Question: Lositan freezing when generating selection table
0
gravatar for andrepleao
3.3 years ago by
andrepleao0
andrepleao0 wrote:

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 • 985 views
ADD COMMENTlink modified 3.2 years ago • written 3.3 years ago by andrepleao0
0
gravatar for andrepleao
3.2 years ago by
andrepleao0
andrepleao0 wrote:

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 COMMENTlink written 3.2 years ago by andrepleao0

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

ADD REPLYlink written 2.9 years ago by ukrz0
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