Lositan freezing when generating selection table
3
0
Entering edit mode
8.4 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 • 2.8k views
ADD COMMENT
0
Entering edit mode
8.4 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?

ADD REPLY

Login before adding your answer.

Traffic: 1582 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6