Entering edit mode
8.8 years ago
ashley.murphy
•
0
I am trying to run LOSITAN (the truckloads of data version) for 5 different species, and had some initial success with two species. But now LOSITAN regularly crashes during either the "Forcing correct mean Fst for first pass" stage or sometimes the second stage. I got a third species to work just by retrying again and again with no changes, but this hasn't worked for the final two species. I have tried on other (Windows) computers, and get the same result, suggesting it is a datafile issue, but the datafiles for all species (even those that previously worked) now always fail, so I'm not sure that is the case.
If anyone could provide any advice (especially tiagoantao) that would be fantastic! Thanks in advance!
The output from the Java console is below:
Java Web Start 11.73.2.02
Using JRE version 1.8.0_73-b02 Java HotSpot(TM) 64-Bit Server VM
User home directory = C:\Users\ashleylm
----------------------------------------------------
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 Permissions manifest attribute in main jar: http://popgen.net/soft/lositan/code2/lib/selwb.jar
Windows 7 C:\Users\ashleylm \
*sys-package-mgr*: can't create package cache dir, 'cachedir\packages'
console: Failed to install '': java.nio.charset.UnsupportedCharsetException: cp0.
1027
0.015494 70
Feb 12, 2016 12:57:24 PM jnr.ffi.util.ref.FinalizableReferenceQueue$SystemLoader loadFinalizer
INFO: Not allowed to access system class loader.
Feb 12, 2016 12:57:27 PM jnr.ffi.util.ref.FinalizableReferenceQueue$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 com.sun.javaws.security.JavaWebStartSecurity.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$9(C:\Users\ashleylm\.lositan\Bio\PopGen\FDist\Async.py:185)
at Bio.PopGen.FDist.Async$py.call_function(C:\Users\ashleylm\.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\ashleylm\.lositan\Main.py:786)
at org.python.pycode._pyx0.call_function(C:\Users\ashleylm\.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\ashleylm\.lositan\Main.py:743)
at org.python.pycode._pyx0.call_function(C:\Users\ashleylm\.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$36(C:\Users\ashleylm\.lositan\Main.py:900)
at org.python.pycode._pyx0.call_function(C:\Users\ashleylm\.lositan\Main.py)
at org.python.core.PyTableCode.call(PyTableCode.java:165)
at org.python.core.PyBaseCode.call(PyBaseCode.java:301)
at org.python.core.PyBaseCode.call(PyBaseCode.java:194)
at org.python.core.PyFunction.__call__(PyFunction.java:417)
at org.python.core.PyMethod.instancemethod___call__(PyMethod.java:232)
at org.python.core.PyMethod.__call__(PyMethod.java:223)
at org.python.core.PyMethod.__call__(PyMethod.java:213)
at org.python.core.PyMethod.__call__(PyMethod.java:208)
at org.python.core.PyObject._jcallexc(PyObject.java:3555)
at org.python.core.PyObject._jcall(PyObject.java:3587)
at org.python.proxies.__main__$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$500(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue$4.run(Unknown Source)
at java.awt.EventQueue$4.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.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)
Feb 12, 2016 12:57:27 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 0x53>>
Traceback (most recent call last):
File "C:\Users\ashleylm\.lositan\Bio\PopGen\FDist\Async.py", line 128, in monitor
self.report_fun(fst)
File "C:\Users\ashleylm\.lositan\Main.py", line 503, in report
os.remove(lpath + os.sep + 'out.dat') #careful, not for 5000 case
OSError: unlink(): an unknown error occurred: C:\Users\ashleylm\.lositan\out.dat
