Lositan freezing when generating selection table
3
0
Entering edit mode
8.3 years ago
andrepleao • 0

Hi,

LOSITAN keeps freezing when producing the selection table. I saw that many people here had the same problems, but I got no answer. So I'll decided to post the console panel here:

java.security.cert.CertificateParsingException: no more data allowed for version 1 certificate
    at sun.security.x509.X509CertInfo.parse(Unknown Source)
    at sun.security.x509.X509CertInfo.<init>(Unknown Source)
    at sun.security.x509.X509CertImpl.parse(Unknown Source)
    at sun.security.x509.X509CertImpl.<init>(Unknown Source)
    at sun.security.provider.X509Factory.parseX509orPKCS7Cert(Unknown Source)
    at sun.security.provider.X509Factory.engineGenerateCertificates(Unknown Source)
    at java.security.cert.CertificateFactory.generateCertificates(Unknown Source)
    at com.sun.deploy.security.WIExplorerCertStore.generateCertificate(Unknown Source)
    at com.sun.deploy.security.WIExplorerCertStore.loadCertificates(Native Method)
    at com.sun.deploy.security.WIExplorerCertStore.load(Unknown Source)
    at com.sun.deploy.security.WIExplorerSigningRootCertStore.load(Unknown Source)
    at com.sun.deploy.security.WIExplorerCertStore.load(Unknown Source)
    at com.sun.deploy.security.WIExplorerSigningRootCertStore.load(Unknown Source)
    at com.sun.deploy.security.LazyRootStore.loadBrowserStore(Unknown Source)
    at com.sun.deploy.security.LazyRootStore.getTrustAnchors(Unknown Source)
    at com.sun.deploy.security.TrustDecider.getValidationState(Unknown Source)
    at com.sun.deploy.security.TrustDecider.validateChain(Unknown Source)
    at com.sun.deploy.security.TrustDecider.isAllPermissionGrantedInt(Unknown Source)
    at com.sun.deploy.security.TrustDecider.isAllPermissionGranted(Unknown Source)
    at com.sun.javaws.security.AppPolicy.grantUnrestrictedAccess(Unknown Source)
    at com.sun.javaws.security.JNLPSignedResourcesHelper.checkSignedResourcesHelper(Unknown Source)
    at com.sun.javaws.security.JNLPSignedResourcesHelper.checkSignedResources(Unknown Source)
    at com.sun.javaws.Launcher.prepareResources(Unknown Source)
    at com.sun.javaws.Launcher.prepareAllResources(Unknown Source)
    at com.sun.javaws.Launcher.prepareToLaunch(Unknown Source)
    at com.sun.javaws.Launcher.prepareToLaunch(Unknown Source)
    at com.sun.javaws.Launcher.launch(Unknown Source)
    at com.sun.javaws.Main.launchApp(Unknown Source)
    at com.sun.javaws.Main.continueInSecureThread(Unknown Source)
    at com.sun.javaws.Main.access$000(Unknown Source)
    at com.sun.javaws.Main$1.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
Missing Permissions manifest attribute in main jar: http://popgen.net/soft/lositan/code2/lib/selwb.jar
Windows 7 C:\Users\andrepl \
console: Failed to install '': java.nio.charset.UnsupportedCharsetException: cp0.
1657
-0.063796 36
Jan 21, 2016 4:03:40 PM jnr.ffi.util.ref.FinalizableReferenceQueue$SystemLoader loadFinalizer
INFO: Not allowed to access system class loader.
Jan 21, 2016 4:03:44 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$9(C:\Users\andrepl\.lositan\Bio\PopGen\FDist\Async.py:185)
    at Bio.PopGen.FDist.Async$py.call_function(C:\Users\andrepl\.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\andrepl\.lositan\Main.py:786)
    at org.python.pycode._pyx0.call_function(C:\Users\andrepl\.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\andrepl\.lositan\Main.py:743)
    at org.python.pycode._pyx0.call_function(C:\Users\andrepl\.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$36(C:\Users\andrepl\.lositan\Main.py:900)
    at org.python.pycode._pyx0.call_function(C:\Users\andrepl\.lositan\Main.py)
    at org.python.core.PyTableCode.call(PyTableCode.java:165)
    at org.python.core.PyBaseCode.call(PyBaseCode.java:301)
    at org.python.core.PyBaseCode.call(PyBaseCode.java:194)
    at org.python.core.PyFunction.__call__(PyFunction.java:417)
    at org.python.core.PyMethod.instancemethod___call__(PyMethod.java:232)
    at org.python.core.PyMethod.__call__(PyMethod.java:223)
    at org.python.core.PyMethod.__call__(PyMethod.java:213)
    at org.python.core.PyMethod.__call__(PyMethod.java:208)
    at org.python.core.PyObject._jcallexc(PyObject.java:3555)
    at org.python.core.PyObject._jcall(PyObject.java:3587)
    at org.python.proxies.__main__$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)

Jan 21, 2016 4:03:44 PM jnr.ffi.util.ref.internal.Finalizer getInheritableThreadLocalsField
INFO: Couldn't access Thread.inheritableThreadLocals. Reference finalizer threads will inherit thread local values.

Please, can someone help me with this issue?
LOSITAN • 2.7k views
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0
Entering edit mode
8.2 years ago
andrepleao • 0

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 COMMENT •
0
Entering edit mode

Hi, I'm having the same problem! What was the error in your data sheet?

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