Question: Why is Lositan crashing when loading input file?
0
gravatar for hazelperry
4.8 years ago by
hazelperry30
European Union
hazelperry30 wrote:

I am using lositan to try and pick out outliers from a couple of large SNP datasets.  I have three input files both in genepop format, two of these contain only two populations and one contains 5.  When I load one of the two population files into lositan it has no problems, the file will load and run fine but when I load in the other it gets as far as loading population 2 and freezes.  The program doesn't freeze completely, I can still look at menu options and the number of loci and populations it shows in the total data are correct but nothing happens (for days), it doesn't give me an Fst value and I can't run the simulation. 

When I load the third file in (the one with 5 populations), if I try to use all of the populaitons it works fine but when I try to use only two of the 5 populations (in the data used menu option) I get the same problem, it says loading population 2 but never gets any further. 

As one of the files runs with no problems and the other two are identical in format I don't think it can be the input file but have no idea what could be the problem.  As the lositan site says to ask for help on here I was hoping someone might be able to tell me what is going wrong?

Thanks

Hazel
 

lositan • 2.8k views
ADD COMMENTlink modified 4.8 years ago by tiagoantao660 • written 4.8 years ago by hazelperry30

Hi Hazel,

Could you please configure your Java virtual machine (On windows, you can find this on the control panel) to start up the console and always show it? Then run your dataset, get the error that gets out and post it here?

 

Tiago

PS - Do not forget to use the version for many loci (there are two available)

ADD REPLYlink written 4.8 years ago by tiagoantao660

Hi Tiago,

When I run lositan with the virtual machine console option open this is what I get (from the point of opening lositan to it freezing).

Missing Permissions manifest attribute in main jar: http://popgen.net/soft/lositan/code2/lib/selwb.jar
Windows 7 C:\Users\bspc26 \
*sys-package-mgr*: can't create package cache dir, 'cachedir\packages'
JNLPClassLoader: Finding library jnidispatch.dll
JNLPClassLoader: Finding library jnidispatch.dll
JNLPClassLoader: Finding library msvcrt.dll
985
0.500562 28
Unhandled exception in thread started by <function endRunDatacal at 0x2>
Traceback (most recent call last):
  File "C:\Users\bspc26\.lositan\Main.py", line 365, in endRunDatacal
    if float(lfst)<-10.0: lfst="nan"
ValueError: invalid literal for __float__: -1.#IND00


I have been using the version for many loci so this shouldn't be the issue. 

Thanks

Hazel

ADD REPLYlink written 4.8 years ago by hazelperry30

This is a bug in Lositan. I will try to patch it today and redeploy it. I will get back to you when it is done.

ADD REPLYlink written 4.8 years ago by tiagoantao660
0
gravatar for tiagoantao
4.8 years ago by
tiagoantao660
United States of America
tiagoantao660 wrote:

I have deployed a new version here:

http://popgen.net/soft/lositan/3264.html

(do not forget to use this link so that the code updates).

If it still fails, please send me the console output again.

ADD COMMENTlink written 4.8 years ago by tiagoantao660

Hi Tiago,

Sorry for not getting back to you sooner I have only just had chance to check the version you deployed above.  Unfortunately it's still not working.  The message I get in the console this time is:

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\bspc26 \
console: Failed to install '': java.nio.charset.UnsupportedCharsetException: cp0.
985
0.500562 28
Unhandled exception in thread started by <function endRunDatacal at 0x3>
Traceback (most recent call last):
  File "C:\Users\bspc26\.lositan\Main.py", line 369, in endRunDatacal
    locusFst.append((float(lhe), float(lfst)))
ValueError: invalid literal for __float__: -1.#IND00

Thanks

Hazel

ADD REPLYlink written 4.7 years ago by hazelperry30

I deployed a new version, could you please try again?

ADD REPLYlink written 4.7 years ago by tiagoantao660

Hi Tiago,

That version now loads my files in with no problem but this time I get the same issue as mhmeek (Lositan freezes when producing selection table) in that it loads the input file, runs but freezes when it gets to the preparing selection table bit.

This time the console shows:

CacheEntry[http://popgen.net/soft/lositan/code2/lib/jfreechart-1.0.13.jar]: updateAvailable=true,lastModified=Wed Jul 16 13:08:10 BST 2014,length=-1
CacheEntry[http://popgen.net/soft/lositan/code2/lib/jython.jar]: updateAvailable=true,lastModified=Wed Jul 16 13:08:12 BST 2014,length=-1
CacheEntry[http://popgen.net/soft/lositan/code2/lib/jcommon-1.0.16.jar]: updateAvailable=true,lastModified=Wed Jul 16 13:08:10 BST 2014,length=-1
CacheEntry[http://popgen.net/soft/lositan/code2/lib/selwb.jar]: updateAvailable=true,lastModified=Wed Jul 16 13:08:12 BST 2014,length=-1
CacheEntry[http://popgen.net/soft/lositan/code2/lib/batik-awt-util.jar]: updateAvailable=true,lastModified=Wed Jul 16 13:08:09 BST 2014,length=-1
CacheEntry[http://popgen.net/soft/lositan/code2/lib/batik-dom.jar]: updateAvailable=true,lastModified=Wed Jul 16 13:08:09 BST 2014,length=-1
CacheEntry[http://popgen.net/soft/lositan/code2/lib/batik-svggen.jar]: updateAvailable=true,lastModified=Wed Jul 16 13:08:09 BST 2014,length=-1
CacheEntry[http://popgen.net/soft/lositan/code2/lib/batik-util.jar]: updateAvailable=true,lastModified=Wed Jul 16 13:08:09 BST 2014,length=-1
CacheEntry[http://popgen.net/soft/lositan/code2/lib/batik-xml.jar]: updateAvailable=true,lastModified=Wed Jul 16 13:08:10 BST 2014,length=-1
CacheEntry[http://popgen.net/soft/lositan/code2/lib/iText-2.1.5.jar]: updateAvailable=true,lastModified=Wed Jul 16 13:08:10 BST 2014,length=-1
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\bspc26 \
console: Failed to install '': java.nio.charset.UnsupportedCharsetException: cp0.
985
0.500562 28
Aug 05, 2014 12:26:05 PM jnr.ffi.util.ref.FinalizableReferenceQueue$SystemLoader loadFinalizer
INFO: Not allowed to access system class loader.
Aug 05, 2014 12:26:05 PM jnr.ffi.util.ref.FinalizableReferenceQueue$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$9(C:\Users\bspc26\.lositan\Bio\PopGen\FDist\Async.py:185)
    at Bio.PopGen.FDist.Async$py.call_function(C:\Users\bspc26\.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\bspc26\.lositan\Main.py:786)
    at org.python.pycode._pyx0.call_function(C:\Users\bspc26\.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\bspc26\.lositan\Main.py:743)
    at org.python.pycode._pyx0.call_function(C:\Users\bspc26\.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$36(C:\Users\bspc26\.lositan\Main.py:900)
    at org.python.pycode._pyx0.call_function(C:\Users\bspc26\.lositan\Main.py)
    at org.python.core.PyTableCode.call(PyTableCode.java:165)
    at org.python.core.PyBaseCode.call(PyBaseCode.java:301)
    at org.python.core.PyBaseCode.call(PyBaseCode.java:194)
    at org.python.core.PyFunction.__call__(PyFunction.java:417)
    at org.python.core.PyMethod.instancemethod___call__(PyMethod.java:232)
    at org.python.core.PyMethod.__call__(PyMethod.java:223)
    at org.python.core.PyMethod.__call__(PyMethod.java:213)
    at org.python.core.PyMethod.__call__(PyMethod.java:208)
    at org.python.core.PyObject._jcallexc(PyObject.java:3555)
    at org.python.core.PyObject._jcall(PyObject.java:3587)
    at org.python.proxies.__main__$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)

Aug 05, 2014 12:26:05 PM jnr.ffi.util.ref.internal.Finalizer getInheritableThreadLocalsField
INFO: Couldn't access Thread.inheritableThreadLocals. Reference finalizer threads will inherit thread local values.

Thanks

Hazel

ADD REPLYlink written 4.7 years ago by hazelperry30

Hi,

 

Could you please send me (in private) your input file? I think the problem is different from the one reported by the other user (in the other case, I think it is a Mac problem).

 

Tiago

ADD REPLYlink written 4.7 years ago by tiagoantao660

Emailed to your gmail address.

Hazel

ADD REPLYlink written 4.7 years ago by hazelperry30

I was able to run this on Linux. I will test it on Windows this evening.

ADD REPLYlink written 4.7 years ago by tiagoantao660

Ok, great thanks. 

On a side note I have some other files which I am running through at the moment.  Having run them through with a confidence interval of 0.995 it has produced a list of loci.  In this list those that have a p value above 0.995 are listed in the FDR column as being outliers (for positive selection) and the majority of these are highlighted red.  However there are a few at least that have p values above 0.995 and are marked in the FDR column as being outliers but they are not highlighted red.  When I save the loci list and the confidence intervals I loose this highlighting so can I ask why some are highlighted and others are not despite having p values above 0.995?

Thanks

Hazel

ADD REPLYlink written 4.7 years ago by hazelperry30

Hi Tiago,

I´m having the same issue as hazelperry. LOSITAN keeps freezing when preparing selection table. Were you able to solve this issue on windows? Or do I have to try it on linux?

Thanks in advance.

Andre Leao

ADD REPLYlink written 3.2 years ago by andrepleao0

Hi again, just writting to say that I found an error in the data sheet and it was it. I was able to run the analyses then. Thanks anyway

ADD REPLYlink written 3.2 years ago by andrepleao0
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