The following error is seen in the console when starting 9.0.2:

08:20:23.980 INFO o.l.i.p.PairedReadPreprocessor - Initializaing PairedReadPreprocessor
ERROR: org.lorainelab.igb.plugins-manager (71): [PluginRepositoryList(80)] The activate method has thrown an exception
com.google.gson.JsonSyntaxException: com.google.gson.stream.MalformedJsonException: Unterminated object at line 10 column 18 path $.prefs.server[0].mirror
at com.google.gson.Gson.fromJson(Gson.java:825)
at com.google.gson.Gson.fromJson(Gson.java:748)
at org.lorainelab.igb.preferences.IgbPreferencesParser.fromJson(IgbPreferencesParser.java:61)
at org.lorainelab.igb.preferences.IgbPreferencesParser.fromDefaultPreferences(IgbPreferencesParser.java:84)
at org.lorainelab.igb.plugin.manager.repos.PluginRepositoryList.activate(PluginRepositoryList.java:46)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.felix.scr.impl.helper.BaseMethod.invokeMethod(BaseMethod.java:231)
at org.apache.felix.scr.impl.helper.BaseMethod.access$500(BaseMethod.java:39)
at org.apache.felix.scr.impl.helper.BaseMethod$Resolved.invoke(BaseMethod.java:624)
at org.apache.felix.scr.impl.helper.BaseMethod.invoke(BaseMethod.java:508)
at org.apache.felix.scr.impl.helper.ActivateMethod.invoke(ActivateMethod.java:149)
at org.apache.felix.scr.impl.manager.SingleComponentManager.createImplementationObject(SingleComponentManager.java:315)
at org.apache.felix.scr.impl.manager.SingleComponentManager.createComponent(SingleComponentManager.java:127)
at org.apache.felix.scr.impl.manager.SingleComponentManager.getService(SingleComponentManager.java:871)
at org.apache.felix.scr.impl.manager.SingleComponentManager.getServiceInternal(SingleComponentManager.java:838)
at org.apache.felix.scr.impl.manager.AbstractComponentManager.activateInternal(AbstractComponentManager.java:850)
at org.apache.felix.scr.impl.manager.DependencyManager$SingleStaticCustomizer.addedService(DependencyManager.java:931)
at org.apache.felix.scr.impl.manager.DependencyManager$SingleStaticCustomizer.addedService(DependencyManager.java:895)
at org.apache.felix.scr.impl.manager.ServiceTracker$Tracked.customizerAdded(ServiceTracker.java:1480)
at org.apache.felix.scr.impl.manager.ServiceTracker$Tracked.customizerAdded(ServiceTracker.java:1401)
at org.apache.felix.scr.impl.manager.ServiceTracker$AbstractTracked.trackAdding(ServiceTracker.java:1210)
at org.apache.felix.scr.impl.manager.ServiceTracker$AbstractTracked.track(ServiceTracker.java:1148)
at org.apache.felix.scr.impl.manager.ServiceTracker$Tracked.serviceChanged(ServiceTracker.java:1432)
at org.apache.felix.framework.util.EventDispatcher.invokeServiceListenerCallback(EventDispatcher.java:987)
at org.apache.felix.framework.util.EventDispatcher.fireEventImmediately(EventDispatcher.java:838)
at org.apache.felix.framework.util.EventDispatcher.fireServiceEvent(EventDispatcher.java:545)
at org.apache.felix.framework.Felix.fireServiceEvent(Felix.java:4560)
at org.apache.felix.framework.Felix.registerService(Felix.java:3542)
at org.apache.felix.framework.BundleContextImpl.registerService(BundleContextImpl.java:348)
at org.apache.felix.scr.impl.manager.AbstractComponentManager$3.register(AbstractComponentManager.java:1003)
at org.apache.felix.scr.impl.manager.AbstractComponentManager$3.register(AbstractComponentManager.java:992)
at org.apache.felix.scr.impl.manager.RegistrationManager.changeRegistration(RegistrationManager.java:134)
at org.apache.felix.scr.impl.manager.AbstractComponentManager.registerService(AbstractComponentManager.java:1044)
at org.apache.felix.scr.impl.manager.AbstractComponentManager.activateInternal(AbstractComponentManager.java:841)
at org.apache.felix.scr.impl.manager.DependencyManager$SingleStaticCustomizer.addedService(DependencyManager.java:931)
at org.apache.felix.scr.impl.manager.DependencyManager$SingleStaticCustomizer.addedService(DependencyManager.java:895)
at org.apache.felix.scr.impl.manager.ServiceTracker$Tracked.customizerAdded(ServiceTracker.java:1480)
at org.apache.felix.scr.impl.manager.ServiceTracker$Tracked.customizerAdded(ServiceTracker.java:1401)
at org.apache.felix.scr.impl.manager.ServiceTracker$AbstractTracked.trackAdding(ServiceTracker.java:1210)
at org.apache.felix.scr.impl.manager.ServiceTracker$AbstractTracked.track(ServiceTracker.java:1148)
at org.apache.felix.scr.impl.manager.ServiceTracker$Tracked.serviceChanged(ServiceTracker.java:1432)
at org.apache.felix.framework.util.EventDispatcher.invokeServiceListenerCallback(EventDispatcher.java:987)
at org.apache.felix.framework.util.EventDispatcher.fireEventImmediately(EventDispatcher.java:838)
at org.apache.felix.framework.util.EventDispatcher.fireServiceEvent(EventDispatcher.java:545)
at org.apache.felix.framework.Felix.fireServiceEvent(Felix.java:4560)
at org.apache.felix.framework.Felix.registerService(Felix.java:3542)
at org.apache.felix.framework.BundleContextImpl.registerService(BundleContextImpl.java:348)
at org.apache.felix.scr.impl.manager.AbstractComponentManager$3.register(AbstractComponentManager.java:1003)
at org.apache.felix.scr.impl.manager.AbstractComponentManager$3.register(AbstractComponentManager.java:992)
at org.apache.felix.scr.impl.manager.RegistrationManager.changeRegistration(RegistrationManager.java:134)
at org.apache.felix.scr.impl.manager.AbstractComponentManager.registerService(AbstractComponentManager.java:1044)
at org.apache.felix.scr.impl.manager.AbstractComponentManager.activateInternal(AbstractComponentManager.java:841)
at org.apache.felix.scr.impl.manager.DependencyManager$SingleStaticCustomizer.addedService(DependencyManager.java:931)
at org.apache.felix.scr.impl.manager.DependencyManager$SingleStaticCustomizer.addedService(DependencyManager.java:895)
at org.apache.felix.scr.impl.manager.ServiceTracker$Tracked.customizerAdded(ServiceTracker.java:1480)
at org.apache.felix.scr.impl.manager.ServiceTracker$Tracked.customizerAdded(ServiceTracker.java:1401)
at org.apache.felix.scr.impl.manager.ServiceTracker$AbstractTracked.trackAdding(ServiceTracker.java:1210)
at org.apache.felix.scr.impl.manager.ServiceTracker$AbstractTracked.track(ServiceTracker.java:1148)
at org.apache.felix.scr.impl.manager.ServiceTracker$Tracked.serviceChanged(ServiceTracker.java:1432)
at org.apache.felix.framework.util.EventDispatcher.invokeServiceListenerCallback(EventDispatcher.java:987)
at org.apache.felix.framework.util.EventDispatcher.fireEventImmediately(EventDispatcher.java:838)
at org.apache.felix.framework.util.EventDispatcher.fireServiceEvent(EventDispatcher.java:545)
at org.apache.felix.framework.Felix.fireServiceEvent(Felix.java:4560)
at org.apache.felix.framework.Felix.registerService(Felix.java:3542)
at org.apache.felix.framework.BundleContextImpl.registerService(BundleContextImpl.java:348)
at org.apache.felix.scr.impl.manager.AbstractComponentManager$3.register(AbstractComponentManager.java:1003)
at org.apache.felix.scr.impl.manager.AbstractComponentManager$3.register(AbstractComponentManager.java:992)
at org.apache.felix.scr.impl.manager.RegistrationManager.changeRegistration(RegistrationManager.java:134)
at org.apache.felix.scr.impl.manager.AbstractComponentManager.registerService(AbstractComponentManager.java:1044)
at org.apache.felix.scr.impl.manager.AbstractComponentManager.activateInternal(AbstractComponentManager.java:841)
at org.apache.felix.scr.impl.manager.AbstractComponentManager.enable(AbstractComponentManager.java:419)
at org.apache.felix.scr.impl.config.ConfigurableComponentHolder.enableComponents(ConfigurableComponentHolder.java:376)
at org.apache.felix.scr.impl.BundleComponentActivator.initialize(BundleComponentActivator.java:172)
at org.apache.felix.scr.impl.BundleComponentActivator.<init>(BundleComponentActivator.java:120)
at org.apache.felix.scr.impl.Activator.loadComponents(Activator.java:258)
at org.apache.felix.scr.impl.Activator.access$000(Activator.java:45)
at org.apache.felix.scr.impl.Activator$ScrExtension.start(Activator.java:185)
at org.apache.felix.utils.extender.AbstractExtender.createExtension(AbstractExtender.java:259)
at org.apache.felix.utils.extender.AbstractExtender.modifiedBundle(AbstractExtender.java:232)
at org.osgi.util.tracker.BundleTracker$Tracked.customizerModified(BundleTracker.java:479)
at org.osgi.util.tracker.BundleTracker$Tracked.customizerModified(BundleTracker.java:414)
at org.osgi.util.tracker.AbstractTracked.track(AbstractTracked.java:232)
at org.osgi.util.tracker.BundleTracker$Tracked.bundleChanged(BundleTracker.java:443)
at org.apache.felix.framework.util.EventDispatcher.invokeBundleListenerCallback(EventDispatcher.java:913)
at org.apache.felix.framework.util.EventDispatcher.fireEventImmediately(EventDispatcher.java:834)
at org.apache.felix.framework.util.EventDispatcher.fireBundleEvent(EventDispatcher.java:516)
at org.apache.felix.framework.Felix.fireBundleEvent(Felix.java:4544)
at org.apache.felix.framework.Felix.startBundle(Felix.java:2166)
at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1365)
at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:308)
at java.lang.Thread.run(Thread.java:748)
Caused by: com.google.gson.stream.MalformedJsonException: Unterminated object at line 10 column 18 path $.prefs.server[0].mirror
at com.google.gson.stream.JsonReader.syntaxError(JsonReader.java:1573)
at com.google.gson.stream.JsonReader.doPeek(JsonReader.java:495)
at com.google.gson.stream.JsonReader.hasNext(JsonReader.java:418)
at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory$Adapter.read(ReflectiveTypeAdapterFactory.java:190)
at com.google.gson.internal.bind.TypeAdapterRuntimeTypeWrapper.read(TypeAdapterRuntimeTypeWrapper.java:40)
at com.google.gson.internal.bind.CollectionTypeAdapterFactory$Adapter.read(CollectionTypeAdapterFactory.java:81)
at com.google.gson.internal.bind.CollectionTypeAdapterFactory$Adapter.read(CollectionTypeAdapterFactory.java:60)
at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory$1.read(ReflectiveTypeAdapterFactory.java:103)
at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory$Adapter.read(ReflectiveTypeAdapterFactory.java:196)
at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory$1.read(ReflectiveTypeAdapterFactory.java:103)
at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory$Adapter.read(ReflectiveTypeAdapterFactory.java:196)
at com.google.gson.Gson.fromJson(Gson.java:810)
... 93 more