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Wrapper plugin creator

PICHON Fabien

I started to create the plugin, but my command line needs an input (FASTA) and a reference file (FASTA), and even if the variable [inputRefSeqFileName]  exists I didn’t find the wayfor the user to assign a file, and it seems to be not possible to have two input fields in the plugin creator. how can I do ?

Thanks.

0

Comments

10 comments

Date Votes
  • Tom Edwards

    Hi Fabien,

    The wrapper plugin supports some basic options and customizability however we unfortunately don't support an option for selecting a file from the file system in the wrapper plugin creator. If you want to do this you would need to create your own full plugin using java code. (See our Plugin Development Kit here)

    One work around may be to always import the .fasta reference sequence into geneious before running the plugin. This way all of your input will be geneious documents, and you don't need to use files from the file system. That should allow you to use the input and command line options in step 2 along with [inputRefSeqFileName] as you found.

    Cheers,
    Tom

    0
  • PICHON Fabien

    Hi,

    Thanks for your answer.

    I imported a reference fasta file in Geneious in 'Reference Features', but it's still not clear for me how to set this fasta file as reference for [inputRefSeqFileName].

    Could provide more information, please ?

    Fabien

    0
  • PICHON Fabien

    I think I found the trick... Have I to set the program as a Mapper even if this is not a mapper... to allow for accessing Reference choice.... ?!

     

    0
  • PICHON Fabien

    So, I gave a try to this and get the following error:

    Data/WrapperPluginDevelopment/Fastani/fastANI_Windows: error while loading shared libraries: libgomp.so.1: cannot open shared object file: No such file or directory

    Since I set the program to "Run using Windows Linux Subsystem", I downloaded the file libgomp1_10.2.1-6_amd64.deb and attached as "Additionnal Bundled file" but get same error...

    Any idea, please ?

    0
  • PICHON Fabien

    I downloaded libgomp.so.1.0.0 from my server and attached as "Additionnal Bundled file" but get same error...

    I renamed it to libgomp.so.1 and attached as "Additionnal Bundled file" but get same error...

    0
  • Tom Edwards

    Hi Fabien,

    Sorry for the late reply. Attaching the library as an Additional Bundled File seems like a good way to go, however it appears that the command line tool you are using is looking for the library in the wrong place.

    Maybe there is some sort of environment variable which you can add at the bottom of the step 2 of 3 section which might point your tool at where the library is located. But exactly what that should be called depends on how the program looking for the library works.

    Cheers,
    Tom

    0
  • PICHON Fabien

    OK, so I installed the library directly in WSL and it seems to work during a while then crash, no idea why. I sent the report.

    Any help would be greatly appreciated!

    Thanks.

    0
  • Tom Edwards
    • Edited

    Would you be able to provide your email and computer username that you used to submit the crash in order to help us identify the crash report?

    Otherwise if you post the details of the crash, found by clicking "Technical Details" button on the crash popup box, we might be able to help identify the problem.

    Cheers,
    Tom

    0
  • PICHON Fabien

    Sequence Alignment 2022.0.2 Exception occurred 2022-05-23 12:09:41

    incidentSequenceNumber: 1
    incidentAge: Current
    applicationName: Geneious Prime
    applicationVersion: 2022.0.2
    applicationPlatform: Microsoft Windows [version 10.0.19044.1288] (amd64)
    applicationBuildDate: 2022-01-26 14:24
    javaVersion: 11.0.12 (64 bit)
    userName: fpn
    stackAnalysis: Sequence Alignment 2022.0.2
    memoryUsage: 219 / 62246 / 65250 MB [After previous GC:  heap total:155/62246   Par Eden Space:0/32   Par Survivor Space:1/4   CMS Old Gen:154/62210]
    dataOnNetworkDrive: false
    dataDirectory: C:\Users\fpn\Geneious 2022.0 Data (exists=true/true)
    applicationDirectory: C:\Program Files\Geneious Prime (exists=true)

    lastSelectedDocuments: 
    <selectedDocumentsXml count="1">
      <document class="com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument">
        <documentName>VAN1645_assembly</documentName>
        <number_of_sequences>432</number_of_sequences>
        <minimumSequenceLength>200</minimumSequenceLength>
        <maximumSequenceLength>467,770</maximumSequenceLength>
        <overrideDocumentType>com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument$NucleotideSequenceList</overrideDocumentType>
      </document>
    </selectedDocumentsXml>
    thread: Thread[.perform an operation on selected documents: Map to Reference...,3,]

    stacktrace: 
    java.lang.UnsupportedOperationException
        at com.biomatters.geneious.publicapi.plugin.DocumentFileImporter.importDocumentsFromMultipleFiles(DocumentFileImporter.java:343)
        at com.biomatters.geneious.publicapi.plugin.DocumentFileImporter.importDocumentsFromMultipleFilesReturningUnimported(DocumentFileImporter.java:365)
        at com.biomatters.geneious.publicapi.utilities.ImportUtilitiesImplementation.importDocuments(ImportUtilitiesImplementation.java:155)
        at com.biomatters.iseek.plugin.wrapperplugins.WrapperOperation.a(WrapperOperation.java:644)
        at com.biomatters.iseek.plugin.wrapperplugins.WrapperOperation.a(WrapperOperation.java:571)
        at com.biomatters.iseek.plugin.wrapperplugins.WrapperAssembler.assemble(WrapperAssembler.java:95)
        at com.biomatters.plugins.alignment.assembly.AssemblyOperation.performOperation(AssemblyOperation.java:528)
        at com.biomatters.iseek.plugin.operations.p.b(OperationManager.java:512)
        at com.biomatters.geneious.common.operations.c.c(OperationsUtilities.java:165)
        at com.biomatters.geneious.common.operations.c.b(OperationsUtilities.java:162)
        at com.biomatters.geneious.common.operations.b$c.a(OperationsUtilities.java:141)
        at com.biomatters.geneious.common.operations.b$d.a(OperationsUtilities.java:168)
        at com.biomatters.iseek.plugin.operations.e.a(OperationManager.java:517)
        at com.biomatters.iseek.plugin.operations.t.a(OperationPerformer.java:110)
        at com.biomatters.iseek.plugin.operations.OperationAction.performAction(OperationAction.java:116)
        at com.biomatters.iseek.plugin.operations.a.run(OperationAction.java:92)
        at java.base/java.lang.Thread.run(Thread.java:829)


    allStacktraces: 
    Thread[AWT-EventQueue-0,6,main] RUNNABLE :
        at java.desktop@11.0.12/sun.awt.windows.WComponentPeer.hide(Native Method)
        at java.desktop@11.0.12/sun.awt.windows.WWindowPeer.hide(WWindowPeer.java:371)
        at java.desktop@11.0.12/sun.awt.windows.WComponentPeer.setVisible(WComponentPeer.java:125)
        at java.desktop@11.0.12/java.awt.Component.hide(Component.java:1753)
        at java.desktop@11.0.12/java.awt.Window.hide(Window.java:1132)
        at java.desktop@11.0.12/java.awt.Component.show(Component.java:1718)
        at java.desktop@11.0.12/java.awt.Component.setVisible(Component.java:1663)
        at java.desktop@11.0.12/java.awt.Window.setVisible(Window.java:1031)
        at app//com.biomatters.geneious.publicapi.components.ProgressFrame$10.run(ProgressFrame.java:890)
        at java.desktop@11.0.12/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)
        at java.desktop@11.0.12/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770)
        at java.desktop@11.0.12/java.awt.EventQueue$4.run(EventQueue.java:721)
        at java.desktop@11.0.12/java.awt.EventQueue$4.run(EventQueue.java:715)
        at java.base@11.0.12/java.security.AccessController.doPrivileged(Native Method)
        at java.base@11.0.12/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
        at java.desktop@11.0.12/java.awt.EventQueue.dispatchEvent(EventQueue.java:740)
        at java.desktop@11.0.12/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
        at java.desktop@11.0.12/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
        at java.desktop@11.0.12/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
        at java.desktop@11.0.12/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
        at java.desktop@11.0.12/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
        at java.desktop@11.0.12/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

    Thread[.perform an operation on selected documents: Map to Reference...,3,main] RUNNABLE :
        at java.base@11.0.12/java.lang.Thread.dumpThreads(Native Method)
        at java.base@11.0.12/java.lang.Thread.getAllStackTraces(Thread.java:1653)
        at app//com.biomatters.utilities.aw.a(HangWatcher.java:96)
        at app//com.biomatters.geneious.common.talkback.geneious.b.a(GeneiousTalkbackIncidentFactory.java:164)
        at app//com.biomatters.geneious.common.talkback.client.e.b(TalkbackIncidentFactory.java:271)
        at app//com.biomatters.geneious.common.talkback.client.e.a(TalkbackIncidentFactory.java:181)
        at app//com.biomatters.geneious.common.ErrorUtilities.a(ErrorUtilities.java:351)
        at app//com.biomatters.iseek.application.ISeekMain$a.uncaughtException(ISeekMain.java:1310)
        at java.base@11.0.12/java.lang.ThreadGroup.uncaughtException(ThreadGroup.java:1055)
        at java.base@11.0.12/java.lang.ThreadGroup.uncaughtException(ThreadGroup.java:1050)
        at java.base@11.0.12/java.lang.Thread.dispatchUncaughtException(Thread.java:1997)

    Thread[Abort polling timer,3,main] TIMED_WAITING :
        at java.base@11.0.12/java.lang.Object.wait(Native Method)
        at java.base@11.0.12/java.util.TimerThread.mainLoop(Timer.java:553)
        at java.base@11.0.12/java.util.TimerThread.run(Timer.java:506)

    Thread[AnimatedIcon repaint thread spawned by AWT-EventQueue-0 for 274806944,6,main] TIMED_WAITING :
        at java.base@11.0.12/java.lang.Thread.sleep(Native Method)
        at app//com.biomatters.geneious.publicapi.components.AnimatedLoadingThrobber$1.run(AnimatedLoadingThrobber.java:83)

    Thread[Attach Listener,5,system] RUNNABLE :

    Thread[AWT-Shutdown,5,system] WAITING :
        at java.base@11.0.12/java.lang.Object.wait(Native Method)
        at java.base@11.0.12/java.lang.Object.wait(Object.java:328)
        at java.desktop@11.0.12/sun.awt.AWTAutoShutdown.run(AWTAutoShutdown.java:291)
        at java.base@11.0.12/java.lang.Thread.run(Thread.java:829)

    Thread[AWT-Windows,6,system] RUNNABLE :
        at java.desktop@11.0.12/sun.awt.windows.WToolkit.eventLoop(Native Method)
        at java.desktop@11.0.12/sun.awt.windows.WToolkit.run(WToolkit.java:305)
        at java.base@11.0.12/java.lang.Thread.run(Thread.java:829)

    ** 2 copies of this thread running:
    Thread[Biomatters-Timer-Thread,5,main] TIMED_WAITING :
        at java.base@11.0.12/java.lang.Thread.sleep(Native Method)
        at app//com.biomatters.iseek.license.au.run(TimerThread.java:50)

    Thread[Calculate sequence viewer statistics in background,1,main] WAITING :
        at java.base@11.0.12/jdk.internal.misc.Unsafe.park(Native Method)
        at java.base@11.0.12/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
        at java.base@11.0.12/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
        at java.base@11.0.12/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
        at java.base@11.0.12/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
        at java.base@11.0.12/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
        at java.base@11.0.12/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
        at java.base@11.0.12/java.lang.Thread.run(Thread.java:829)

    Thread[Common-Cleaner,8,InnocuousThreadGroup] TIMED_WAITING :
        at java.base@11.0.12/java.lang.Object.wait(Native Method)
        at java.base@11.0.12/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:155)
        at java.base@11.0.12/jdk.internal.ref.CleanerImpl.run(CleanerImpl.java:148)
        at java.base@11.0.12/java.lang.Thread.run(Thread.java:829)
        at java.base@11.0.12/jdk.internal.misc.InnocuousThread.run(InnocuousThread.java:134)

    Thread[ConflictDetectionTimer,5,main] TIMED_WAITING :
        at java.base@11.0.12/java.lang.Thread.sleep(Native Method)
        at app//com.biomatters.geneious.publicapi.utilities.ThreadUtilities.sleep(ThreadUtilities.java:35)
        at app//com.biomatters.iseek.application.z.run(DataDirectoryLock.java:417)

    Thread[DataDirectoryExistsTimer,5,main] TIMED_WAITING :
        at java.base@11.0.12/java.lang.Thread.sleep(Native Method)
        at app//com.biomatters.geneious.publicapi.utilities.ThreadUtilities.sleep(ThreadUtilities.java:35)
        at app//com.biomatters.iseek.application.A.run(DataDirectoryLock.java:430)

    Thread[DestroyJavaVM,5,main] RUNNABLE :

    Thread[DirectoryRepository: Document Indexer,1,main] TIMED_WAITING :
        at java.base@11.0.12/java.lang.Thread.sleep(Native Method)
        at app//com.biomatters.geneious.publicapi.utilities.ThreadUtilities.sleep(ThreadUtilities.java:35)
        at com.biomatters.plugins.local.DirectoryRepositorySearchIndex.a(DirectoryRepositorySearchIndex.java:639)
        at com.biomatters.plugins.local.DirectoryRepositorySearchIndex.y(DirectoryRepositorySearchIndex.java:841)
        at com.biomatters.plugins.local.s.run(DirectoryRepositorySearchIndex.java:219)

    Thread[Finalizer,8,system] WAITING :
        at java.base@11.0.12/java.lang.Object.wait(Native Method)
        at java.base@11.0.12/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:155)
        at java.base@11.0.12/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:176)
        at java.base@11.0.12/java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:170)

    Thread[FLEXlm Heartbeat,5,main] TIMED_WAITING :
        at java.base@11.0.12/java.lang.Thread.sleep(Native Method)
        at app//com.macrovision.flexlm.licsource.LicenseServer.runHeartbeat(LicenseServer.java:1891)
        at app//com.macrovision.flexlm.licsource.LicenseServer$1.run(LicenseServer.java:1847)

    Thread[GarbageCollectionNotifier,6,main] WAITING :
        at java.base@11.0.12/java.lang.Object.wait(Native Method)
        at java.base@11.0.12/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:155)
        at java.base@11.0.12/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:176)
        at app//com.biomatters.geneious.publicapi.utilities.GarbageCollectionNotifier$1.run(GarbageCollectionNotifier.java:48)

    Thread[Hang Watcher,10,main] TIMED_WAITING :
        at java.base@11.0.12/java.lang.Thread.sleep(Native Method)
        at app//com.biomatters.utilities.ay.run(HangWatcher.java:75)

    Thread[Java2D Disposer,10,system] WAITING :
        at java.base@11.0.12/java.lang.Object.wait(Native Method)
        at java.base@11.0.12/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:155)
        at java.base@11.0.12/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:176)
        at java.desktop@11.0.12/sun.java2d.Disposer.run(Disposer.java:144)
        at java.base@11.0.12/java.lang.Thread.run(Thread.java:829)

    Thread[Memory Monitor,1,main] TIMED_WAITING :
        at java.base@11.0.12/java.lang.Thread.sleep(Native Method)
        at app//com.biomatters.utilities.aR.run(MemoryMonitor.java:41)
        at java.base@11.0.12/java.lang.Thread.run(Thread.java:829)

    Thread[mysql-cj-abandoned-connection-cleanup,5,main] TIMED_WAITING :
        at java.base@11.0.12/java.lang.Object.wait(Native Method)
        at java.base@11.0.12/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:155)
        at com.mysql.cj.jdbc.AbandonedConnectionCleanupThread.run(AbandonedConnectionCleanupThread.java:91)
        at java.base@11.0.12/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
        at java.base@11.0.12/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
        at java.base@11.0.12/java.lang.Thread.run(Thread.java:829)

    Thread[pool-4-thread-1,5,main] TIMED_WAITING :
        at java.base@11.0.12/jdk.internal.misc.Unsafe.park(Native Method)
        at java.base@11.0.12/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
        at java.base@11.0.12/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2123)
        at java.base@11.0.12/java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:1182)
        at java.base@11.0.12/java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:899)
        at java.base@11.0.12/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
        at java.base@11.0.12/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
        at java.base@11.0.12/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
        at java.base@11.0.12/java.lang.Thread.run(Thread.java:829)

    Thread[Reference Handler,10,system] RUNNABLE :
        at java.base@11.0.12/java.lang.ref.Reference.waitForReferencePendingList(Native Method)
        at java.base@11.0.12/java.lang.ref.Reference.processPendingReferences(Reference.java:241)
        at java.base@11.0.12/java.lang.ref.Reference$ReferenceHandler.run(Reference.java:213)

    Thread[Repository_Firing_Thread,5,main] WAITING :
        at java.base@11.0.12/java.lang.Object.wait(Native Method)
        at java.base@11.0.12/java.lang.Object.wait(Object.java:328)
        at app//com.biomatters.utilities.aD.b(InvokeLaterThread.java:77)
        at app//com.biomatters.utilities.aE.run(InvokeLaterThread.java:45)

    Thread[Run immediate task group LocalDocuments,5,main] WAITING :
        at java.base@11.0.12/jdk.internal.misc.Unsafe.park(Native Method)
        at java.base@11.0.12/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
        at java.base@11.0.12/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
        at java.base@11.0.12/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
        at java.base@11.0.12/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
        at java.base@11.0.12/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
        at java.base@11.0.12/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
        at java.base@11.0.12/java.lang.Thread.run(Thread.java:829)

    Thread[Run immediate task group NCBI_genomic,5,main] WAITING :
        at java.base@11.0.12/jdk.internal.misc.Unsafe.park(Native Method)
        at java.base@11.0.12/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
        at java.base@11.0.12/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
        at java.base@11.0.12/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
        at java.base@11.0.12/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
        at java.base@11.0.12/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
        at java.base@11.0.12/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
        at java.base@11.0.12/java.lang.Thread.run(Thread.java:829)

    Thread[Run immediate task group NCBI_rRNA_typestrains,5,main] WAITING :
        at java.base@11.0.12/jdk.internal.misc.Unsafe.park(Native Method)
        at java.base@11.0.12/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
        at java.base@11.0.12/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
        at java.base@11.0.12/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
        at java.base@11.0.12/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
        at java.base@11.0.12/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
        at java.base@11.0.12/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
        at java.base@11.0.12/java.lang.Thread.run(Thread.java:829)

    Thread[Run immediate task group NCBI_TL,5,main] WAITING :
        at java.base@11.0.12/jdk.internal.misc.Unsafe.park(Native Method)
        at java.base@11.0.12/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
        at java.base@11.0.12/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
        at java.base@11.0.12/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
        at java.base@11.0.12/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
        at java.base@11.0.12/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
        at java.base@11.0.12/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
        at java.base@11.0.12/java.lang.Thread.run(Thread.java:829)

    Thread[Signal Dispatcher,9,system] RUNNABLE :

    Thread[SwingWorker-pool-6-thread-1,5,main] WAITING :
        at java.base@11.0.12/jdk.internal.misc.Unsafe.park(Native Method)
        at java.base@11.0.12/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
        at java.base@11.0.12/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
        at java.base@11.0.12/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
        at java.base@11.0.12/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
        at java.base@11.0.12/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
        at java.base@11.0.12/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
        at java.base@11.0.12/java.lang.Thread.run(Thread.java:829)

    Thread[Thread-1,5,main] TIMED_WAITING :
        at java.base@11.0.12/java.lang.Thread.sleep(Native Method)
        at app//com.biomatters.geneious.publicapi.utilities.ThreadUtilities.sleep(ThreadUtilities.java:35)
        at app//com.biomatters.geneious.common.z.run(GeneiousUtilities.java:505)
        at java.base@11.0.12/java.lang.Thread.run(Thread.java:829)

    Thread[Thread-3,5,main] WAITING :
        at java.base@11.0.12/java.lang.Object.wait(Native Method)
        at java.base@11.0.12/java.lang.Object.wait(Object.java:328)
        at app//com.biomatters.utilities.G.run(FilePreferences.java:73)

    Thread[Thread-6,5,main] RUNNABLE :
        at app//com.sun.jna.Native.invokeInt(Native Method)
        at app//com.sun.jna.Function.invoke(Function.java:418)
        at app//com.sun.jna.Function.invoke(Function.java:361)
        at app//com.sun.jna.Library$Handler.invoke(Library.java:265)
        at app//com.sun.proxy.$Proxy14.ReadFile(Unknown Source)
        at app//com.biomatters.windows.WindowsPipeClient.readMessage(WindowsPipeClient.java:52)
        at app//com.biomatters.iseek.application.launcherwrapper.w.a(WindowsEventsReceivingThread.java:35)
        at app//com.biomatters.iseek.application.launcherwrapper.a.run(EventsReceivingThread.java:35)

    Thread[Timer: FilePreferences sync timer (daemon),5,main] TIMED_WAITING :
        at java.base@11.0.12/java.lang.Object.wait(Native Method)
        at java.base@11.0.12/java.util.TimerThread.mainLoop(Timer.java:553)
        at java.base@11.0.12/java.util.TimerThread.run(Timer.java:506)

    Thread[Timer: UpdatingProperties - null.properties,5,main] TIMED_WAITING :
        at java.base@11.0.12/java.lang.Object.wait(Native Method)
        at java.base@11.0.12/java.util.TimerThread.mainLoop(Timer.java:553)
        at java.base@11.0.12/java.util.TimerThread.run(Timer.java:506)

    Thread[Timer: UpdatingProperties - properties.txt,6,main] TIMED_WAITING :
        at java.base@11.0.12/java.lang.Object.wait(Native Method)
        at java.base@11.0.12/java.util.TimerThread.mainLoop(Timer.java:553)
        at java.base@11.0.12/java.util.TimerThread.run(Timer.java:506)

    Thread[TimerQueue,5,system] TIMED_WAITING :
        at java.base@11.0.12/jdk.internal.misc.Unsafe.park(Native Method)
        at java.base@11.0.12/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
        at java.base@11.0.12/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2123)
        at java.base@11.0.12/java.util.concurrent.DelayQueue.take(DelayQueue.java:229)
        at java.desktop@11.0.12/javax.swing.TimerQueue.run(TimerQueue.java:171)
        at java.base@11.0.12/java.lang.Thread.run(Thread.java:829)

    Thread[UsageTrackingUploadServiceTimer,5,main] TIMED_WAITING :
        at java.base@11.0.12/java.lang.Object.wait(Native Method)
        at java.base@11.0.12/java.util.TimerThread.mainLoop(Timer.java:553)
        at java.base@11.0.12/java.util.TimerThread.run(Timer.java:506)

     

    systemProperties: 
    VM options: -Xmx0M
    -Xms256M
    -XX:+UseConcMarkSweepGC
    -XX:MaxNewSize=40M
    -XX:MaxJavaStackTraceDepth=99999
    -Djava.net.preferIPv4Stack=true
    -XX:ReservedCodeCacheSize=128m
    -Dfile.encoding=UTF8
    -Dsun.awt.nopixfmt=true
    --add-opens=java.base/jdk.internal.reflect=ALL-UNNAMED
    -Djava.net.useSystemProxies=false

    System memory: 65,250 MB
    {java.specification.version=11, install4j.launcherId=6, sun.cpu.isalist=amd64, sun.arch.data.model=64, java.vendor.url=https://adoptium.net/, sun.boot.library.path=c:\program files\geneious prime\jre\bin, sun.java.command=com.biomatters.iseek.application.ISeekMain -distributionVersion -windowsNamedPipe=geneious-38a4f20b-13dd-435c-a0e9-998f6c1acfa0, jdk.debug=release, sun.awt.exception.handler=com.biomatters.iseek.application.ISeekMain$a, java.specification.vendor=Oracle Corporation, java.version.date=2021-07-20, java.home=c:\program files\geneious prime\jre, java.specification.name=Java Platform API Specification, java.vm.specification.vendor=Oracle Corporation, apple.awt.antialiasing=on, user.script=, sun.management.compiler=HotSpot 64-Bit Tiered Compilers, java.runtime.version=11.0.12+7, apple.awt.rendering=VALUE_RENDER_SPEED, file.encoding=UTF8, jnidispatch.path=C:\Program Files\Geneious Prime\resources\jna_windows\win64\jnidispatch.dll, java.vendor.version=Temurin-11.0.12+7, java.io.tmpdir=C:\Users\fpn\AppData\Local\Temp\, java.version=11.0.12, java.vm.specification.name=Java Virtual Machine Specification, sun.awt.nopixfmt=true, java.awt.printerjob=sun.awt.windows.WPrinterJob, java.library.path=c:\program files\geneious prime\jre\bin;C:\Program Files\Geneious Prime\.\.;C:\Program Files\Common Files\Oracle\Java\javapath;C:\Rtools\bin;C:\Program Files (x86)\Common Files\Oracle\Java\javapath;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Windows\System32\OpenSSH\;C:\Program Files (x86)\CheckPoint\Endpoint Security\Endpoint Common\bin;C:\Program Files (x86)\NVIDIA Corporation\PhysX\Common;C:\Program Files\Git\cmd;C:\Program Files (x86)\Pandoc\;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0\;C:\WINDOWS\System32\OpenSSH\;C:\Program Files\R\R-4.1.2\bin\x64;C:\Users\fpn\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.7_qbz5n2kfra8p0\LocalCache\local-packages\Python37\Scripts;;C:\Program Files\Docker\Docker\resources\bin;C:\ProgramData\DockerDesktop\version-bin;C:\Program Files\Geneious Prime;C:\Program Files\NCBI\blast-2.11.0+\bin;C:\Users\fpn\AppData\Local\Microsoft\WindowsApps;C:\Users\fpn\AppData\Local\atom\bin;C:\Users\fpn\AppData\Local\Programs\MiKTeX\miktex\bin\x64\;C:\Users\fpn\AppData\Local\Microsoft\WindowsApps;;C:\Program Files\domino, java.vendor=Eclipse Foundation, sun.io.unicode.encoding=UnicodeLittle, launchISeekMain:16496=, install4j.swt=false, sun.desktop=windows, sun.java2d.print.shapetext=true, sun.awt.enableExtraMouseButtons=true, https.proxyPort=8080, user.timezone=Europe/Paris, os.name=Windows 10, java.vm.specification.version=11, JDK_1_3_Compatibility=YES, user.home=C:\Users\fpn, java.util.prefs.PreferencesFactory=com.biomatters.utilities.FilePreferencesFactory, java.awt.graphicsenv=sun.awt.Win32GraphicsEnvironment, networkaddress.cache.ttl=600, exe4j.consoleCodepage=cp0, exe4j.isInstall4j=true, java.net.preferIPv4Stack=true, path.separator=;, os.version=10.0, java.vm.name=OpenJDK 64-Bit Server VM, os.arch=amd64, java.vm.info=mixed mode, java.class.version=55.0, http.proxyPort=8080, awt.toolkit=sun.awt.windows.WToolkit, sun.jnu.encoding=Cp1252, exe4j.unextractedPosition=0, file.separator=\, line.separator=
    , exe4j.moduleName=C:\Program Files\Geneious Prime\Geneious Prime.exe, apple.awt.textantialiasing=on, java.util.logging.config.file=logging.properties, user.name=fpn, java.net.useSystemProxies=false, apple.awt.showGrowBox=true, exe4j.semaphoreName=Local\c:_program_files_geneious_prime_geneious_prime.exe, jna.loaded=true, sun.os.patch.level=, http.proxyHost=srvproxy01.lesaffre.fr, java.class.path=<snip>, java.vm.vendor=Eclipse Foundation, user.variant=, jna.debug_load=true, apple.laf.useScreenMenuBar=true, jna.boot.library.path=C:\Program Files\Geneious Prime\resources\jna_windows\win32;C:\Program Files\Geneious Prime\resources\jna_windows\win64, sun.java.launcher=SUN_STANDARD, user.country=FR, sun.cpu.endian=little, user.language=fr, https.proxyHost=srvproxy01.lesaffre.fr, geneious.runFromLauncher=true, exe4j.tempDir=, com.apple.macos.useScreenMenuBar=true, sun.java2d.d3d=false, javax.xml.parsers.SAXParserFactory=com.sun.org.apache.xerces.internal.jaxp.SAXParserFactoryImpl, java.runtime.name=OpenJDK Runtime Environment, java.vendor.url.bug=https://github.com/adoptium/adoptium-support/issues, user.dir=C:\Program Files\Geneious Prime, java.vm.version=11.0.12+7}

    warningHistory: 
    2022 May 23 - 12:06:46.091: WARNING: Running Geneious 2022.0.2 (2022-01-26 14:24) under 64 bit Java 11.0.12 with max memory=65,269,661,696 DataDirectory=C:\Users\fpn\Geneious 2022.0 Data TempDirectory=C:\Users\fpn\Geneious 2022.0 Data\transient\1653300406062\x
    2022 May 23 - 12:07:46.722: WARNING: Geneious hung:
    Thread[AWT-EventQueue-0,6,main] WAITING :
        at java.base@11.0.12/jdk.internal.misc.Unsafe.park(Native Method)
        at java.base@11.0.12/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
        at java.base@11.0.12/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
        at java.desktop@11.0.12/java.awt.EventQueue.getNextEvent(EventQueue.java:566)
        at java.desktop@11.0.12/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:190)
        at java.desktop@11.0.12/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
        at java.desktop@11.0.12/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
        at java.desktop@11.0.12/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
        at java.desktop@11.0.12/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
        at java.desktop@11.0.12/java.awt.EventDispatc...
    2022 May 23 - 12:07:46.723: Hang occurred:
    Thread[AWT-EventQueue-0,6,main] WAITING :
        at java.base@11.0.12/jdk.internal.misc.Unsafe.park(Native Method)
        at java.base@11.0.12/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
        at java.base@11.0.12/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
        at java.desktop@11.0.12/java.awt.EventQueue.getNextEvent(EventQueue.java:566)
        at java.desktop@11.0.12/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:190)
        at java.desktop@11.0.12/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
        at java.desktop@11.0.12/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
        at java.desktop@11.0.12/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
        at java.desktop@11.0.12/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
        at java.desktop@11.0.12/java.awt.EventDispatchThread.r...
    2022 May 23 - 12:07:57.803: Looks like it wasn't really a hang - deleting incident
    2022 May 23 - 12:09:25.094: Can't delete folder C:\Users\fpn\Geneious 2022.0 Data\transient\1653300406062\x\4
    2022 May 23 - 12:09:41.764: WARNING: Exception: java.lang.UnsupportedOperationException
        at com.biomatters.geneious.publicapi.plugin.DocumentFileImporter.importDocumentsFromMultipleFiles(DocumentFileImporter.java:343)
        at com.biomatters.geneious.publicapi.plugin.DocumentFileImporter.importDocumentsFromMultipleFilesReturningUnimported(DocumentFileImporter.java:365)
        at com.biomatters.geneious.publicapi.utilities.ImportUtilitiesImplementation.importDocuments(ImportUtilitiesImplementation.java:155)
        at com.biomatters.iseek.plugin.wrapperplugins.WrapperOperation.a(WrapperOperation.java:644)
        at com.biomatters.iseek.plugin.wrapperplugins.WrapperOperation.a(WrapperOperation.java:571)
        at com.biomatters.iseek.plugin.wrapperplugins.WrapperAssembler.assemble(WrapperAssembler.java:95)
        at com.biomatters.plugins.alignment.assembly.AssemblyOperation.performOperation(AssemblyOperation.java:528)
        at com.biomatters.iseek.plugin.operations.p.b(OperationManager.java:512)
        at com.biomatters.geneious.common.opera...
    2022 May 23 - 12:09:43.521: end of warning history

    infoHistory: 
    2022 May 23 - 12:06:44.112: lockDataDirectory result=success for C:\Users\fpn\Geneious 2022.0 Data. Running under 64 bit Java 11.0.12 with max memory=65,269,661,696
    2022 May 23 - 12:06:46.089: Running Geneious 2022.0.2 (2022-01-26 14:24) under 64 bit Java 11.0.12 with max memory=65,269,661,696 DataDirectory=C:\Users\fpn\Geneious 2022.0 Data TempDirectory=C:\Users\fpn\Geneious 2022.0 Data\transient\1653300406062\x
    2022 May 23 - 12:06:46.091: WARNING: Running Geneious 2022.0.2 (2022-01-26 14:24) under 64 bit Java 11.0.12 with max memory=65,269,661,696 DataDirectory=C:\Users\fpn\Geneious 2022.0 Data TempDirectory=C:\Users\fpn\Geneious 2022.0 Data\transient\1653300406062\x
    2022 May 23 - 12:06:46.147: creating https socket to avoid flexnet ssl bug
    2022 May 23 - 12:06:48.803: documentsSelectedXml=<selectedDocumentsXml count="0" />
    2022 May 23 - 12:06:49.229: Loading plugins from: C:\Program Files\Common Files\Geneious\plugins - C:\Program Files\Common Files\Geneious\plugins\com.biomatters.plugins.wrapperPluginCreator.WrapperPluginCreatorPlugin, C:\Program Files\Common Files\Geneious\plugins\mauve.plugin.MauveAlignmentPlugin, C:\Program Files\Common Files\Geneious\plugins\Minimap2
    2022 May 23 - 12:06:49.301: Loading plugins from: bundledPlugins - bundledPlugins\Clustal_Omega, bundledPlugins\com.biomatters.plugins.abi.ChromatographPlugin, bundledPlugins\com.biomatters.plugins.alignment.AlignmentPlugin, bundledPlugins\com.biomatters.plugins.annotationTableViewer.AnnotationTableViewerPlugin, bundledPlugins\com.biomatters.plugins.batchRename.BatchRenamePlugin, bundledPlugins\com.biomatters.plugins.bbtools.BBToolsPlugin, bundledPlugins\com.biomatters.plugins.bedimporter.BedImporterPlugin, bundledPlugins\com.biomatters.plugins.chimerafiltering.ChimeraFilteringPlugin, bundledPlugins\com.biomatters.plugins.chromatogramPlugin.ChromatogramPlugin, bundledPlugins\com.biomatters.plugins.ChromatogramViewer.ChromatogramViewerPlugin, bundledPlugins\com.biomatters.plugins.clonemanager.CloneManagerImporterPlugin, bundledPlugins\com.biomatters.plugins.cloning.CloningPlugin, bundledPlugins\com.biomatters.plugins.codonOptimization.CodonOptimizationPlugin, bundledPlugins\com.biomatters.plugins.consens...
    2022 May 23 - 12:07:16.385: Program has hung for 30285 milliseconds. Will generate crash log when time reaches 60000
    2022 May 23 - 12:07:17.388: Program has hung for 31293 milliseconds. Will generate crash log when time reaches 60000
    2022 May 23 - 12:07:18.401: Program has hung for 32305 milliseconds. Will generate crash log when time reaches 60000
    2022 May 23 - 12:07:19.402: Program has hung for 33307 milliseconds. Will generate crash log when time reaches 60000
    2022 May 23 - 12:07:20.415: Program has hung for 34320 milliseconds. Will generate crash log when time reaches 60000
    2022 May 23 - 12:07:21.427: Program has hung for 35331 milliseconds. Will generate crash log when time reaches 60000
    2022 May 23 - 12:07:22.441: Program has hung for 36346 milliseconds. Will generate crash log when time reaches 60000
    2022 May 23 - 12:07:23.451: Program has hung for 37356 milliseconds. Will generate crash log when time reaches 60000
    2022 May 23 - 12:07:24.461: Program has hung for 38366 milliseconds. Will generate crash log when time reaches 60000
    2022 May 23 - 12:07:25.461: Program has hung for 39366 milliseconds. Will generate crash log when time reaches 60000
    2022 May 23 - 12:07:26.463: Program has hung for 40368 milliseconds. Will generate crash log when time reaches 60000
    2022 May 23 - 12:07:27.466: Program has hung for 41371 milliseconds. Will generate crash log when time reaches 60000
    2022 May 23 - 12:07:28.476: Program has hung for 42381 milliseconds. Will generate crash log when time reaches 60000
    2022 May 23 - 12:07:29.491: Program has hung for 43396 milliseconds. Will generate crash log when time reaches 60000
    2022 May 23 - 12:07:30.500: Program has hung for 44405 milliseconds. Will generate crash log when time reaches 60000
    2022 May 23 - 12:07:31.507: Program has hung for 45412 milliseconds. Will generate crash log when time reaches 60000
    2022 May 23 - 12:07:32.513: Program has hung for 46418 milliseconds. Will generate crash log when time reaches 60000
    2022 May 23 - 12:07:33.519: Program has hung for 47424 milliseconds. Will generate crash log when time reaches 60000
    2022 May 23 - 12:07:34.526: Program has hung for 48431 milliseconds. Will generate crash log when time reaches 60000
    2022 May 23 - 12:07:35.529: Program has hung for 49434 milliseconds. Will generate crash log when time reaches 60000
    2022 May 23 - 12:07:36.537: Program has hung for 50442 milliseconds. Will generate crash log when time reaches 60000
    2022 May 23 - 12:07:37.541: Program has hung for 51446 milliseconds. Will generate crash log when time reaches 60000
    2022 May 23 - 12:07:38.547: Program has hung for 52452 milliseconds. Will generate crash log when time reaches 60000
    2022 May 23 - 12:07:39.550: Program has hung for 53455 milliseconds. Will generate crash log when time reaches 60000
    2022 May 23 - 12:07:40.556: Program has hung for 54460 milliseconds. Will generate crash log when time reaches 60000
    2022 May 23 - 12:07:41.560: Program has hung for 55465 milliseconds. Will generate crash log when time reaches 60000
    2022 May 23 - 12:07:42.575: Program has hung for 56479 milliseconds. Will generate crash log when time reaches 60000
    2022 May 23 - 12:07:43.590: Program has hung for 57495 milliseconds. Will generate crash log when time reaches 60000
    2022 May 23 - 12:07:44.302: programDataXml=<programDataXml>
      <geneiousVersion>2022.0.2</geneiousVersion>
      <programBuildDate>2022-01-26 14:24</programBuildDate>
      <runningFromADistribution>true</runningFromADistribution>
      <isProVersion>true</isProVersion>
      <status>Pro_Purchased</status>
      <subtype>Commercial</subtype>
      <cloud>false</cloud>
      <type>floating</type>
      <period>Subscription</period>
      <javaVersion>11.0.12 (64 bit)</javaVersion>
      <osPlatformString>Microsoft Windows [version 10.0.19044.1288]</osPlatformString>
      <osName>Windows 10</osName>
      <osVersionNum>10.0</osVersionNum>
      <osArch>amd64</osArch>
      <maxMemory>65,269,661,696</maxMemory>
    </programDataXml>
    2022 May 23 - 12:07:44.303: usageTrackingServiceTimer scheduled to start in 120000ms with period 300000
    2022 May 23 - 12:07:44.590: Program has hung for 58495 milliseconds. Will generate crash log when time reaches 60000
    2022 May 23 - 12:07:45.593: Program has hung for 59498 milliseconds. Will generate crash log when time reaches 60000
    2022 May 23 - 12:07:46.599: Program has hung for 60504 milliseconds. Will generate crash log when time reaches 60000
    2022 May 23 - 12:07:46.722: WARNING: Geneious hung:
    Thread[AWT-EventQueue-0,6,main] WAITING :
        at java.base@11.0.12/jdk.internal.misc.Unsafe.park(Native Method)
        at java.base@11.0.12/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
        at java.base@11.0.12/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
        at java.desktop@11.0.12/java.awt.EventQueue.getNextEvent(EventQueue.java:566)
        at java.desktop@11.0.12/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:190)
        at java.desktop@11.0.12/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
        at java.desktop@11.0.12/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
        at java.desktop@11.0.12/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
        at java.desktop@11.0.12/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
        at java.desktop@11.0.12/java.awt.EventDispatc...
    2022 May 23 - 12:07:46.723: Geneious hung
    2022 May 23 - 12:07:46.723: Hang occurred:
    Thread[AWT-EventQueue-0,6,main] WAITING :
        at java.base@11.0.12/jdk.internal.misc.Unsafe.park(Native Method)
        at java.base@11.0.12/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
        at java.base@11.0.12/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
        at java.desktop@11.0.12/java.awt.EventQueue.getNextEvent(EventQueue.java:566)
        at java.desktop@11.0.12/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:190)
        at java.desktop@11.0.12/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
        at java.desktop@11.0.12/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
        at java.desktop@11.0.12/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
        at java.desktop@11.0.12/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
        at java.desktop@11.0.12/java.awt.EventDispatchThread.r...
    2022 May 23 - 12:07:47.746: Initializing local database at 'C:\Users\fpn\Geneious 2022.0 Data\.localDatabase'
    2022 May 23 - 12:07:49.686: Plugin Initialization Round 2 started 20 plugins: [com.biomatters.plugins.wrapperPluginCreator.WrapperPluginCreatorPlugin, mauve.plugin.MauveAlignmentPlugin, Minimap2, Clustal_Omega, com.biomatters.plugins.alignment.AlignmentPlugin, com.biomatters.plugins.bbtools.BBToolsPlugin, com.biomatters.plugins.cloning.CloningPlugin, com.biomatters.plugins.crispr.CRISPRPlugin, com.biomatters.plugins.emboss.EmbossToolsPlugin, com.biomatters.plugins.identifyOrganism.IdentifyOrganismPlugin, com.biomatters.plugins.microsats.MicrosatsPlugin, com.biomatters.plugins.operationsTable.OperationsTablePlugin, com.biomatters.plugins.primerDesign.PrimerDesignPlugin, com.biomatters.plugins.rnafold.RNAFoldPlugin, com.biomatters.plugins.sequenceConcatenation.SequenceConcatenationPlugin, com.biomatters.plugins.sequenceviewer.SequenceViewerPlugin, com.biomatters.plugins.serverDatabase.ServerDatabasePlugin, com.biomatters.plugins.spades.SPAdesPlugin, com.biomatters.plugins.textImporter.TextImporterPlugin, ...
    2022 May 23 - 12:07:50.546: initialize LocalDatabasePlugin took 7,378 ms
    2022 May 23 - 12:07:50.678: UserDataDirectory=C:\Users\fpn\Geneious 2022.0 Data
    2022 May 23 - 12:07:51.159: Downloading new enzyme sets from rebase now...
    2022 May 23 - 12:07:51.780: optionValueUsedXml=<optionValueXml optionName="SequenceViewer_Dna:colorScheme" newValue="DefaultForeground1" />
    2022 May 23 - 12:07:51.782: optionValueUsedXml=<optionValueXml optionName="SequenceViewer_Dna:wrap" newValue="true" />
    2022 May 23 - 12:07:52.640: Created NucleotideSequenceViewer #Seqs=1 maxLen=7 circAlign=0 hasSequenceListSummary=false refSeq=-1 #visibleAnnos=1 #annos=1/0/0/0 #selected=0 selected= graphs=0 #docs=1 doc=class com.biomatters.geneious.publicapi.implementations.sequence.DefaultNucleotideSequence name=sequenceViewerTestSequenceForPerformanceImprovement
    2022 May 23 - 12:07:52.768: documentsSelectedXml=<selectedDocumentsXml count="0" />
    2022 May 23 - 12:07:52.861: optionValueUsedXml=<optionValueXml optionName="SequenceViewer_Dna:colorScheme" newValue="DefaultForeground1" />
    2022 May 23 - 12:07:52.862: optionValueUsedXml=<optionValueXml optionName="SequenceViewer_Dna:wrap" newValue="true" />
    2022 May 23 - 12:07:52.955: Created NucleotideSequenceViewer #Seqs=1 maxLen=7 circAlign=0 hasSequenceListSummary=false refSeq=-1 #visibleAnnos=0 #annos=0/0/0/0 #selected=0 selected= graphs=0 #docs=1 doc=class com.biomatters.geneious.publicapi.implementations.sequence.DefaultNucleotideSequence name=Dummy sequence for performance improvement
    2022 May 23 - 12:07:53.146: dialogShownXml=<dialog dialogTitle="Could not connect to shared database" dialogHashCode="1562493697" />
    2022 May 23 - 12:07:53.539: Save error log to C:\Users\fpn\Geneious 2022.0 Data\incident.txt
    2022 May 23 - 12:07:55.099: dialogClosedXml=<dialog dialogTitle="Could not connect to shared database" dialogHashCode="1562493697" dialogClosedButtonId="ok" dialogClosedButtonLabel="OK" />
    2022 May 23 - 12:07:55.740: serviceSelectedClass=com.biomatters.plugins.local.LocalDatabaseService
    2022 May 23 - 12:07:56.202: documentsSelectedXml=<selectedDocumentsXml count="0" />
    2022 May 23 - 12:07:57.384: Initialization Complete. Took 85,943 milliseconds to initialize Geneious 2022.0.2 with data location=C:\Users\fpn\Geneious 2022.0 Data
    2022 May 23 - 12:07:57.385: geneiousStartupDuration=85943
    2022 May 23 - 12:07:57.803: Looks like it wasn't really a hang - deleting incident
    2022 May 23 - 12:07:57.803: deleting error log C:\Users\fpn\Geneious 2022.0 Data\incident.txt
    2022 May 23 - 12:07:58.055: databaseSizeXml=<databaseSize sharedDbConnections="0">
      <localDatabase folderCount="20" docCount="2683" />
    </databaseSize>
    2022 May 23 - 12:07:58.629: dialogShownXml=<dialog dialogTitle="Software Update" dialogHashCode="1811676321" />
    2022 May 23 - 12:07:58.844: documentsSelectedXml=<selectedDocumentsXml count="1">
      <document class="com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument">
        <number_of_sequences>432</number_of_sequences>
        <minimumSequenceLength>200</minimumSequenceLength>
        <maximumSequenceLength>467,770</maximumSequenceLength>
        <overrideDocumentType>com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument$NucleotideSequenceList</overrideDocumentType>
      </document>
    </selectedDocumentsXml>
    2022 May 23 - 12:08:00.005: optionValueUsedXml=<optionValueXml optionName="SequenceViewer_DnaGenomeUnaligned:colorScheme" newValue="DefaultForeground1" />
    2022 May 23 - 12:08:00.006: optionValueUsedXml=<optionValueXml optionName="SequenceViewer_DnaGenomeUnaligned:wrap" newValue="false" />
    2022 May 23 - 12:08:00.583: delayDialogShownLabel=Loading annotation tracks
    2022 May 23 - 12:08:01.862: displayDimensionXml=<displayDimensions width="1920" height="1080" />
    2022 May 23 - 12:08:02.972: Created NucleotideSequenceViewer #Seqs=432 maxLen=467770 circAlign=0 hasSequenceListSummary=false refSeq=-1 #visibleAnnos=53697 #annos=0/0/0/53697 #selected=1 selected=99:1:44 graphs=0 #docs=1 doc=class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument name=VAN1645_assembly
    2022 May 23 - 12:08:03.212: mainFrameDimensionsXml=<mainFrameDimensions width="1936" height="1056" />
    2022 May 23 - 12:08:03.226: delayDialogHiddenLabel=Loading annotation tracks
    2022 May 23 - 12:08:04.633: dialogClosedXml=<dialog dialogTitle="Software Update" dialogHashCode="1811676321" dialogClosedButtonId="cancel" dialogClosedButtonLabel="Remind Me Later" />
    2022 May 23 - 12:08:05.898: menuBarActivated=File
    2022 May 23 - 12:08:06.249: menuBarActivated=New
    2022 May 23 - 12:08:07.238: menuItemButtonClicked=Create/Edit Wrapper Plugin...
    2022 May 23 - 12:08:07.362: dialogShownXml=<dialog dialogTitle="CreateEdit Wrapper Plugins" dialogHashCode="291130930" />
    2022 May 23 - 12:08:13.559: Shutting down license heart-beat
    2022 May 23 - 12:08:14.372: Completed license heart-beat shutdown
    2022 May 23 - 12:08:18.064: toolbarButtonClicked=Edit...
    2022 May 23 - 12:09:01.984: dialogClosedXml=<dialog dialogTitle="CreateEdit Wrapper Plugins" dialogHashCode="291130930" dialogClosedButtonId="closeWindowButton" dialogClosedButtonLabel="" />
    2022 May 23 - 12:09:03.988: menuBarActivated=File
    2022 May 23 - 12:09:04.486: menuBarActivated=Edit
    2022 May 23 - 12:09:04.623: menuBarActivated=Sequence
    2022 May 23 - 12:09:05.739: menuBarActivated=Tools
    2022 May 23 - 12:09:06.322: subMenuActivated=Align/Assemble
    2022 May 23 - 12:09:06.672: subMenuActivated=Primers
    2022 May 23 - 12:09:06.957: subMenuActivated=Align/Assemble
    2022 May 23 - 12:09:09.417: menuItemButtonClicked=Map to Reference...
    2022 May 23 - 12:09:11.136: dialogShownXml=<dialog dialogTitle="Map to Reference" dialogHashCode="1968981708" />
    2022 May 23 - 12:09:25.094: Can't delete folder C:\Users\fpn\Geneious 2022.0 Data\transient\1653300406062\x\4
    2022 May 23 - 12:09:25.157: dialogClosedXml=<dialog dialogTitle="Map to Reference" dialogHashCode="1968981708" dialogClosedButtonId="ok" dialogClosedButtonLabel="OK" />
    2022 May 23 - 12:09:25.161: dialogOptionsXml=<root name="com.biomatters.plugins.alignment.assembly.AssemblyOptions">
      <childOptions name="data">
        <option name="groupAssemblies" class="java.lang.Boolean" isDefault="true">false</option>
        <option name="namePart" class="com.biomatters.geneious.publicapi.plugin.Options$OptionValue" isDefault="true">0</option>
        <option name="assembleListsSeparately" class="java.lang.Boolean" isDefault="true">false</option>
      </childOptions>
      <childOptions name="method">
        <childOptions name="algorithm">
          <option name="referenceAssembly" class="com.biomatters.geneious.publicapi.plugin.Options$OptionValue" isDefault="false">Fastani_Fabien_Pichon</option>
        </childOptions>
        <childOptions name="Fastani_Fabien_Pichon">
          <childOptions name="options" />
        </childOptions>
      </childOptions>
      <childOptions name="trimOptions">
        <option name="method" class="com.biomatters.geneious.publicapi.plugin.Options$OptionValue" isDefault="true">noTr...
    2022 May 23 - 12:09:25.377: operationStarted=<OperationManagerCallbackXml operationUniqueId="com.biomatters.plugins.alignment.AssemblyOperation_Reference" callbackHashCode="125555570" />
    2022 May 23 - 12:09:26.277: progressFrameShownXml=<progressFrameXml progressFrameTitle=" - Fastani" progressFrameHashCode="732911100" />
    2022 May 23 - 12:09:41.751: operationFinishedWithRuntimeExceptionOrError=<OperationManagerCallbackXml operationUniqueId="com.biomatters.plugins.alignment.AssemblyOperation_Reference" callbackHashCode="125555570" />
    2022 May 23 - 12:09:41.751: progressFrameHiddenCompletedXml=<progressFrameXml progressFrameTitle=" - Fastani" progressFrameHashCode="732911100" />
    2022 May 23 - 12:09:41.764: WARNING: Exception: java.lang.UnsupportedOperationException
        at com.biomatters.geneious.publicapi.plugin.DocumentFileImporter.importDocumentsFromMultipleFiles(DocumentFileImporter.java:343)
        at com.biomatters.geneious.publicapi.plugin.DocumentFileImporter.importDocumentsFromMultipleFilesReturningUnimported(DocumentFileImporter.java:365)
        at com.biomatters.geneious.publicapi.utilities.ImportUtilitiesImplementation.importDocuments(ImportUtilitiesImplementation.java:155)
        at com.biomatters.iseek.plugin.wrapperplugins.WrapperOperation.a(WrapperOperation.java:644)
        at com.biomatters.iseek.plugin.wrapperplugins.WrapperOperation.a(WrapperOperation.java:571)
        at com.biomatters.iseek.plugin.wrapperplugins.WrapperAssembler.assemble(WrapperAssembler.java:95)
        at com.biomatters.plugins.alignment.assembly.AssemblyOperation.performOperation(AssemblyOperation.java:528)
        at com.biomatters.iseek.plugin.operations.p.b(OperationManager.java:512)
        at com.biomatters.geneious.common.opera...
    2022 May 23 - 12:09:43.525: end of info history

    debugHistory: 
    2022 May 23 - 12:08:02.832: Updating translationAnnotations for seq 6 #translationAnnotations=302 seqLength=279697
    2022 May 23 - 12:08:02.833: Updating translationAnnotations for seq 7 #translationAnnotations=298 seqLength=270838
    2022 May 23 - 12:08:02.835: Updating translationAnnotations for seq 8 #translationAnnotations=294 seqLength=265592
    2022 May 23 - 12:08:02.836: Updating translationAnnotations for seq 9 #translationAnnotations=272 seqLength=264373
    2022 May 23 - 12:08:02.838: Updating translationAnnotations for seq 10 #translationAnnotations=273 seqLength=250071
    2022 May 23 - 12:08:02.839: Updating translationAnnotations for seq 11 #translationAnnotations=280 seqLength=246342
    2022 May 23 - 12:08:02.841: Updating translationAnnotations for seq 12 #translationAnnotations=231 seqLength=230931
    2022 May 23 - 12:08:02.842: Updating translationAnnotations for seq 13 #translationAnnotations=254 seqLength=227377
    2022 May 23 - 12:08:02.843: Updating translationAnnotations for seq 14 #translationAnnotations=192 seqLength=210770
    2022 May 23 - 12:08:02.844: Updating translationAnnotations for seq 15 #translationAnnotations=202 seqLength=192375
    2022 May 23 - 12:08:02.845: Updating translationAnnotations for seq 16 #translationAnnotations=190 seqLength=192256
    2022 May 23 - 12:08:02.845: Updating translationAnnotations for seq 17 #translationAnnotations=180 seqLength=176682
    2022 May 23 - 12:08:02.846: Updating translationAnnotations for seq 18 #translationAnnotations=173 seqLength=176593
    2022 May 23 - 12:08:02.846: Updating translationAnnotations for seq 19 #translationAnnotations=167 seqLength=161373
    2022 May 23 - 12:08:02.847: Updating translationAnnotations for seq 20 #translationAnnotations=168 seqLength=155050
    2022 May 23 - 12:08:02.847: Updating translationAnnotations for seq 21 #translationAnnotations=168 seqLength=152083
    2022 May 23 - 12:08:02.848: Updating translationAnnotations for seq 22 #translationAnnotations=141 seqLength=149885
    2022 May 23 - 12:08:02.848: Updating translationAnnotations for seq 23 #translationAnnotations=150 seqLength=148782
    2022 May 23 - 12:08:02.849: Updating translationAnnotations for seq 24 #translationAnnotations=144 seqLength=139279
    2022 May 23 - 12:08:02.849: Updating translationAnnotations for seq 25 #translationAnnotations=138 seqLength=137462
    2022 May 23 - 12:08:02.850: Updating translationAnnotations for seq 26 #translationAnnotations=155 seqLength=136322
    2022 May 23 - 12:08:02.850: Updating translationAnnotations for seq 27 #translationAnnotations=138 seqLength=133056
    2022 May 23 - 12:08:02.851: Updating translationAnnotations for seq 28 #translationAnnotations=155 seqLength=132837
    2022 May 23 - 12:08:02.851: Updating translationAnnotations for seq 29 #translationAnnotations=134 seqLength=132643
    2022 May 23 - 12:08:02.852: Updating translationAnnotations for seq 30 #translationAnnotations=134 seqLength=125299
    2022 May 23 - 12:08:02.852: Updating translationAnnotations for seq 31 #translationAnnotations=111 seqLength=122592
    2022 May 23 - 12:08:02.852: Updating translationAnnotations for seq 32 #translationAnnotations=126 seqLength=118165
    2022 May 23 - 12:08:02.853: Updating translationAnnotations for seq 33 #translationAnnotations=113 seqLength=117999
    2022 May 23 - 12:08:02.853: Updating translationAnnotations for seq 34 #translationAnnotations=119 seqLength=117234
    2022 May 23 - 12:08:02.853: Updating translationAnnotations for seq 35 #translationAnnotations=101 seqLength=115027
    2022 May 23 - 12:08:02.854: Updating translationAnnotations for seq 36 #translationAnnotations=124 seqLength=113188
    2022 May 23 - 12:08:02.855: Updating translationAnnotations for seq 37 #translationAnnotations=104 seqLength=110457
    2022 May 23 - 12:08:02.855: Updating translationAnnotations for seq 38 #translationAnnotations=114 seqLength=107104
    2022 May 23 - 12:08:02.855: Updating translationAnnotations for seq 39 #translationAnnotations=101 seqLength=103273
    2022 May 23 - 12:08:02.856: Updating translationAnnotations for seq 41 #translationAnnotations=104 seqLength=102825
    2022 May 23 - 12:08:02.857: Updating translationAnnotations for seq 43 #translationAnnotations=124 seqLength=102621
    2022 May 23 - 12:08:02.857: Updating translationAnnotations for seq 44 #translationAnnotations=104 seqLength=97991
    2022 May 23 - 12:08:02.955: consider repopulateAnnotationOptionsNow
    2022 May 23 - 12:08:02.955: Getting active annotation types for 12 available types
    2022 May 23 - 12:08:02.955: Found 9 annotation types to show
    2022 May 23 - 12:08:02.957: Updated annotation type options, setting them selected now: true
    2022 May 23 - 12:08:02.972: Should have activated annotation options for 53,697 annotations
    2022 May 23 - 12:08:02.972: finished repopulateAnnotationOptionsNow
    2022 May 23 - 12:08:02.972: Created NucleotideSequenceViewer #Seqs=432 maxLen=467770 circAlign=0 hasSequenceListSummary=false refSeq=-1 #visibleAnnos=53697 #annos=0/0/0/53697 #selected=1 selected=99:1:44 graphs=0 #docs=1 doc=class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument name=VAN1645_assembly
    2022 May 23 - 12:08:02.972: Took 3,616 ms SequenceViewerPanel.initialize
    2022 May 23 - 12:08:03.064: Creating SequenceViewer. Active viewers=2: 4:NucleotideSequenceViewer on 1 documents for com.biomatters.plugins.annotationTableViewer.AnnotationTableViewerPlugin$1@4d463d11 name=VAN1645_assembly location=LocalDocuments/Sample Documents/Genomes/Yeasts Creation StackTrace:  at com.biomatters.iseek.gui.ViewersPanel.createViewer(ViewersPanel.java:770)
     at com.biomatters.iseek.gui.ViewersPanel.createViewerWrapper(ViewersPanel.java:633)
     at com.biomatters.iseek.gui.ViewersPanel.handleSetDocumentComplete(ViewersPanel.java:553)
     at com.biomatters.iseek.gui.bv.run(ViewersPanel.java:309)
     at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)
     at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770)
     at java.awt.EventQueue$4.run(EventQueue.java:721)
     at java.awt.EventQueue$4.run(EventQueue.java:715)
     at java.security.AccessController.doPrivileged(AccessController.java:-2)
     at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDoma...
    2022 May 23 - 12:08:03.116: Took 122 ms sort 53697 annotations do
    2022 May 23 - 12:08:03.212: mainFrameDimensionsXml=<mainFrameDimensions width="1936" height="1056" />
    2022 May 23 - 12:08:03.226: delay dialog hidden
    2022 May 23 - 12:08:03.226: delayDialogHiddenLabel=Loading annotation tracks
    2022 May 23 - 12:08:03.650: size was null -1/-1 newSize=java.awt.Dimension[width=5613358,height=44263] redrawIfChanged=true changingDimensions=0 dimensionsChanged=true viewportSize=java.awt.Dimension[width=1319,height=497] scrollBounds=java.awt.Rectangle[x=0,y=0,width=1331,height=509] scrollVert=20/true scrollHoriz=30/true
    2022 May 23 - 12:08:03.668: size was java.awt.Dimension[width=5613358,height=44263] 109/14 newSize=java.awt.Dimension[width=5613358,height=18851] redrawIfChanged=true changingDimensions=0 dimensionsChanged=true viewportSize=java.awt.Dimension[width=1319,height=497] scrollBounds=java.awt.Rectangle[x=0,y=0,width=1331,height=509] scrollVert=20/true scrollHoriz=30/true
    2022 May 23 - 12:08:03.672: scrollPositionChanged visible visibleRectangle =java.awt.Rectangle[x=144,y=14,width=1210,height=483], getBounds =java.awt.Rectangle[x=-35,y=0,width=5613249,height=18837] scroll bounds=java.awt.Rectangle[x=0,y=0,width=1331,height=509] panel getBounds=java.awt.Rectangle[x=0,y=31,width=1628,height=556]
    2022 May 23 - 12:08:03.674: scrollPositionChanged visible visibleRectangle =java.awt.Rectangle[x=144,y=14,width=1210,height=483], getBounds =java.awt.Rectangle[x=-35,y=0,width=5613249,height=18837] scroll bounds=java.awt.Rectangle[x=0,y=0,width=1331,height=509] panel getBounds=java.awt.Rectangle[x=0,y=31,width=1628,height=556]
    2022 May 23 - 12:08:03.751: For 'A' transformedOutline=java.awt.Rectangle[x=-5,y=-5,width=10,height=10] outline=java.awt.Rectangle[x=0,y=-5,width=9,height=10] baseOffsetFromCentre=5 font=java.awt.Font[family=Open Sans,name=Open Sans,style=plain,size=13] transform=AffineTransform[[1.1, 0.0, -4.52890625], [0.0, 1.0, 0.0]] context=AffineTransform[[1.0, 0.0, 0.0], [0.0, 1.0, 0.0]]/Antialiased text mode/Integer text metrics mode outline= bounds=java.awt.Rectangle[x=0,y=-5,width=9,height=10]/java.awt.geom.Rectangle2D$Float[x=0.0,y=-4.3125,w=8.234375,h=9.3125] width=9.0 type:0:[7.109375, 5.0, 0.0, 0.0, 0.0, 0.0] type:1:[5.953125, 2.046875, 0.0, 0.0, 0.0, 0.0] type:1:[2.234375, 2.046875, 0.0, 0.0, 0.0, 0.0] type:1:[1.09375, 5.0, 0.0, 0.0, 0.0, 0.0] type:1:[0.0, 5.0, 0.0, 0.0, 0.0, 0.0] type:1:[3.671875, -4.3125, 0.0, 0.0, 0.0, 0.0] type:1:[4.578125, -4.3125, 0.0, 0.0, 0.0, 0.0] type:1:[8.234375, 5.0, 0.0, 0.0, 0.0, 0.0] type:1:[7.109375, 5.0, 0.0, 0.0, 0.0, 0.0] type:4:[0.0, 0.0, 0.0, 0.0, 0.0, 0.0] type:0:[5.6...
    2022 May 23 - 12:08:03.768: For 'A' transformedOutline=java.awt.Rectangle[x=-5,y=-5,width=10,height=10] outline=java.awt.Rectangle[x=0,y=-5,width=9,height=10] baseOffsetFromCentre=5 font=java.awt.Font[family=Open Sans,name=Open Sans,style=plain,size=13] transform=AffineTransform[[1.1, 0.0, -4.52890625], [0.0, 1.0, 0.0]] context=AffineTransform[[1.0, 0.0, 0.0], [0.0, 1.0, 0.0]]/Antialiased text mode/Integer text metrics mode outline= bounds=java.awt.Rectangle[x=0,y=-5,width=9,height=10]/java.awt.geom.Rectangle2D$Float[x=0.0,y=-4.3125,w=8.234375,h=9.3125] width=9.0 type:0:[7.109375, 5.0, 0.0, 0.0, 0.0, 0.0] type:1:[5.953125, 2.046875, 0.0, 0.0, 0.0, 0.0] type:1:[2.234375, 2.046875, 0.0, 0.0, 0.0, 0.0] type:1:[1.09375, 5.0, 0.0, 0.0, 0.0, 0.0] type:1:[0.0, 5.0, 0.0, 0.0, 0.0, 0.0] type:1:[3.671875, -4.3125, 0.0, 0.0, 0.0, 0.0] type:1:[4.578125, -4.3125, 0.0, 0.0, 0.0, 0.0] type:1:[8.234375, 5.0, 0.0, 0.0, 0.0, 0.0] type:1:[7.109375, 5.0, 0.0, 0.0, 0.0, 0.0] type:4:[0.0, 0.0, 0.0, 0.0, 0.0, 0.0] type:0:[5.6...
    2022 May 23 - 12:08:03.785: For 'A' transformedOutline=java.awt.Rectangle[x=-5,y=-5,width=10,height=10] outline=java.awt.Rectangle[x=0,y=-5,width=9,height=10] baseOffsetFromCentre=5 font=java.awt.Font[family=Open Sans,name=Open Sans,style=plain,size=13] transform=AffineTransform[[1.1, 0.0, -4.52890625], [0.0, 1.0, 0.0]] context=AffineTransform[[1.0, 0.0, 0.0], [0.0, 1.0, 0.0]]/Antialiased text mode/Integer text metrics mode outline= bounds=java.awt.Rectangle[x=0,y=-5,width=9,height=10]/java.awt.geom.Rectangle2D$Float[x=0.0,y=-4.3125,w=8.234375,h=9.3125] width=9.0 type:0:[7.109375, 5.0, 0.0, 0.0, 0.0, 0.0] type:1:[5.953125, 2.046875, 0.0, 0.0, 0.0, 0.0] type:1:[2.234375, 2.046875, 0.0, 0.0, 0.0, 0.0] type:1:[1.09375, 5.0, 0.0, 0.0, 0.0, 0.0] type:1:[0.0, 5.0, 0.0, 0.0, 0.0, 0.0] type:1:[3.671875, -4.3125, 0.0, 0.0, 0.0, 0.0] type:1:[4.578125, -4.3125, 0.0, 0.0, 0.0, 0.0] type:1:[8.234375, 5.0, 0.0, 0.0, 0.0, 0.0] type:1:[7.109375, 5.0, 0.0, 0.0, 0.0, 0.0] type:4:[0.0, 0.0, 0.0, 0.0, 0.0, 0.0] type:0:[5.6...
    2022 May 23 - 12:08:03.805: Successfully loaded and registered font OpenSans-Bold.ttf
    2022 May 23 - 12:08:03.825: Slow rendering of 105 millseconds. Going into low quality mode
    2022 May 23 - 12:08:03.944: Slow rendering of 113 millseconds. Going into low quality mode
    2022 May 23 - 12:08:04.036: scrollPositionChanged visible visibleRectangle =java.awt.Rectangle[x=144,y=14,width=1210,height=483], getBounds =java.awt.Rectangle[x=-35,y=0,width=5613249,height=18837] scroll bounds=java.awt.Rectangle[x=0,y=0,width=1331,height=509] panel getBounds=java.awt.Rectangle[x=0,y=31,width=1628,height=556]
    2022 May 23 - 12:08:04.227: Delay has elapsed. Go back to high quality rendering now
    2022 May 23 - 12:08:04.633: dialogClosedXml=<dialog dialogTitle="Software Update" dialogHashCode="1811676321" dialogClosedButtonId="cancel" dialogClosedButtonLabel="Remind Me Later" />
    2022 May 23 - 12:08:05.898: menuBarActivated=File
    2022 May 23 - 12:08:06.249: menuBarActivated=New
    2022 May 23 - 12:08:07.238: menuItemButtonClicked=Create/Edit Wrapper Plugin...
    2022 May 23 - 12:08:07.362: dialogShownXml=<dialog dialogTitle="CreateEdit Wrapper Plugins" dialogHashCode="291130930" />
    2022 May 23 - 12:08:11.752: HeartbeatRequest{activationId=null,licenseStatus=Active,licenseType=SubscriptionlicenseKey=-409123041,email=965773757,machineId=dZ5GpXblGB/AjGR4j/V3Kw==,macAddresses=00155dcde7a2 00155dcde7a2 00155dcde7a2 00155dcde7a2 00155dcde7a2 58a023d0db35 58a023d0db35 58a023d0db35 58a023d0db35 58a023d0db35 58a023d0db35 58a023d0db35 58a023d0db35 8c04ba79cf21 8c04ba79cf21 8c04ba79cf21 8c04ba79cf21 8c04ba79cf21 8c04ba79cf21,version=2022.0.2,releaseLevel=full,osName=Windows 10,osVersion=10.0,computerUser=fpn,computerName=FR18-LIL-L-9786}
    2022 May 23 - 12:08:13.559: HeartbeatResponse{keyType=FLEXNET_FLOATING, licenseeName=Mathieu Clément-Ziza, companyName=Lesaffre International Corporation, segment=COMMERCIAL, modality=FLOATING, licenseStartDate=2021-06-10T00:00:00Z, licenseExpirationDate=2022-06-21T16:31:00Z, activation=null}
    2022 May 23 - 12:08:13.559: has license been updated ? false
    2022 May 23 - 12:08:13.559: Shutting down license heart-beat
    2022 May 23 - 12:08:14.372: Completed license heart-beat shutdown
    2022 May 23 - 12:08:18.064: toolbarButtonClicked=Edit...
    2022 May 23 - 12:09:01.984: dialogClosedXml=<dialog dialogTitle="CreateEdit Wrapper Plugins" dialogHashCode="291130930" dialogClosedButtonId="closeWindowButton" dialogClosedButtonLabel="" />
    2022 May 23 - 12:09:03.988: menuBarActivated=File
    2022 May 23 - 12:09:04.486: menuBarActivated=Edit
    2022 May 23 - 12:09:04.623: menuBarActivated=Sequence
    2022 May 23 - 12:09:05.739: menuBarActivated=Tools
    2022 May 23 - 12:09:06.322: subMenuActivated=Align/Assemble
    2022 May 23 - 12:09:06.672: subMenuActivated=Primers
    2022 May 23 - 12:09:06.957: subMenuActivated=Align/Assemble
    2022 May 23 - 12:09:09.417: menuItemButtonClicked=Map to Reference...
    2022 May 23 - 12:09:09.419: doing operation Map to Reference...
    2022 May 23 - 12:09:09.497: Found class com.biomatters.plugins.alignment.trimannotations.VectorTrimOptions$DatabaseOptions in class loader of plugin com.biomatters.plugins.alignment.AlignmentPlugin
    2022 May 23 - 12:09:09.498: Found class com.biomatters.plugins.alignment.vectorscreening.VectorDatabaseOptionValue in class loader of plugin com.biomatters.plugins.alignment.AlignmentPlugin
    2022 May 23 - 12:09:11.136: dialogShownXml=<dialog dialogTitle="Map to Reference" dialogHashCode="1968981708" />
    2022 May 23 - 12:09:25.094: Can't delete folder C:\Users\fpn\Geneious 2022.0 Data\transient\1653300406062\x\4
    2022 May 23 - 12:09:25.157: dialogClosedXml=<dialog dialogTitle="Map to Reference" dialogHashCode="1968981708" dialogClosedButtonId="ok" dialogClosedButtonLabel="OK" />
    2022 May 23 - 12:09:25.161: dialogOptionsXml=<root name="com.biomatters.plugins.alignment.assembly.AssemblyOptions">
      <childOptions name="data">
        <option name="groupAssemblies" class="java.lang.Boolean" isDefault="true">false</option>
        <option name="namePart" class="com.biomatters.geneious.publicapi.plugin.Options$OptionValue" isDefault="true">0</option>
        <option name="assembleListsSeparately" class="java.lang.Boolean" isDefault="true">false</option>
      </childOptions>
      <childOptions name="method">
        <childOptions name="algorithm">
          <option name="referenceAssembly" class="com.biomatters.geneious.publicapi.plugin.Options$OptionValue" isDefault="false">Fastani_Fabien_Pichon</option>
        </childOptions>
        <childOptions name="Fastani_Fabien_Pichon">
          <childOptions name="options" />
        </childOptions>
      </childOptions>
      <childOptions name="trimOptions">
        <option name="method" class="com.biomatters.geneious.publicapi.plugin.Options$OptionValue" isDefault="true">noTr...
    2022 May 23 - 12:09:25.283: Slow rendering of 91 millseconds. Going into low quality mode
    2022 May 23 - 12:09:25.377: operationStarted=<OperationManagerCallbackXml operationUniqueId="com.biomatters.plugins.alignment.AssemblyOperation_Reference" callbackHashCode="125555570" />
    2022 May 23 - 12:09:25.772: Delay has elapsed. Go back to high quality rendering now
    2022 May 23 - 12:09:26.277: progressFrameShownXml=<progressFrameXml progressFrameTitle=" - Fastani" progressFrameHashCode="732911100" />
    2022 May 23 - 12:09:26.929: Slow rendering of 85 millseconds. Going into low quality mode
    2022 May 23 - 12:09:27.232: Delay has elapsed. Go back to high quality rendering now
    2022 May 23 - 12:09:41.739: remove document
    2022 May 23 - 12:09:41.751: operationFinishedWithRuntimeExceptionOrError=<OperationManagerCallbackXml operationUniqueId="com.biomatters.plugins.alignment.AssemblyOperation_Reference" callbackHashCode="125555570" />
    2022 May 23 - 12:09:41.751: progressFrameHiddenCompletedXml=<progressFrameXml progressFrameTitle=" - Fastani" progressFrameHashCode="732911100" />
    2022 May 23 - 12:09:41.764: WARNING: Exception: java.lang.UnsupportedOperationException
        at com.biomatters.geneious.publicapi.plugin.DocumentFileImporter.importDocumentsFromMultipleFiles(DocumentFileImporter.java:343)
        at com.biomatters.geneious.publicapi.plugin.DocumentFileImporter.importDocumentsFromMultipleFilesReturningUnimported(DocumentFileImporter.java:365)
        at com.biomatters.geneious.publicapi.utilities.ImportUtilitiesImplementation.importDocuments(ImportUtilitiesImplementation.java:155)
        at com.biomatters.iseek.plugin.wrapperplugins.WrapperOperation.a(WrapperOperation.java:644)
        at com.biomatters.iseek.plugin.wrapperplugins.WrapperOperation.a(WrapperOperation.java:571)
        at com.biomatters.iseek.plugin.wrapperplugins.WrapperAssembler.assemble(WrapperAssembler.java:95)
        at com.biomatters.plugins.alignment.assembly.AssemblyOperation.performOperation(AssemblyOperation.java:528)
        at com.biomatters.iseek.plugin.operations.p.b(OperationManager.java:512)
        at com.biomatters.geneious.common.opera...
    2022 May 23 - 12:09:41.787: CommandLine: cmd.exe /c ver
    2022 May 23 - 12:09:43.528: end of debug history
    pluginList: Wrapper Plugin Creator 1.0,Mauve Plugin 1.1.3,Minimap2 2.2.0

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  • Tom Edwards

    Hi Fabien,

    Unfortunately it looks like you have run into a bug with our wrapper plugin when it tries to import multiple files at once. From what I can find looking into the code, there doesn't appear to be a workaround apart from only importing one file :(. We will endeavor to fix this bug as soon as possible and release an updated version of Geneious.

    Apologies for the problems this is causing,
    Tom

    0

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