15:42:07.081 INFO o.l.i.appstore.IgbAppServerLauncher - setPlugingManagerService START 15:42:07.082 INFO o.l.i.appstore.IgbAppServerLauncher - setPluginManagerService DONE 15:42:07.083 INFO o.l.i.appstore.IgbAppServerLauncher - activate START 15:42:07.083 INFO o.l.i.appstore.IgbAppServerLauncher - org.lorainelab.igb.plugin.manager.service.impl.PluginManagerServiceImpl@39652a30 15:42:07.084 INFO o.l.i.appstore.IgbAppServerLauncher - activate DONE 15:42:07.560 INFO c.a.igb.util.IGBTrustManager - Trusted Certificates:CN=*.bioviz.org,O=Ann Loraine,L=Concord,ST=North Carolina,C=US; CN=DigiCert TLS RSA SHA256 2020 CA1,O=DigiCert Inc,C=US 15:42:07.656 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.HomeAction. But action class com.affymetrix.igb.action.HomeAction exists with same keystroke "ctrl pressed H". Using keystroke with latest action. 15:42:08.563 INFO c.a.igb.util.IGBTrustManager - Trusted Certificates:CN=*.bioviz.org,O=Ann Loraine,L=Concord,ST=North Carolina,C=US; CN=DigiCert TLS RSA SHA256 2020 CA1,O=DigiCert Inc,C=US 15:42:08.795 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://lorainelab-quickload.scidas.org/bar/ 15:42:08.955 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://lorainelab-quickload.scidas.org/bar/synonyms.txt 15:42:08.961 INFO com.affymetrix.igb.Activator - IGB Started 15:42:09.005 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.tukaani.xz 15:42:09.005 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: affymetrix-common 15:42:09.008 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: annotation-tab 15:42:09.032 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://lorainelab-quickload.scidas.org/bar/species.txt 15:42:09.034 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://lorainelab-quickload.scidas.org/chipseq/ 15:42:09.042 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: apollo-library 15:42:09.048 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: appstore 15:42:09.055 INFO o.l.i.appstore.IgbAppServerLauncher - setPlugingManagerService START 15:42:09.055 INFO o.l.i.appstore.IgbAppServerLauncher - setPluginManagerService DONE 15:42:09.055 INFO o.l.i.appstore.IgbAppServerLauncher - activate START 15:42:09.055 INFO o.l.i.appstore.IgbAppServerLauncher - org.lorainelab.igb.plugin.manager.service.impl.PluginManagerServiceImpl@39652a30 15:42:09.056 INFO o.l.i.appstore.IgbAppServerLauncher - activate DONE 15:42:09.056 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.bai 15:42:09.065 ERROR c.a.genometry.parsers.FileTypeHolder - duplicate SymLoaderFactory for extension {0}!!! 15:42:09.065 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.bam 15:42:09.074 ERROR c.a.genometry.parsers.FileTypeHolder - duplicate SymLoaderFactory for extension {0}!!! 15:42:09.075 ERROR c.a.genometry.parsers.FileTypeHolder - duplicate SymLoaderFactory for extension {0}!!! 15:42:09.076 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.bed 15:42:09.082 ERROR c.a.genometry.parsers.FileTypeHolder - duplicate SymLoaderFactory for extension {0}!!! 15:42:09.083 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: bigBedHandler 15:42:09.090 ERROR c.a.genometry.parsers.FileTypeHolder - duplicate SymLoaderFactory for extension {0}!!! 15:42:09.090 ERROR c.a.genometry.parsers.FileTypeHolder - duplicate SymLoaderFactory for extension {0}!!! 15:42:09.090 ERROR c.a.genometry.parsers.FileTypeHolder - duplicate SymLoaderFactory for extension {0}!!! 15:42:09.090 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: bigWigHandler 15:42:09.096 ERROR c.a.genometry.parsers.FileTypeHolder - duplicate SymLoaderFactory for extension {0}!!! 15:42:09.097 ERROR c.a.genometry.parsers.FileTypeHolder - duplicate SymLoaderFactory for extension {0}!!! 15:42:09.097 ERROR c.a.genometry.parsers.FileTypeHolder - duplicate SymLoaderFactory for extension {0}!!! 15:42:09.097 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: bookmark 15:42:09.117 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.bookmarks.action.AddBookmarkAction. But action class com.affymetrix.igb.bookmarks.action.AddBookmarkAction exists with same keystroke "ctrl pressed D". Using keystroke with latest action. 15:42:09.193 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.cache 15:42:09.194 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://lorainelab-quickload.scidas.org/chipseq/synonyms.txt 15:42:09.215 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.cache-api 15:42:09.217 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: console-tab 15:42:09.226 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: context-menu-service 15:42:09.231 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: das 15:42:09.237 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.external-sort 15:42:09.241 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: externalView 15:42:09.251 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://lorainelab-quickload.scidas.org/chipseq/species.txt 15:42:09.255 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server https://bioviz.org/quickload/genome-in-a-bottle/ 15:42:09.316 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.feedback 15:42:09.365 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: frameManager 15:42:09.375 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: genometry 15:42:09.431 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.genotyping 15:42:09.439 ERROR c.a.genometry.parsers.FileTypeHolder - duplicate SymLoaderFactory for extension {0}!!! 15:42:09.439 ERROR c.a.genometry.parsers.FileTypeHolder - duplicate SymLoaderFactory for extension {0}!!! 15:42:09.443 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: graphTab 15:42:09.468 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: heatmap-editor 15:42:09.471 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb 15:42:09.500 INFO c.a.igb.IgbServiceDependencyManager - AnnotationContextMenuRegistryI now available. 15:42:09.501 INFO c.a.igb.IgbServiceDependencyManager - ChromosomeSynonymLookupService now available. 15:42:09.501 INFO c.a.igb.IgbServiceDependencyManager - FrameManagerService now available. 15:42:09.501 INFO c.a.igb.IgbServiceDependencyManager - GenomeVersionSynonymLookupService now available. 15:42:09.501 INFO c.a.igb.IgbServiceDependencyManager - QuickloadFactory now available. 15:42:09.502 INFO c.a.igb.IgbServiceDependencyManager - SpeciesSynonymLookupService now available. 15:42:09.502 INFO c.a.igb.IgbServiceDependencyManager - Window Service now available. 15:42:09.502 INFO c.a.igb.IgbServiceDependencyManager - Igb Module Service Dependencies are now available. 15:42:09.570 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from https://bioviz.org/quickload/genome-in-a-bottle/synonyms.txt 15:42:09.650 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.ZoomOutXAction. But action class com.affymetrix.igb.action.ZoomOutXAction exists with same keystroke "shift ctrl pressed LEFT". Using keystroke with latest action. 15:42:09.652 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.ZoomInXAction. But action class com.affymetrix.igb.action.ZoomInXAction exists with same keystroke "shift ctrl pressed RIGHT". Using keystroke with latest action. 15:42:09.653 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.RefreshDataAction. But action class com.affymetrix.igb.action.RefreshDataAction exists with same keystroke "ctrl pressed R". Using keystroke with latest action. 15:42:09.657 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.ZoomOutYAction. But action class com.affymetrix.igb.action.ZoomOutYAction exists with same keystroke "shift ctrl pressed UP". Using keystroke with latest action. 15:42:09.659 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.ZoomInYAction. But action class com.affymetrix.igb.action.ZoomInYAction exists with same keystroke "shift ctrl pressed DOWN". Using keystroke with latest action. 15:42:09.668 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: https://bioviz.org/quickload/genome-in-a-bottle/species.txt 15:42:09.676 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.HomeAction. But action class com.affymetrix.igb.action.HomeAction exists with same keystroke "ctrl pressed H". Using keystroke with latest action. 15:42:09.704 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.HomeAction. But action class com.affymetrix.igb.action.HomeAction exists with same keystroke "ctrl pressed H". Using keystroke with latest action. 15:42:09.706 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.HomeAction. But action class com.affymetrix.igb.action.HomeAction exists with same keystroke "ctrl pressed H". Using keystroke with latest action. 15:42:09.739 INFO o.l.i.appstore.IgbAppServerLauncher - Started REST endpoint. 15:42:09.914 ERROR o.l.i.appstore.IgbAppServerLauncher - Could not start REST endpoint. 15:42:09.915 ERROR c.a.i.bookmarks.SimpleBookmarkServer - Could not start bookmark server, turning off IGB's URL-based control features. 15:42:09.977 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://igbquickload.org/rnaseq/ 15:42:10.188 INFO c.a.i.p.IgbPreferencesLoadingOrchestrator - Loading server preferences from the Java preferences subsystem 15:42:10.189 INFO c.a.i.p.IgbPreferencesLoadingOrchestrator - Completed loading server preferences from the Java preferences subsystem 15:42:10.279 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.LoadFileAction. But action class com.affymetrix.igb.action.LoadFileAction exists with same keystroke "ctrl pressed O". Using keystroke with latest action. 15:42:10.282 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.shared.LoadURLAction. But action class com.affymetrix.igb.shared.LoadURLAction exists with same keystroke "shift ctrl pressed O". Using keystroke with latest action. 15:42:10.283 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.ExportFileAction. But action class com.affymetrix.igb.action.ExportFileAction exists with same keystroke "ctrl pressed S". Using keystroke with latest action. 15:42:10.285 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.PreferencesAction. But action class com.affymetrix.igb.action.PreferencesAction exists with same keystroke "alt pressed P". Using keystroke with latest action. 15:42:10.288 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.ExitAction. But action class com.affymetrix.igb.action.ExitAction exists with same keystroke "ctrl pressed Q". Using keystroke with latest action. 15:42:10.290 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.CopyResiduesAction. But action class com.affymetrix.igb.action.CopyResiduesAction exists with same keystroke "ctrl pressed C". Using keystroke with latest action. 15:42:10.291 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.shared.SelectAllAction. But action class com.affymetrix.igb.shared.SelectAllAction exists with same keystroke "ctrl pressed A". Using keystroke with latest action. 15:42:10.295 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://igbquickload.org/rnaseq/synonyms.txt 15:42:10.323 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.DocumentationAction. But action class com.affymetrix.igb.action.DocumentationAction exists with same keystroke "pressed F1". Using keystroke with latest action. 15:42:10.356 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://igbquickload.org/rnaseq/species.txt Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at com.google.common.base.Preconditions.checkNotNull(Preconditions.java:213) at com.google.common.collect.SingletonImmutableSet.(SingletonImmutableSet.java:47) at com.google.common.collect.ImmutableSet.of(ImmutableSet.java:94) at com.google.common.collect.ImmutableSet.construct(ImmutableSet.java:185) at com.google.common.collect.ImmutableSet.copyOf(ImmutableSet.java:375) at com.affymetrix.igb.view.load.GeneralLoadUtils.getLoadedSpeciesNames(GeneralLoadUtils.java:188) at com.affymetrix.igb.view.load.GeneralLoadUtils.retrieveDataContainer(GeneralLoadUtils.java:167) at com.affymetrix.igb.general.DataProviderManager.loadSupportedGenomeVersions(DataProviderManager.java:451) at com.affymetrix.igb.general.DataProviderManager.initializeDataProvider(DataProviderManager.java:339) at com.affymetrix.igb.general.DataProviderManager.lambda$addDataProvider$70(DataProviderManager.java:324) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) 15:42:10.477 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://igbquickload.org/quickload/ Aug 02, 2022 3:42:10 PM com.google.common.eventbus.EventBus$LoggingSubscriberExceptionHandler handleException SEVERE: Could not dispatch event: com.affymetrix.igb.view.SeqGroupView@14bd523b to public void com.affymetrix.igb.view.SeqGroupView.dataProviderInit(com.affymetrix.igb.general.DataProviderManager$DataProviderServiceChangeEvent) 15:42:10.909 INFO com.affymetrix.igb.Activator - Verifying Jidesoft license 15:42:10.910 INFO com.affymetrix.igb.Activator - Starting IGB 15:42:10.911 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.LoadFileAction. But action class com.affymetrix.igb.action.LoadFileAction exists with same keystroke "ctrl pressed O". Using keystroke with latest action. 15:42:10.912 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.ZoomInXAction. But action class com.affymetrix.igb.action.ZoomInXAction exists with same keystroke "shift ctrl pressed RIGHT". Using keystroke with latest action. 15:42:10.912 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.RefreshDataAction. But action class com.affymetrix.igb.action.RefreshDataAction exists with same keystroke "ctrl pressed R". Using keystroke with latest action. 15:42:10.912 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.ScrollDownAction. But action class com.affymetrix.igb.action.ScrollDownAction exists with same keystroke "ctrl pressed DOWN". Using keystroke with latest action. 15:42:10.912 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.ZoomInYAction. But action class com.affymetrix.igb.action.ZoomInYAction exists with same keystroke "shift ctrl pressed DOWN". Using keystroke with latest action. 15:42:10.913 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.ZoomOutXAction. But action class com.affymetrix.igb.action.ZoomOutXAction exists with same keystroke "shift ctrl pressed LEFT". Using keystroke with latest action. 15:42:10.913 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.bookmarks.action.AddBookmarkAction. But action class com.affymetrix.igb.bookmarks.action.AddBookmarkAction exists with same keystroke "ctrl pressed D". Using keystroke with latest action. 15:42:10.914 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.shared.LoadURLAction. But action class com.affymetrix.igb.shared.LoadURLAction exists with same keystroke "shift ctrl pressed O". Using keystroke with latest action. 15:42:10.915 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.ScrollLeftAction. But action class com.affymetrix.igb.action.ScrollLeftAction exists with same keystroke "ctrl pressed LEFT". Using keystroke with latest action. 15:42:10.915 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.ZoomOutYAction. But action class com.affymetrix.igb.action.ZoomOutYAction exists with same keystroke "shift ctrl pressed UP". Using keystroke with latest action. 15:42:10.916 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.shared.SelectAllAction. But action class com.affymetrix.igb.shared.SelectAllAction exists with same keystroke "ctrl pressed A". Using keystroke with latest action. 15:42:10.916 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.CopyResiduesAction. But action class com.affymetrix.igb.action.CopyResiduesAction exists with same keystroke "ctrl pressed C". Using keystroke with latest action. 15:42:10.917 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.DocumentationAction. But action class com.affymetrix.igb.action.DocumentationAction exists with same keystroke "pressed F1". Using keystroke with latest action. 15:42:10.917 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.ExportFileAction. But action class com.affymetrix.igb.action.ExportFileAction exists with same keystroke "ctrl pressed S". Using keystroke with latest action. 15:42:10.918 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.PreferencesAction. But action class com.affymetrix.igb.action.PreferencesAction exists with same keystroke "alt pressed P". Using keystroke with latest action. 15:42:10.919 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.ScrollRightAction. But action class com.affymetrix.igb.action.ScrollRightAction exists with same keystroke "ctrl pressed RIGHT". Using keystroke with latest action. 15:42:10.919 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.ScrollUpAction. But action class com.affymetrix.igb.action.ScrollUpAction exists with same keystroke "ctrl pressed UP". Using keystroke with latest action. 15:42:10.920 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.ExitAction. But action class com.affymetrix.igb.action.ExitAction exists with same keystroke "ctrl pressed Q". Using keystroke with latest action. 15:42:10.920 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.HomeAction. But action class com.affymetrix.igb.action.HomeAction exists with same keystroke "ctrl pressed H". Using keystroke with latest action. 15:42:10.928 INFO com.affymetrix.igb.IGB - Starting: Integrated Genome Browser 9.1.10 15:42:10.928 INFO com.affymetrix.igb.IGB - Java version: 1.8.0_332 from Azul Systems, Inc. 15:42:10.929 INFO com.affymetrix.igb.IGB - System memory: 3.8 GB Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at com.google.common.base.Preconditions.checkNotNull(Preconditions.java:213) at com.google.common.collect.SingletonImmutableSet.(SingletonImmutableSet.java:47) at com.google.common.collect.ImmutableSet.of(ImmutableSet.java:94) at com.google.common.collect.ImmutableSet.construct(ImmutableSet.java:185) at com.google.common.collect.ImmutableSet.copyOf(ImmutableSet.java:375) at com.affymetrix.igb.view.load.GeneralLoadUtils.getLoadedSpeciesNames(GeneralLoadUtils.java:188) at com.affymetrix.igb.view.load.GeneralLoadUtils.retrieveDataContainer(GeneralLoadUtils.java:167) at com.affymetrix.igb.general.DataProviderManager.loadSupportedGenomeVersions(DataProviderManager.java:451) at com.affymetrix.igb.general.DataProviderManager.initializeDataProvider(DataProviderManager.java:339) at com.affymetrix.igb.general.DataProviderManager.lambda$addDataProvider$70(DataProviderManager.java:324) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) 15:42:11.200 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://lorainelab-quickload.scidas.org/blueberry/ 15:42:11.314 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.ScrollUpAction. But action class com.affymetrix.igb.action.ScrollUpAction exists with same keystroke "ctrl pressed UP". Using keystroke with latest action. 15:42:11.314 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.ScrollUpAction. But action class com.affymetrix.igb.action.ScrollUpAction exists with same keystroke "ctrl pressed UP". Using keystroke with latest action. 15:42:11.315 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.ScrollDownAction. But action class com.affymetrix.igb.action.ScrollDownAction exists with same keystroke "ctrl pressed DOWN". Using keystroke with latest action. 15:42:11.315 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.ScrollDownAction. But action class com.affymetrix.igb.action.ScrollDownAction exists with same keystroke "ctrl pressed DOWN". Using keystroke with latest action. 15:42:11.316 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.ScrollLeftAction. But action class com.affymetrix.igb.action.ScrollLeftAction exists with same keystroke "ctrl pressed LEFT". Using keystroke with latest action. 15:42:11.316 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.ScrollLeftAction. But action class com.affymetrix.igb.action.ScrollLeftAction exists with same keystroke "ctrl pressed LEFT". Using keystroke with latest action. 15:42:11.318 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.ScrollRightAction. But action class com.affymetrix.igb.action.ScrollRightAction exists with same keystroke "ctrl pressed RIGHT". Using keystroke with latest action. 15:42:11.318 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.ScrollRightAction. But action class com.affymetrix.igb.action.ScrollRightAction exists with same keystroke "ctrl pressed RIGHT". Using keystroke with latest action. 15:42:11.343 ERROR c.a.i.bookmarks.SimpleBookmarkServer - Couldn't find an available port for IGB to listen to control requests on port 7085! Turning off IGB's URL-based control features 15:42:11.344 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.bookmarks.action.AddBookmarkAction. But action class com.affymetrix.igb.bookmarks.action.AddBookmarkAction exists with same keystroke "ctrl pressed D". Using keystroke with latest action. 15:42:11.344 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.bookmarks.action.AddBookmarkAction. But action class com.affymetrix.igb.bookmarks.action.AddBookmarkAction exists with same keystroke "ctrl pressed D". Using keystroke with latest action. 15:42:11.364 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://lorainelab-quickload.scidas.org/blueberry/synonyms.txt 15:42:11.405 INFO c.a.igb.util.IGBTrustManager - Authenticated CN=DigiCert TLS RSA SHA256 2020 CA1,O=DigiCert Inc,C=US,CN=DigiCert Global Root CA,OU=www.digicert.com,O=DigiCert Inc,C=US, certificates using default trust store 15:42:11.420 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://lorainelab-quickload.scidas.org/blueberry/species.txt Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at com.google.common.base.Preconditions.checkNotNull(Preconditions.java:213) at com.google.common.collect.SingletonImmutableSet.(SingletonImmutableSet.java:47) at com.google.common.collect.ImmutableSet.of(ImmutableSet.java:94) at com.google.common.collect.ImmutableSet.construct(ImmutableSet.java:185) at com.google.common.collect.ImmutableSet.copyOf(ImmutableSet.java:375) at com.affymetrix.igb.view.load.GeneralLoadUtils.getLoadedSpeciesNames(GeneralLoadUtils.java:188) at com.affymetrix.igb.view.load.GeneralLoadUtils.retrieveDataContainer(GeneralLoadUtils.java:167) at com.affymetrix.igb.general.DataProviderManager.loadSupportedGenomeVersions(DataProviderManager.java:451) at com.affymetrix.igb.general.DataProviderManager.initializeDataProvider(DataProviderManager.java:339) at com.affymetrix.igb.general.DataProviderManager.lambda$addDataProvider$70(DataProviderManager.java:324) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) 15:42:11.530 INFO c.a.igb.util.IGBTrustManager - Authenticated CN=DigiCert TLS RSA SHA256 2020 CA1,O=DigiCert Inc,C=US,CN=DigiCert Global Root CA,OU=www.digicert.com,O=DigiCert Inc,C=US, certificates using default trust store Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at com.google.common.base.Preconditions.checkNotNull(Preconditions.java:213) at com.google.common.collect.SingletonImmutableSet.(SingletonImmutableSet.java:47) 15:42:11.683 INFO com.affymetrix.igb.Activator - IGB Started at com.google.common.collect.ImmutableSet.of(ImmutableSet.java:94) 15:42:11.683 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-genoviz-extensions at com.google.common.collect.ImmutableSet.construct(ImmutableSet.java:185) at com.google.common.collect.ImmutableSet.copyOf(ImmutableSet.java:375) at com.affymetrix.igb.view.load.GeneralLoadUtils.getLoadedSpeciesNames(GeneralLoadUtils.java:188) at com.affymetrix.igb.view.load.GeneralLoadUtils.retrieveDataContainer(GeneralLoadUtils.java:167) at com.affymetrix.igb.general.DataProviderManager.loadSupportedGenomeVersions(DataProviderManager.java:451) at com.affymetrix.igb.general.DataProviderManager.initializeDataProvider(DataProviderManager.java:339) at com.affymetrix.igb.general.DataProviderManager.lambda$addDataProvider$70(DataProviderManager.java:324) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) 15:42:11.687 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://lorainelab-quickload.scidas.org/bar/ 15:42:11.688 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-javafx-util 15:42:11.691 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-preferences 15:42:11.714 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-services 15:42:11.717 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igbScript 15:42:11.727 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igbSwingExt 15:42:11.730 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: image-exporter 15:42:11.827 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://lorainelab-quickload.scidas.org/bar/synonyms.txt 15:42:11.838 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: keyWordSearch 15:42:11.843 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: keybinding-registry 15:42:11.896 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://lorainelab-quickload.scidas.org/bar/species.txt Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at com.google.common.base.Preconditions.checkNotNull(Preconditions.java:213) at com.google.common.collect.SingletonImmutableSet.(SingletonImmutableSet.java:47) at com.google.common.collect.ImmutableSet.of(ImmutableSet.java:94) at com.google.common.collect.ImmutableSet.construct(ImmutableSet.java:185) at com.google.common.collect.ImmutableSet.copyOf(ImmutableSet.java:375) at com.affymetrix.igb.view.load.GeneralLoadUtils.getLoadedSpeciesNames(GeneralLoadUtils.java:188) at com.affymetrix.igb.view.load.GeneralLoadUtils.retrieveDataContainer(GeneralLoadUtils.java:167) at com.affymetrix.igb.general.DataProviderManager.loadSupportedGenomeVersions(DataProviderManager.java:451) at com.affymetrix.igb.general.DataProviderManager.initializeDataProvider(DataProviderManager.java:339) at com.affymetrix.igb.general.DataProviderManager.lambda$addDataProvider$70(DataProviderManager.java:324) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) 15:42:11.900 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://lorainelab-quickload.scidas.org/chipseq/ 15:42:11.995 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.logging-config 15:42:11.995 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.narrowpeak 15:42:11.999 ERROR c.a.genometry.parsers.FileTypeHolder - duplicate SymLoaderFactory for extension {0}!!! 15:42:11.999 ERROR c.a.genometry.parsers.FileTypeHolder - duplicate SymLoaderFactory for extension {0}!!! 15:42:11.999 ERROR c.a.genometry.parsers.FileTypeHolder - duplicate SymLoaderFactory for extension {0}!!! 15:42:11.999 ERROR c.a.genometry.parsers.FileTypeHolder - duplicate SymLoaderFactory for extension {0}!!! 15:42:12.000 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: ncbiBlast 15:42:12.006 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.error.reporter.manager 15:42:12.008 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.menu.api 15:42:12.011 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: paired-data-preprocessor 15:42:12.014 INFO o.l.i.p.PairedReadPreprocessor - Initializaing PairedReadPreprocessor 15:42:12.015 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.plugins-manager 15:42:12.070 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://lorainelab-quickload.scidas.org/chipseq/synonyms.txt 15:42:12.128 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://lorainelab-quickload.scidas.org/chipseq/species.txt Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at com.google.common.base.Preconditions.checkNotNull(Preconditions.java:213) at com.google.common.collect.SingletonImmutableSet.(SingletonImmutableSet.java:47) at com.google.common.collect.ImmutableSet.of(ImmutableSet.java:94) at com.google.common.collect.ImmutableSet.construct(ImmutableSet.java:185) at com.google.common.collect.ImmutableSet.copyOf(ImmutableSet.java:375) at com.affymetrix.igb.view.load.GeneralLoadUtils.getLoadedSpeciesNames(GeneralLoadUtils.java:188) at com.affymetrix.igb.view.load.GeneralLoadUtils.retrieveDataContainer(GeneralLoadUtils.java:167) at com.affymetrix.igb.general.DataProviderManager.loadSupportedGenomeVersions(DataProviderManager.java:451) at com.affymetrix.igb.general.DataProviderManager.initializeDataProvider(DataProviderManager.java:339) at com.affymetrix.igb.general.DataProviderManager.lambda$addDataProvider$70(DataProviderManager.java:324) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) 15:42:12.132 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server https://bioviz.org/quickload/genome-in-a-bottle/ 15:42:12.427 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from https://bioviz.org/quickload/genome-in-a-bottle/synonyms.txt 15:42:12.553 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: https://bioviz.org/quickload/genome-in-a-bottle/species.txt Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at com.google.common.base.Preconditions.checkNotNull(Preconditions.java:213) at com.google.common.collect.SingletonImmutableSet.(SingletonImmutableSet.java:47) at com.google.common.collect.ImmutableSet.of(ImmutableSet.java:94) at com.google.common.collect.ImmutableSet.construct(ImmutableSet.java:185) at com.google.common.collect.ImmutableSet.copyOf(ImmutableSet.java:375) at com.affymetrix.igb.view.load.GeneralLoadUtils.getLoadedSpeciesNames(GeneralLoadUtils.java:188) at com.affymetrix.igb.view.load.GeneralLoadUtils.retrieveDataContainer(GeneralLoadUtils.java:167) at com.affymetrix.igb.general.DataProviderManager.loadSupportedGenomeVersions(DataProviderManager.java:451) at com.affymetrix.igb.general.DataProviderManager.initializeDataProvider(DataProviderManager.java:339) at com.affymetrix.igb.general.DataProviderManager.lambda$addDataProvider$70(DataProviderManager.java:324) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) 15:42:12.850 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://igbquickload.org/rnaseq/ 15:42:13.134 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://igbquickload.org/rnaseq/synonyms.txt 15:42:13.192 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://igbquickload.org/rnaseq/species.txt Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at com.google.common.base.Preconditions.checkNotNull(Preconditions.java:213) at com.google.common.collect.SingletonImmutableSet.(SingletonImmutableSet.java:47) at com.google.common.collect.ImmutableSet.of(ImmutableSet.java:94) at com.google.common.collect.ImmutableSet.construct(ImmutableSet.java:185) at com.google.common.collect.ImmutableSet.copyOf(ImmutableSet.java:375) at com.affymetrix.igb.view.load.GeneralLoadUtils.getLoadedSpeciesNames(GeneralLoadUtils.java:188) at com.affymetrix.igb.view.load.GeneralLoadUtils.retrieveDataContainer(GeneralLoadUtils.java:167) at com.affymetrix.igb.general.DataProviderManager.loadSupportedGenomeVersions(DataProviderManager.java:451) at com.affymetrix.igb.general.DataProviderManager.initializeDataProvider(DataProviderManager.java:339) at com.affymetrix.igb.general.DataProviderManager.lambda$addDataProvider$70(DataProviderManager.java:324) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) 15:42:13.275 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://igbquickload.org/rnaseq/ 15:42:13.328 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: propertyView 15:42:13.339 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: quickload 15:42:13.345 INFO c.a.igb.util.IGBTrustManager - Authenticated CN=DigiCert TLS RSA SHA256 2020 CA1,O=DigiCert Inc,C=US,CN=DigiCert Global Root CA,OU=www.digicert.com,O=DigiCert Inc,C=US, certificates using default trust store 15:42:13.347 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: restrictionSites 15:42:13.356 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: searchModelIdOrProps 15:42:13.364 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: searchView 15:42:13.391 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: sequenceViewer 15:42:13.584 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://igbquickload.org/rnaseq/synonyms.txt 15:42:13.644 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://igbquickload.org/rnaseq/species.txt 15:42:13.687 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: session-manager 15:42:13.689 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://igbquickload.org/quickload/ 15:42:13.835 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: shared-lib-wrapper 15:42:13.841 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: survey 15:42:14.063 INFO c.a.igb.util.IGBTrustManager - Authenticated CN=DigiCert TLS RSA SHA256 2020 CA1,O=DigiCert Inc,C=US,CN=DigiCert Global Root CA,OU=www.digicert.com,O=DigiCert Inc,C=US, certificates using default trust store 15:42:14.067 INFO c.a.igb.util.IGBTrustManager - Authenticated CN=DigiCert TLS RSA SHA256 2020 CA1,O=DigiCert Inc,C=US,CN=DigiCert Global Root CA,OU=www.digicert.com,O=DigiCert Inc,C=US, certificates using default trust store 15:42:14.121 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: synonym-lookup 15:42:14.128 ERROR c.a.i.bookmarks.SimpleBookmarkServer - Couldn't find an available port for IGB to listen to control requests on port 7085! Turning off IGB's URL-based control features 15:42:14.129 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.bookmarks.action.AddBookmarkAction. But action class com.affymetrix.igb.bookmarks.action.AddBookmarkAction exists with same keystroke "ctrl pressed D". Using keystroke with latest action. 15:42:14.129 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.bookmarks.action.AddBookmarkAction. But action class com.affymetrix.igb.bookmarks.action.AddBookmarkAction exists with same keystroke "ctrl pressed D". Using keystroke with latest action. 15:42:14.142 ERROR c.a.i.bookmarks.SimpleBookmarkServer - Couldn't find an available port for IGB to listen to control requests on port 7085! Turning off IGB's URL-based control features 15:42:14.144 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.bookmarks.action.AddBookmarkAction. But action class com.affymetrix.igb.bookmarks.action.AddBookmarkAction exists with same keystroke "ctrl pressed D". Using keystroke with latest action. 15:42:14.144 WARN com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.bookmarks.action.AddBookmarkAction. But action class com.affymetrix.igb.bookmarks.action.AddBookmarkAction exists with same keystroke "ctrl pressed D". Using keystroke with latest action. 15:42:14.156 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: thresholding Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at com.google.common.base.Preconditions.checkNotNull(Preconditions.java:213) at com.google.common.collect.SingletonImmutableSet.(SingletonImmutableSet.java:47) at com.google.common.collect.ImmutableSet.of(ImmutableSet.java:94) at com.google.common.collect.ImmutableSet.construct(ImmutableSet.java:185) at com.google.common.collect.ImmutableSet.copyOf(ImmutableSet.java:375) at com.affymetrix.igb.view.load.GeneralLoadUtils.getLoadedSpeciesNames(GeneralLoadUtils.java:188) at com.affymetrix.igb.view.load.GeneralLoadUtils.retrieveDataContainer(GeneralLoadUtils.java:167) at com.affymetrix.igb.general.DataProviderManager.loadSupportedGenomeVersions(DataProviderManager.java:451) at com.affymetrix.igb.general.DataProviderManager.initializeDataProvider(DataProviderManager.java:339) at com.affymetrix.igb.general.DataProviderManager.lambda$addDataProvider$70(DataProviderManager.java:324) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) 15:42:14.428 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: track-operations-panel at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) 15:42:14.429 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://igbquickload.org/quickload/ 15:42:14.447 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: update 15:42:14.531 INFO c.a.igb.util.IGBTrustManager - Authenticated CN=DigiCert TLS RSA SHA256 2020 CA1,O=DigiCert Inc,C=US,CN=DigiCert Global Root CA,OU=www.digicert.com,O=DigiCert Inc,C=US, certificates using default trust store 15:42:14.597 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: weblinks 15:42:14.903 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: window-service 15:42:14.911 [main] INFO com.affymetrix.main.OSGiHandler - OSGi is started with org.apache.felix.framework version 5.2.0 15:42:15.158 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://lorainelab-quickload.scidas.org/blueberry/ 15:42:15.304 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://lorainelab-quickload.scidas.org/blueberry/synonyms.txt 15:42:15.360 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://lorainelab-quickload.scidas.org/blueberry/species.txt Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at com.google.common.base.Preconditions.checkNotNull(Preconditions.java:213) at com.google.common.collect.SingletonImmutableSet.(SingletonImmutableSet.java:47) at com.google.common.collect.ImmutableSet.of(ImmutableSet.java:94) at com.google.common.collect.ImmutableSet.construct(ImmutableSet.java:185) at com.google.common.collect.ImmutableSet.copyOf(ImmutableSet.java:375) at com.affymetrix.igb.view.load.GeneralLoadUtils.getLoadedSpeciesNames(GeneralLoadUtils.java:188) at com.affymetrix.igb.view.load.GeneralLoadUtils.retrieveDataContainer(GeneralLoadUtils.java:167) at com.affymetrix.igb.general.DataProviderManager.loadSupportedGenomeVersions(DataProviderManager.java:451) at com.affymetrix.igb.general.DataProviderManager.initializeDataProvider(DataProviderManager.java:339) at com.affymetrix.igb.general.DataProviderManager.lambda$addDataProvider$70(DataProviderManager.java:324) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) 15:42:15.364 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://lorainelab-quickload.scidas.org/blueberry/ 15:42:15.529 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://lorainelab-quickload.scidas.org/blueberry/synonyms.txt 15:42:15.588 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://lorainelab-quickload.scidas.org/blueberry/species.txt Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at com.google.common.base.Preconditions.checkNotNull(Preconditions.java:213) at com.google.common.collect.SingletonImmutableSet.(SingletonImmutableSet.java:47) at com.google.common.collect.ImmutableSet.of(ImmutableSet.java:94) at com.google.common.collect.ImmutableSet.construct(ImmutableSet.java:185) at com.google.common.collect.ImmutableSet.copyOf(ImmutableSet.java:375) at com.affymetrix.igb.view.load.GeneralLoadUtils.getLoadedSpeciesNames(GeneralLoadUtils.java:188) at com.affymetrix.igb.view.load.GeneralLoadUtils.retrieveDataContainer(GeneralLoadUtils.java:167) at com.affymetrix.igb.general.DataProviderManager.loadSupportedGenomeVersions(DataProviderManager.java:451) at com.affymetrix.igb.general.DataProviderManager.initializeDataProvider(DataProviderManager.java:339) at com.affymetrix.igb.general.DataProviderManager.lambda$addDataProvider$70(DataProviderManager.java:324) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) 15:42:16.167 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://lorainelab-quickload.scidas.org/bar/ 15:42:16.314 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://lorainelab-quickload.scidas.org/bar/synonyms.txt 15:42:16.369 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://lorainelab-quickload.scidas.org/bar/species.txt Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at com.google.common.base.Preconditions.checkNotNull(Preconditions.java:213) at com.google.common.collect.SingletonImmutableSet.(SingletonImmutableSet.java:47) at com.google.common.collect.ImmutableSet.of(ImmutableSet.java:94) at com.google.common.collect.ImmutableSet.construct(ImmutableSet.java:185) at com.google.common.collect.ImmutableSet.copyOf(ImmutableSet.java:375) at com.affymetrix.igb.view.load.GeneralLoadUtils.getLoadedSpeciesNames(GeneralLoadUtils.java:188) at com.affymetrix.igb.view.load.GeneralLoadUtils.retrieveDataContainer(GeneralLoadUtils.java:167) at com.affymetrix.igb.general.DataProviderManager.loadSupportedGenomeVersions(DataProviderManager.java:451) at com.affymetrix.igb.general.DataProviderManager.initializeDataProvider(DataProviderManager.java:339) at com.affymetrix.igb.general.DataProviderManager.lambda$addDataProvider$70(DataProviderManager.java:324) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) 15:42:16.374 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://lorainelab-quickload.scidas.org/bar/ 15:42:16.527 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://lorainelab-quickload.scidas.org/bar/synonyms.txt 15:42:17.104 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://lorainelab-quickload.scidas.org/bar/species.txt 15:42:17.112 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://lorainelab-quickload.scidas.org/chipseq/ 15:42:18.164 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://lorainelab-quickload.scidas.org/chipseq/synonyms.txt 15:42:18.225 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://lorainelab-quickload.scidas.org/chipseq/species.txt Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at com.google.common.base.Preconditions.checkNotNull(Preconditions.java:213) at com.google.common.collect.SingletonImmutableSet.(SingletonImmutableSet.java:47) at com.google.common.collect.ImmutableSet.of(ImmutableSet.java:94) at com.google.common.collect.ImmutableSet.construct(ImmutableSet.java:185) at com.google.common.collect.ImmutableSet.copyOf(ImmutableSet.java:375) at com.affymetrix.igb.view.load.GeneralLoadUtils.getLoadedSpeciesNames(GeneralLoadUtils.java:188) at com.affymetrix.igb.view.load.GeneralLoadUtils.retrieveDataContainer(GeneralLoadUtils.java:167) at com.affymetrix.igb.general.DataProviderManager.loadSupportedGenomeVersions(DataProviderManager.java:451) at com.affymetrix.igb.general.DataProviderManager.initializeDataProvider(DataProviderManager.java:339) at com.affymetrix.igb.general.DataProviderManager.lambda$addDataProvider$70(DataProviderManager.java:324) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) 15:42:18.229 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://lorainelab-quickload.scidas.org/chipseq/ 15:42:18.378 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://lorainelab-quickload.scidas.org/chipseq/synonyms.txt 15:42:19.151 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://lorainelab-quickload.scidas.org/chipseq/species.txt 15:42:19.156 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server https://bioviz.org/quickload/genome-in-a-bottle/ 15:42:19.467 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from https://bioviz.org/quickload/genome-in-a-bottle/synonyms.txt 15:42:19.605 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: https://bioviz.org/quickload/genome-in-a-bottle/species.txt Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at com.google.common.base.Preconditions.checkNotNull(Preconditions.java:213) at com.google.common.collect.SingletonImmutableSet.(SingletonImmutableSet.java:47) at com.google.common.collect.ImmutableSet.of(ImmutableSet.java:94) at com.google.common.collect.ImmutableSet.construct(ImmutableSet.java:185) at com.google.common.collect.ImmutableSet.copyOf(ImmutableSet.java:375) at com.affymetrix.igb.view.load.GeneralLoadUtils.getLoadedSpeciesNames(GeneralLoadUtils.java:188) at com.affymetrix.igb.view.load.GeneralLoadUtils.retrieveDataContainer(GeneralLoadUtils.java:167) at com.affymetrix.igb.general.DataProviderManager.loadSupportedGenomeVersions(DataProviderManager.java:451) at com.affymetrix.igb.general.DataProviderManager.initializeDataProvider(DataProviderManager.java:339) at com.affymetrix.igb.general.DataProviderManager.lambda$addDataProvider$70(DataProviderManager.java:324) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) 15:42:19.607 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server https://bioviz.org/quickload/genome-in-a-bottle/ 15:42:19.928 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from https://bioviz.org/quickload/genome-in-a-bottle/synonyms.txt 15:42:20.056 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: https://bioviz.org/quickload/genome-in-a-bottle/species.txt Aug 02, 2022 3:42:20 PM com.google.common.eventbus.EventBus$LoggingSubscriberExceptionHandler handleException SEVERE: Could not dispatch event: com.affymetrix.igb.view.SeqGroupView@14bd523b to public void com.affymetrix.igb.view.SeqGroupView.dataProviderInit(com.affymetrix.igb.general.DataProviderManager$DataProviderServiceChangeEvent)