
Oct 07, 2016 1:34:20 PM dr.app.beast.BeastMain <init>
SEVERE: Parsing error - poorly formed BEAST file, result7oct.xml:
Error parsing '<rescaledTree>' element with id, 'startingTree':
Clade defined by taxon Set, untitled1, is not found in the guide tree
java.lang.RuntimeException: Terminate
at dr.app.beast.BeastMain.<init>(Unknown Source)
at dr.app.beast.BeastMain.main(Unknown Source)

BEAST has terminated with an error. Please select QUIT from the menu.


Does anyone have any idea about this error? T.T 
Thank you so much. 

Manuel

Andrew Rambaut

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Oct 7, 2016, 11:00:38 AM10/7/16
to beast...@googlegroups.com
Dear Manuel,

The problem is that the starting tree you have used doesn’t actually contain the clade that you have defined (called untitled1). It may be a mistake
defining the clade. Generally it is not a good idea to use a starting tree as it is often difficult to make it compatible with the priors and settings. The
default random tree is automatically set to be compatible with your constraints.

Andrew


On 7 Oct 2016, at 12:44, Manuel Jesús Gil López <manuelj...@uca.es> wrote:

Hi there! I would like to run BEAST with some chloroplast sequences but I got this message and I have no idea about what is the problem: 

Manuel Jesús Gil López

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Oct 10, 2016, 6:16:56 AM10/10/16
to beast-users
Thank you so much Rambaut!

I correct this problem changing the tree as you said. But now I got this (see below). I think is a problem about Java, but I got the last version of it. Does anyone have any idea about that error running BEAST? thank you!




# A fatal error has been detected by the Java Runtime Environment:
#
#  EXCEPTION_ACCESS_VIOLATION (0xc0000005) at pc=0x47efb6c0, pid=3980, tid=0x00001f2c
#
# JRE version: Java(TM) SE Runtime Environment (8.0_101-b13) (build 1.8.0_101-b13)
# Java VM: Java HotSpot(TM) Client VM (25.101-b13 mixed mode windows-x86 )
# Problematic frame:
# C  [hmsbeagle-cpu-sse32-21.DLL+0xb6c0]
#
# Failed to write core dump. Minidumps are not enabled by default on client versions of Windows
#
# If you would like to submit a bug report, please visit:
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#

---------------  T H R E A D  ---------------

Current thread (0x45e37400):  JavaThread "pool-1-thread-1" [_thread_in_native, id=7980, stack(0x4d780000,0x4d7d0000)]

siginfo: ExceptionCode=0xc0000005, reading address 0x00000000

Registers:
EAX=0x00000080, EBX=0x4d7cef70, ECX=0x00000000, EDX=0x4df7cef8
ESP=0x4d7cedb0, EBP=0x4d7cef60, ESI=0x00000000, EDI=0x4df77b30
EIP=0x47efb6c0, EFLAGS=0x00010202

Top of Stack: (sp=0x4d7cedb0)
0x4d7cedb0:   4df7cef8 00630978 ffffffff 00000000
0x4d7cedc0:   00000086 4b835c90 4b83d0d8 00630978
0x4d7cedd0:   00000000 3ff00000 00000000 00000000
0x4d7cede0:   00000000 00000000 00000000 00000000
0x4d7cedf0:   00000000 00000000 00000002 3ff00000
0x4d7cee00:   00000000 3cc00000 00000000 3cc00000
0x4d7cee10:   00000000 00000000 00000000 00000000
0x4d7cee20:   00000000 3ff00000 00000000 00000000 

Instructions: (pc=0x47efb6c0)
0x47efb6a0:   66 0f 59 c5 66 0f 58 c8 66 0f 28 85 80 fe ff ff
0x47efb6b0:   c1 e0 05 66 0f 59 c3 66 0f 59 8c 05 30 ff ff ff
0x47efb6c0:   66 0f 29 0a 66 0f 28 8d a0 fe ff ff 66 0f 59 cc
0x47efb6d0:   66 0f 58 c8 66 0f 28 85 c0 fe ff ff 66 0f 59 c2 


Register to memory mapping:

EAX=0x00000080 is an unknown value
EBX=0x4d7cef70 is pointing into the stack for thread: 0x45e37400
ECX=0x00000000 is an unknown value
EDX=0x4df7cef8 is an unknown value
ESP=0x4d7cedb0 is pointing into the stack for thread: 0x45e37400
EBP=0x4d7cef60 is pointing into the stack for thread: 0x45e37400
ESI=0x00000000 is an unknown value
EDI=0x4df77b30 is an unknown value


Stack: [0x4d780000,0x4d7d0000],  sp=0x4d7cedb0,  free space=315k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
C  [hmsbeagle-cpu-sse32-21.DLL+0xb6c0]
C  [hmsbeagle-cpu-sse32-21.DLL+0x113bc]
C  [hmsbeagle32.dll+0x693e]
C  [hmsbeagle32.dll+0x7679]
j  beagle.BeagleJNIWrapper.updatePartials(I[III)I+0
j  beagle.BeagleJNIImpl.updatePartials([III)V+10
j  dr.app.beagle.evomodel.treelikelihood.BeagleTreeLikelihood.calculateLogLikelihood()D+489
j  dr.app.beagle.evomodel.treelikelihood.AbstractTreeLikelihood.getLogLikelihood()D+9
j  dr.inference.model.CompoundLikelihood$LikelihoodCaller.call()Ljava/lang/Double;+8
j  dr.inference.model.CompoundLikelihood$LikelihoodCaller.call()Ljava/lang/Object;+1
j  java.util.concurrent.FutureTask.run()V+42
j  java.util.concurrent.ThreadPoolExecutor.runWorker(Ljava/util/concurrent/ThreadPoolExecutor$Worker;)V+95
j  java.util.concurrent.ThreadPoolExecutor$Worker.run()V+5
j  java.lang.Thread.run()V+11
v  ~StubRoutines::call_stub
V  [jvm.dll+0x15a2e5]
V  [jvm.dll+0x21ff6e]
V  [jvm.dll+0x15a37e]
V  [jvm.dll+0x15a506]
V  [jvm.dll+0x15a577]
V  [jvm.dll+0xfe92f]
V  [jvm.dll+0x17d7dc]
V  [jvm.dll+0x17d8ca]
V  [jvm.dll+0x1c1ed6]
C  [msvcr100.dll+0x5c556]
C  [msvcr100.dll+0x5c600]
C  [kernel32.dll+0x1336a]
C  [ntdll.dll+0x39882]
C  [ntdll.dll+0x39855]
C  0x00000000

Java frames: (J=compiled Java code, j=interpreted, Vv=VM code)
j  beagle.BeagleJNIWrapper.updatePartials(I[III)I+0
j  beagle.BeagleJNIImpl.updatePartials([III)V+10
j  dr.app.beagle.evomodel.treelikelihood.BeagleTreeLikelihood.calculateLogLikelihood()D+489
j  dr.app.beagle.evomodel.treelikelihood.AbstractTreeLikelihood.getLogLikelihood()D+9
j  dr.inference.model.CompoundLikelihood$LikelihoodCaller.call()Ljava/lang/Double;+8
j  dr.inference.model.CompoundLikelihood$LikelihoodCaller.call()Ljava/lang/Object;+1
j  java.util.concurrent.FutureTask.run()V+42
j  java.util.concurrent.ThreadPoolExecutor.runWorker(Ljava/util/concurrent/ThreadPoolExecutor$Worker;)V+95
j  java.util.concurrent.ThreadPoolExecutor$Worker.run()V+5
j  java.lang.Thread.run()V+11
v  ~StubRoutines::call_stub

---------------  P R O C E S S  ---------------

Java Threads: ( => current thread )
  0x4e119000 JavaThread "pool-1-thread-2" [_thread_blocked, id=7596, stack(0x4d710000,0x4d760000)]
=>0x45e37400 JavaThread "pool-1-thread-1" [_thread_in_native, id=7980, stack(0x4d780000,0x4d7d0000)]
  0x45e39c00 JavaThread "TimerQueue" daemon [_thread_blocked, id=4192, stack(0x485d0000,0x48620000)]
  0x45e00800 JavaThread "Thread-3" [_thread_blocked, id=712, stack(0x48a80000,0x48ad0000)]
  0x45e00000 JavaThread "Thread-2" [_thread_blocked, id=6160, stack(0x48b00000,0x48b50000)]
  0x45dfb800 JavaThread "D3D Screen Updater" daemon [_thread_blocked, id=6748, stack(0x487d0000,0x48820000)]
  0x45d5d400 JavaThread "AWT-EventQueue-0" [_thread_blocked, id=1164, stack(0x46480000,0x464d0000)]
  0x45038800 JavaThread "AWT-Windows" daemon [_thread_in_native, id=5456, stack(0x45800000,0x45850000)]
  0x45038000 JavaThread "AWT-Shutdown" [_thread_blocked, id=5104, stack(0x456d0000,0x45720000)]
  0x45035400 JavaThread "Java2D Disposer" daemon [_thread_blocked, id=5228, stack(0x45520000,0x45570000)]
  0x44efc000 JavaThread "Service Thread" daemon [_thread_blocked, id=7676, stack(0x45260000,0x452b0000)]
  0x44ed1000 JavaThread "C1 CompilerThread0" daemon [_thread_blocked, id=5800, stack(0x451f0000,0x45240000)]
  0x00a0e400 JavaThread "Attach Listener" daemon [_thread_blocked, id=8124, stack(0x45070000,0x450c0000)]
  0x00a0d800 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=6324, stack(0x45100000,0x45150000)]
  0x00a01400 JavaThread "Finalizer" daemon [_thread_blocked, id=6680, stack(0x01250000,0x012a0000)]
  0x009fbc00 JavaThread "Reference Handler" daemon [_thread_blocked, id=7576, stack(0x012a0000,0x012f0000)]
  0x00acc000 JavaThread "main" [_thread_blocked, id=5052, stack(0x00a60000,0x00ab0000)]

Other Threads:
  0x009f4800 VMThread [stack: 0x00a10000,0x00a60000] [id=6908]
  0x44eff400 WatcherThread [stack: 0x45440000,0x45490000] [id=7820]

VM state:not at safepoint (normal execution)

VM Mutex/Monitor currently owned by a thread: None

Heap:
 def new generation   total 78720K, used 9416K [0x04a00000, 0x09f60000, 0x19f50000)
  eden space 70016K,  13% used [0x04a00000, 0x053320c0, 0x08e60000)
  from space 8704K,   0% used [0x08e60000, 0x08e60000, 0x096e0000)
  to   space 8704K,   0% used [0x096e0000, 0x096e0000, 0x09f60000)
 tenured generation   total 174784K, used 10511K [0x19f50000, 0x24a00000, 0x44a00000)
   the space 174784K,   6% used [0x19f50000, 0x1a993d10, 0x1a993e00, 0x24a00000)
 Metaspace       used 13295K, capacity 13473K, committed 13568K, reserved 13696K

Card table byte_map: [0x00e20000,0x01030000] byte_map_base: 0x00dfb000

Polling page: 0x000a0000

CodeCache: size=32768Kb used=1860Kb max_used=1863Kb free=30907Kb
 bounds [0x02810000, 0x029e8000, 0x04810000]
 total_blobs=1167 nmethods=876 adapters=221
 compilation: enabled

Compilation events (10 events):
Event: 22.027 Thread 0x44ed1000  870  s          java.lang.Throwable::fillInStackTrace (29 bytes)
Event: 22.028 Thread 0x44ed1000 nmethod 870 0x029e0a08 code [0x029e0b10, 0x029e0d1c]
Event: 22.029 Thread 0x44ed1000  872             java.io.FilterInputStream::<init> (10 bytes)
Event: 22.030 Thread 0x44ed1000 nmethod 872 0x029e0dc8 code [0x029e0ec0, 0x029e0f60]
Event: 22.031 Thread 0x44ed1000  873             java.util.jar.JarFile::getEntry (22 bytes)
Event: 22.031 Thread 0x44ed1000 nmethod 873 0x029e12c8 code [0x029e13e0, 0x029e1508]
Event: 22.031 Thread 0x44ed1000  874   !         java.util.zip.ZipFile::getEntry (86 bytes)
Event: 22.032 Thread 0x44ed1000 nmethod 874 0x029e15c8 code [0x029e1710, 0x029e1ab8]
Event: 22.059 Thread 0x44ed1000  875             java.util.Objects::requireNonNull (15 bytes)
Event: 22.060 Thread 0x44ed1000 nmethod 875 0x029e1ec8 code [0x029e1fd0, 0x029e20ac]

GC Heap History (2 events):
Event: 18.592 GC heap before
{Heap before GC invocations=0 (full 0):
 def new generation   total 78656K, used 58780K [0x04a00000, 0x09f50000, 0x19f50000)
  eden space 69952K,  84% used [0x04a00000, 0x08367158, 0x08e50000)
  from space 8704K,   0% used [0x08e50000, 0x08e50000, 0x096d0000)
  to   space 8704K,   0% used [0x096d0000, 0x096d0000, 0x09f50000)
 tenured generation   total 174784K, used 0K [0x19f50000, 0x24a00000, 0x44a00000)
   the space 174784K,   0% used [0x19f50000, 0x19f50000, 0x19f50200, 0x24a00000)
 Metaspace       used 12006K, capacity 12193K, committed 12288K, reserved 12672K
Event: 18.685 GC heap after
Heap after GC invocations=1 (full 1):
 def new generation   total 78720K, used 0K [0x04a00000, 0x09f60000, 0x19f50000)
  eden space 70016K,   0% used [0x04a00000, 0x04a00000, 0x08e60000)
  from space 8704K,   0% used [0x08e60000, 0x08e60000, 0x096e0000)
  to   space 8704K,   0% used [0x096e0000, 0x096e0000, 0x09f60000)
 tenured generation   total 174784K, used 10511K [0x19f50000, 0x24a00000, 0x44a00000)
   the space 174784K,   6% used [0x19f50000, 0x1a993d10, 0x1a993e00, 0x24a00000)
 Metaspace       used 12006K, capacity 12193K, committed 12288K, reserved 12672K
}

Deoptimization events (0 events):
No events

Internal exceptions (10 events):
Event: 0.069 Thread 0x00acc000 Exception <a 'java/lang/NoSuchMethodError': Method sun.misc.Unsafe.defineClass(Ljava/lang/String;[BII)Ljava/lang/Class; name or signature does not match> (0x04a06ea8) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u101\7261\hotspot\src\share\\»C DZ?
Event: 0.069 Thread 0x00acc000 Exception <a 'java/lang/NoSuchMethodError': Method sun.misc.Unsafe.prefetchRead(Ljava/lang/Object;J)V name or signature does not match> (0x04a07178) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u101\7261\hotspot\src\share\vm\prims\jni.cpp, ¿ 2$ômÏ?
Event: 0.246 Thread 0x00acc000 Exception <a 'java/security/PrivilegedActionException'> (0x04ae5360) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u101\7261\hotspot\src\share\vm\prims\jvm.cpp, line 1386]
Event: 0.246 Thread 0x00acc000 Exception <a 'java/security/PrivilegedActionException'> (0x04ae5560) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u101\7261\hotspot\src\share\vm\prims\jvm.cpp, line 1386]
Event: 0.248 Thread 0x00acc000 Exception <a 'java/security/PrivilegedActionException'> (0x04ae9398) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u101\7261\hotspot\src\share\vm\prims\jvm.cpp, line 1386]
Event: 0.248 Thread 0x00acc000 Exception <a 'java/security/PrivilegedActionException'> (0x04ae9598) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u101\7261\hotspot\src\share\vm\prims\jvm.cpp, line 1386]
Event: 0.261 Thread 0x00acc000 Exception <a 'java/io/FileNotFoundException'> (0x04aed808) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u101\7261\hotspot\src\share\vm\prims\jni.cpp, line 709]
Event: 0.333 Thread 0x00acc000 Exception <a 'java/lang/NoSuchFieldError': method resolution failed> (0x04d05c38) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u101\7261\hotspot\src\share\vm\prims\methodHandles.cpp, line 1146]
Event: 0.337 Thread 0x00acc000 Exception <a 'java/lang/NoSuchFieldError': method resolution failed> (0x04d11dd8) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u101\7261\hotspot\src\share\vm\prims\methodHandles.cpp, line 1146]
Event: 0.505 Thread 0x00acc000 Exception <a 'java/io/FileNotFoundException'> (0x04e18e28) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u101\7261\hotspot\src\share\vm\prims\jni.cpp, line 709]

Events (10 events):
Event: 22.059 loading class dr/math/ErrorFunction
Event: 22.059 loading class dr/math/ErrorFunction done
Event: 22.059 Executing VM operation: RevokeBias
Event: 22.059 Executing VM operation: RevokeBias done
Event: 22.060 Thread 0x44ed1000 flushing nmethod 0x028b6908
Event: 22.060 loading class dr/app/beagle/evomodel/branchmodel/BranchModel$1
Event: 22.060 loading class dr/app/beagle/evomodel/branchmodel/BranchModel$1 done
Event: 22.060 Thread 0x44ed1000 flushing nmethod 0x02916008
Event: 22.060 Executing VM operation: RevokeBias
Event: 22.060 Executing VM operation: RevokeBias done


Dynamic libraries:
0x013d0000 - 0x01403000 C:\Program Files (x86)\Java\jre1.8.0_101\bin\javaw.exe
0x770b0000 - 0x77230000 C:\Windows\SysWOW64\ntdll.dll
0x76100000 - 0x76210000 C:\Windows\syswow64\kernel32.dll
0x76c20000 - 0x76c67000 C:\Windows\syswow64\KERNELBASE.dll
0x75310000 - 0x753b1000 C:\Windows\syswow64\ADVAPI32.dll
0x74d30000 - 0x74ddc000 C:\Windows\syswow64\msvcrt.dll
0x767d0000 - 0x767e9000 C:\Windows\SysWOW64\sechost.dll
0x74fc0000 - 0x750b0000 C:\Windows\syswow64\RPCRT4.dll
0x74a20000 - 0x74a80000 C:\Windows\syswow64\SspiCli.dll
0x74a10000 - 0x74a1c000 C:\Windows\syswow64\CRYPTBASE.dll
0x76a30000 - 0x76b30000 C:\Windows\syswow64\USER32.dll
0x766c0000 - 0x76750000 C:\Windows\syswow64\GDI32.dll
0x74b50000 - 0x74b5a000 C:\Windows\syswow64\LPK.dll
0x75200000 - 0x7529d000 C:\Windows\syswow64\USP10.dll
0x6b870000 - 0x6ba0e000 C:\Windows\WinSxS\x86_microsoft.windows.common-controls_6595b64144ccf1df_6.0.7601.18837_none_41e855142bd5705d\COMCTL32.dll
0x74cc0000 - 0x74d17000 C:\Windows\syswow64\SHLWAPI.dll
0x76b30000 - 0x76b90000 C:\Windows\system32\IMM32.DLL
0x74a80000 - 0x74b4c000 C:\Windows\syswow64\MSCTF.dll
0x55c20000 - 0x55cdf000 C:\Program Files (x86)\Java\jre1.8.0_101\bin\msvcr100.dll
0x6ca60000 - 0x6ce2c000 C:\Program Files (x86)\Java\jre1.8.0_101\bin\client\jvm.dll
0x74150000 - 0x74157000 C:\Windows\system32\WSOCK32.dll
0x76c70000 - 0x76ca5000 C:\Windows\syswow64\WS2_32.dll
0x74cb0000 - 0x74cb6000 C:\Windows\syswow64\NSI.dll
0x70a50000 - 0x70a82000 C:\Windows\system32\WINMM.dll
0x73f30000 - 0x73f39000 C:\Windows\system32\VERSION.dll
0x765d0000 - 0x765d5000 C:\Windows\syswow64\PSAPI.DLL
0x5c7d0000 - 0x5c7dc000 C:\Program Files (x86)\Java\jre1.8.0_101\bin\verify.dll
0x5c7a0000 - 0x5c7c1000 C:\Program Files (x86)\Java\jre1.8.0_101\bin\java.dll
0x5c780000 - 0x5c793000 C:\Program Files (x86)\Java\jre1.8.0_101\bin\zip.dll
0x753d0000 - 0x7601b000 C:\Windows\syswow64\SHELL32.dll
0x76470000 - 0x765cc000 C:\Windows\syswow64\ole32.dll
0x752a0000 - 0x752ab000 C:\Windows\syswow64\profapi.dll
0x52b80000 - 0x52cc5000 C:\Program Files (x86)\Java\jre1.8.0_101\bin\awt.dll
0x76b90000 - 0x76c1f000 C:\Windows\syswow64\OLEAUT32.dll
0x6df10000 - 0x6df90000 C:\Windows\system32\uxtheme.dll
0x45610000 - 0x456ad000 C:\Program Files (x86)\DigitalPersona\Bin\DpoFeedb.dll
0x74b60000 - 0x74b77000 C:\Windows\syswow64\USERENV.dll
0x6b5d0000 - 0x6b5e3000 C:\Windows\system32\dwmapi.dll
0x6b310000 - 0x6b346000 C:\Program Files (x86)\DigitalPersona\Bin\DpoSet.dll
0x66090000 - 0x66253000 C:\Windows\system32\d3d9.dll
0x684b0000 - 0x684b6000 C:\Windows\system32\d3d8thk.dll
0x66000000 - 0x66086000 C:\Windows\system32\aticfx32.dll
0x673d0000 - 0x673da000 C:\Windows\system32\atiu9pag.dll
0x63900000 - 0x63cde000 C:\Windows\system32\atiumdag.dll
0x65ca0000 - 0x65ff3000 C:\Windows\system32\atiumdva.dll
0x59090000 - 0x590c9000 C:\Program Files (x86)\Java\jre1.8.0_101\bin\fontmanager.dll
0x76040000 - 0x760c3000 C:\Windows\syswow64\CLBCatQ.DLL
0x66370000 - 0x664a1000 C:\Windows\system32\WindowsCodecs.dll
0x6f470000 - 0x6f4bc000 C:\Windows\system32\apphelp.dll
0x5c830000 - 0x5c868000 C:\Users\Gil-Lo\AppData\Roaming\Dropbox\bin\DropboxExt.65536.dll
0x5c7f0000 - 0x5c821000 C:\Windows\system32\EhStorShell.dll
0x74e20000 - 0x74fbd000 C:\Windows\syswow64\SETUPAPI.dll
0x760d0000 - 0x760f7000 C:\Windows\syswow64\CFGMGR32.dll
0x76400000 - 0x76412000 C:\Windows\syswow64\DEVOBJ.dll
0x72280000 - 0x72375000 C:\Windows\system32\PROPSYS.dll
0x524e0000 - 0x526ff000 C:\Program Files (x86)\Microsoft Office\Office12\GrooveShellExtensions.dll
0x55da0000 - 0x55e93000 C:\Program Files (x86)\Microsoft Office\Office12\GrooveUtil.DLL
0x76210000 - 0x763f4000 C:\Windows\syswow64\WININET.dll
0x76030000 - 0x76034000 C:\Windows\syswow64\api-ms-win-downlevel-user32-l1-1-0.dll
0x76020000 - 0x76024000 C:\Windows\syswow64\api-ms-win-downlevel-shlwapi-l1-1-0.dll
0x753c0000 - 0x753c4000 C:\Windows\syswow64\api-ms-win-downlevel-version-l1-1-0.dll
0x74d20000 - 0x74d23000 C:\Windows\syswow64\api-ms-win-downlevel-normaliz-l1-1-0.dll
0x766b0000 - 0x766b3000 C:\Windows\syswow64\normaliz.DLL
0x767f0000 - 0x76a22000 C:\Windows\syswow64\iertutil.dll
0x76670000 - 0x76675000 C:\Windows\syswow64\api-ms-win-downlevel-advapi32-l1-1-0.dll
0x74b80000 - 0x74ca1000 C:\Windows\syswow64\CRYPT32.dll
0x74de0000 - 0x74dec000 C:\Windows\syswow64\MSASN1.dll
0x6dd50000 - 0x6ddeb000 C:\Windows\WinSxS\x86_microsoft.vc80.crt_1fc8b3b9a1e18e3b_8.0.50727.6195_none_d09154e044272b9a\MSVCR80.dll
0x658a0000 - 0x658a7000 C:\Program Files (x86)\Microsoft Office\Office12\GrooveNew.DLL
0x5d4e0000 - 0x5d4fb000 C:\Windows\WinSxS\x86_microsoft.vc80.atl_1fc8b3b9a1e18e3b_8.0.50727.6195_none_d1cb102c435421de\ATL80.DLL
0x73b90000 - 0x73ba7000 C:\Windows\system32\CRYPTSP.dll
0x73b50000 - 0x73b8b000 C:\Windows\system32\rsaenh.dll
0x6ec00000 - 0x6ec05000 C:\Windows\system32\MSImg32.dll
0x59410000 - 0x59480000 C:\Windows\system32\ntshrui.dll
0x73540000 - 0x73559000 C:\Windows\system32\srvcli.dll
0x6b5f0000 - 0x6b5fb000 C:\Windows\system32\cscapi.dll
0x5dd00000 - 0x5dd0a000 C:\Windows\system32\slc.dll
0x5c760000 - 0x5c776000 C:\Program Files (x86)\Java\jre1.8.0_101\bin\net.dll
0x71a70000 - 0x71aac000 C:\Windows\system32\mswsock.dll
0x71870000 - 0x71876000 C:\Windows\System32\wship6.dll
0x5c870000 - 0x5c87f000 C:\Program Files (x86)\Java\jre1.8.0_101\bin\nio.dll
0x590d0000 - 0x59102000 C:\Program Files (x86)\Java\jre1.8.0_101\bin\t2k.dll
0x76750000 - 0x767cb000 C:\Windows\syswow64\COMDLG32.dll
0x70f40000 - 0x70f61000 C:\Windows\system32\ntmarta.dll
0x76420000 - 0x76465000 C:\Windows\syswow64\WLDAP32.dll
0x73380000 - 0x7338e000 C:\Windows\system32\RpcRtRemote.dll
0x55d40000 - 0x55d9c000 C:\Windows\System32\StructuredQuery.dll
0x71ac0000 - 0x71ac8000 C:\Windows\System32\Secur32.dll
0x55ed0000 - 0x55f1e000 C:\Windows\SysWOW64\actxprxy.dll
0x55cf0000 - 0x55d39000 C:\Program Files (x86)\Internet Explorer\ieproxy.dll
0x73130000 - 0x73134000 C:\Windows\system32\api-ms-win-downlevel-shlwapi-l2-1-0.dll
0x55c00000 - 0x55c16000 C:\Windows\SysWOW64\thumbcache.dll
0x5d470000 - 0x5d49f000 C:\Windows\system32\SHDOCVW.dll
0x4c020000 - 0x4cc68000 C:\Windows\system32\ieframe.DLL
0x59400000 - 0x59404000 C:\Windows\system32\api-ms-win-downlevel-shell32-l1-1-0.dll
0x55b60000 - 0x55c00000 C:\Windows\system32\SearchFolder.dll
0x5c880000 - 0x5c8ad000 C:\Program Files (x86)\Microsoft Office\Office12\GrooveSystemServices.dll
0x6b620000 - 0x6b754000 C:\Windows\System32\msxml3.dll
0x6e7f0000 - 0x6e807000 C:\Windows\System32\bcrypt.dll
0x6d190000 - 0x6d1cd000 C:\Windows\SysWOW64\bcryptprimitives.dll
0x59080000 - 0x5908c000 C:\Program Files (x86)\Common Files\Microsoft Shared\OFFICE12\MSOXEV.DLL
0x750b0000 - 0x751fa000 C:\Windows\syswow64\urlmon.dll
0x77080000 - 0x77084000 C:\Windows\syswow64\api-ms-win-downlevel-ole32-l1-1-0.dll
0x47d00000 - 0x47d36000 C:\Program Files (x86)\Common Files\libhmsbeagle\hmsbeagle32.dll
0x47d40000 - 0x47d7d000 C:\Program Files (x86)\Common Files\libhmsbeagle\hmsbeagle-cpu32-21.DLL
0x47ef0000 - 0x47f2c000 C:\Program Files (x86)\Common Files\libhmsbeagle\hmsbeagle-cpu-sse32-21.DLL
0x720a0000 - 0x7218b000 C:\Windows\system32\dbghelp.dll

VM Arguments:
jvm_args: -Xms256m -Xmx1024m 
java_command: C:\Users\Gil-Lo\Desktop\BEAST oct 2016\BEAST v1.8.3\BEAST v1.8.3.exe -window -working -options
java_class_path (initial): C:\Users\Gil-Lo\Desktop\BEAST oct 2016\BEAST v1.8.3\BEAST v1.8.3.exe
Launcher Type: SUN_STANDARD

Environment Variables:
CLASSPATH=.;C:\Program Files (x86)\Java\jre6\lib\ext\QTJava.zip
PATH=C:\ProgramData\Oracle\Java\javapath;C:\Program Files (x86)\Common Files\libhmsbeagle\;%CommonProgramFiles%\Microsoft Shared\Windows Live;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program Files (x86)\ATI Technologies\ATI.ACE\Core-Static;C:\Program Files (x86)\QuickTime\QTSystem\;C:\strawberry\c\bin;C:\strawberry\perl\site\bin;C:\strawberry\perl\bin;C:\Program Files (x86)\OpenVPN\bin;C:\Program Files (x86)\Skype\Phone\;;C:\Program Files (x86)\Java\jre1.8.0_101\bin
USERNAME=Gil-Lo
OS=Windows_NT
PROCESSOR_IDENTIFIER=Intel64 Family 6 Model 30 Stepping 5, GenuineIntel



---------------  S Y S T E M  ---------------

OS: Windows 7 , 64 bit Build 7601 (6.1.7601.18933)

CPU:total 8 (4 cores per cpu, 2 threads per core) family 6 model 30 stepping 5, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, ht, tsc, tscinvbit

Memory: 4k page, physical 4126576k(1225116k free), swap 8251312k(4197708k free)

vm_info: Java HotSpot(TM) Client VM (25.101-b13) for windows-x86 JRE (1.8.0_101-b13), built on Jun 22 2016 00:45:44 by "java_re" with MS VC++ 10.0 (VS2010)

time: Mon Oct 10 12:11:34 2016
elapsed time: 22 seconds (0d 0h 0m 22s)

thompso...@gmail.com

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May 8, 2021, 2:56:22 PM5/8/21
to beast-users
Hi,

I've got the same problem, however when I choose random tree BEAST doesn't work, with the error "SEVERE: Parsing error - poorly formed XML (possibly not an XML file): XML document structures must start and end within the same entity."  In the XML file, this is what the end looks like.  It keeps doing this pattern until line 12,419.  How can I correct this?

Best,
Jamiecoalescent simulator.jpg

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