Question: Why is LOSITAN not running the simulations?
0
gravatar for carolw1
4.5 years ago by
carolw10
Australia
carolw10 wrote:

I am using LOSITAN to identify outliers. I can open the genepop file, load the populations and obtain the fst as well as see the loci on the graph. However once I click run simulations with standard number of 50x1000 sims, the program simply freezes, it doesn't crash, I can still click on the Help tab, but nothing else works. I've left it for many hours and still nothing works.

I have pasted the error messages from the java console below and since the lositan website says to ask here, I'm hoping someone can answer this question.

Thanks

Carol

 

Java Web Start 10.60.2.19
Using JRE version 1.7.0_60-b19 Java HotSpot(TM) Client VM
User home directory = C:\Users\Dell
----------------------------------------------------
c:   clear console window
f:   finalize objects on finalization queue
g:   garbage collect
h:   display this help message
m:   print memory usage
o:   trigger logging
p:   reload proxy configuration
q:   hide console
r:   reload policy configuration
s:   dump system and deployment properties
t:   dump thread list
v:   dump thread stack
0-5: set trace level to <n>
----------------------------------------------------
Missing Application-Name manifest attribute for: http://popgen.net/soft/lositan/code2/lib/selwb.jar
Missing Permissions manifest attribute in main jar: http://popgen.net/soft/lositan/code2/lib/selwb.jar
Windows 7 C:\Users\Dell \
console: Failed to install '': java.nio.charset.UnsupportedCharsetException: cp0.
2290
0.015213 16
Oct 05, 2014 9:15:34 PM jnr.ffi.util.ref.FinalizableReferenceQueue$SystemLoader loadFinalizer
INFO: Not allowed to access system class loader.
Oct 05, 2014 9:15:38 PM jnr.ffi.util.ref.FinalizableReferenceQueue$DecoupledLoader loadFinalizer
WARNING: Could not load Finalizer in its own class loader.Loading Finalizer in the current class loader instead. As a result, you will not be ableto garbage collect this class loader. To support reclaiming this class loader, eitherresolve the underlying issue, or move Google Collections to your system class path.
java.security.AccessControlException: access denied ("java.lang.RuntimePermission" "createClassLoader")
    at java.security.AccessControlContext.checkPermission(Unknown Source)
    at java.security.AccessController.checkPermission(Unknown Source)
    at java.lang.SecurityManager.checkPermission(Unknown Source)
    at java.lang.SecurityManager.checkCreateClassLoader(Unknown Source)
    at java.lang.ClassLoader.checkCreateClassLoader(Unknown Source)
    at java.lang.ClassLoader.<init>(Unknown Source)
    at java.security.SecureClassLoader.<init>(Unknown Source)
    at java.net.URLClassLoader.<init>(Unknown Source)
    at jnr.ffi.util.ref.FinalizableReferenceQueue$DecoupledLoader.newLoader(FinalizableReferenceQueue.java:257)
    at jnr.ffi.util.ref.FinalizableReferenceQueue$DecoupledLoader.loadFinalizer(FinalizableReferenceQueue.java:227)
    at jnr.ffi.util.ref.FinalizableReferenceQueue.loadFinalizer(FinalizableReferenceQueue.java:155)
    at jnr.ffi.util.ref.FinalizableReferenceQueue.<clinit>(FinalizableReferenceQueue.java:84)
    at jnr.ffi.provider.jffi.NativeFinalizer.<init>(NativeFinalizer.java:9)
    at jnr.ffi.provider.jffi.NativeFinalizer$SingletonHolder.<clinit>(NativeFinalizer.java:12)
    at jnr.ffi.provider.jffi.NativeFinalizer.getInstance(NativeFinalizer.java:16)
    at jnr.ffi.provider.jffi.TransientNativeMemory$Magazine.<init>(TransientNativeMemory.java:104)
    at jnr.ffi.provider.jffi.TransientNativeMemory.allocate(TransientNativeMemory.java:44)
    at jnr.ffi.provider.jffi.NativeMemoryManager.allocateDirect(NativeMemoryManager.java:43)
    at jnr.ffi.Memory.allocateDirect(Memory.java:88)
    at jnr.posix.WString$1.toNative(WString.java:33)
    at jnr.posix.WString$1.toNative(WString.java:26)
    at jnr.ffi.provider.jffi.ParameterConverter.toNative(ParameterConverter.java:41)
    at jnr.posix.WindowsLibC$jaffl$0._wmkdir(Unknown Source)
    at jnr.posix.WindowsPOSIX.mkdir(WindowsPOSIX.java:458)
    at jnr.posix.LazyPOSIX.mkdir(LazyPOSIX.java:207)
    at org.python.modules.posix.PosixModule.mkdir(PosixModule.java:521)
    at org.python.modules.posix.PosixModule.mkdir(PosixModule.java:517)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
    at java.lang.reflect.Method.invoke(Unknown Source)
    at org.python.core.PyReflectedFunction.__call__(PyReflectedFunction.java:186)
    at org.python.core.PyReflectedFunction.__call__(PyReflectedFunction.java:204)
    at org.python.core.PyObject.__call__(PyObject.java:403)
    at org.python.core.PyObject.__call__(PyObject.java:407)
    at Bio.PopGen.FDist.Async$py.run_fdist$9(C:\Users\Dell\.lositan\Bio\PopGen\FDist\Async.py:185)
    at Bio.PopGen.FDist.Async$py.call_function(C:\Users\Dell\.lositan\Bio\PopGen\FDist\Async.py)
    at org.python.core.PyTableCode.call(PyTableCode.java:165)
    at org.python.core.PyBaseCode.call(PyBaseCode.java:301)
    at org.python.core.PyBaseCode.call(PyBaseCode.java:194)
    at org.python.core.PyFunction.__call__(PyFunction.java:417)
    at org.python.core.PyMethod.instancemethod___call__(PyMethod.java:232)
    at org.python.core.PyMethod.__call__(PyMethod.java:223)
    at org.python.core.PyMethod.__call__(PyMethod.java:213)
    at org.python.pycode._pyx0.runFDistPart$30(C:\Users\Dell\.lositan\Main.py:786)
    at org.python.pycode._pyx0.call_function(C:\Users\Dell\.lositan\Main.py)
    at org.python.core.PyTableCode.call(PyTableCode.java:165)
    at org.python.core.PyBaseCode.call(PyBaseCode.java:301)
    at org.python.core.PyFunction.function___call__(PyFunction.java:406)
    at org.python.core.PyFunction.__call__(PyFunction.java:401)
    at org.python.core.PyFunction.__call__(PyFunction.java:391)
    at org.python.pycode._pyx0.runFDist$28(C:\Users\Dell\.lositan\Main.py:743)
    at org.python.pycode._pyx0.call_function(C:\Users\Dell\.lositan\Main.py)
    at org.python.core.PyTableCode.call(PyTableCode.java:165)
    at org.python.core.PyBaseCode.call(PyBaseCode.java:301)
    at org.python.core.PyBaseCode.call(PyBaseCode.java:114)
    at org.python.core.PyFunction.__call__(PyFunction.java:337)
    at org.python.pycode._pyx0.actionPerformed$36(C:\Users\Dell\.lositan\Main.py:900)
    at org.python.pycode._pyx0.call_function(C:\Users\Dell\.lositan\Main.py)
    at org.python.core.PyTableCode.call(PyTableCode.java:165)
    at org.python.core.PyBaseCode.call(PyBaseCode.java:301)
    at org.python.core.PyBaseCode.call(PyBaseCode.java:194)
    at org.python.core.PyFunction.__call__(PyFunction.java:417)
    at org.python.core.PyMethod.instancemethod___call__(PyMethod.java:232)
    at org.python.core.PyMethod.__call__(PyMethod.java:223)
    at org.python.core.PyMethod.__call__(PyMethod.java:213)
    at org.python.core.PyMethod.__call__(PyMethod.java:208)
    at org.python.core.PyObject._jcallexc(PyObject.java:3555)
    at org.python.core.PyObject._jcall(PyObject.java:3587)
    at org.python.proxies.__main__$doAction$16.actionPerformed(Unknown Source)
    at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
    at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
    at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
    at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
    at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)
    at java.awt.Component.processMouseEvent(Unknown Source)
    at javax.swing.JComponent.processMouseEvent(Unknown Source)
    at java.awt.Component.processEvent(Unknown Source)
    at java.awt.Container.processEvent(Unknown Source)
    at java.awt.Component.dispatchEventImpl(Unknown Source)
    at java.awt.Container.dispatchEventImpl(Unknown Source)
    at java.awt.Component.dispatchEvent(Unknown Source)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
    at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
    at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
    at java.awt.Container.dispatchEventImpl(Unknown Source)
    at java.awt.Window.dispatchEventImpl(Unknown Source)
    at java.awt.Component.dispatchEvent(Unknown Source)
    at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
    at java.awt.EventQueue.access$200(Unknown Source)
    at java.awt.EventQueue$3.run(Unknown Source)
    at java.awt.EventQueue$3.run(Unknown Source)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
    at java.awt.EventQueue$4.run(Unknown Source)
    at java.awt.EventQueue$4.run(Unknown Source)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
    at java.awt.EventQueue.dispatchEvent(Unknown Source)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
    at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
    at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    at java.awt.EventDispatchThread.run(Unknown Source)

Oct 05, 2014 9:15:38 PM jnr.ffi.util.ref.internal.Finalizer getInheritableThreadLocalsField
INFO: Couldn't access Thread.inheritableThreadLocals. Reference finalizer threads will inherit thread local values.
Unhandled exception in thread started by <bound method SplitFDist.monitor of <Bio.PopGen.FDist.Async.SplitFDist object at 0x7>>
Traceback (most recent call last):
  File "C:\Users\Dell\.lositan\Bio\PopGen\FDist\Async.py", line 124, in monitor
    os.remove(self.parts[done] + os.sep + file)
OSError: unlink(): an unknown error occurred: C:\Users\Dell\.lositan\2\out.dat

 

lositan • 1.6k views
ADD COMMENTlink modified 4.5 years ago by tiagoantao660 • written 4.5 years ago by carolw10
0
gravatar for tiagoantao
4.5 years ago by
tiagoantao660
United States of America
tiagoantao660 wrote:

This is really a strange error and I have never seen this, for now I would recommend trying to run this on another PC and see if the problem repeats...

ADD COMMENTlink written 4.5 years ago by tiagoantao660
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