10:22:08.785 INFO c.a.i.b.action.BookmarkActionManager - Loading bookmarks from file /Users/pkulzer/.igb/bookmarks.html 10:22:08.792 INFO c.a.i.b.action.BookmarkActionManager - Saving bookmarks to file /Users/pkulzer/.igb/bookmarks.html~ 10:22:08.840 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://igbquickload.org/blueberry/ 10:22:09.122 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://igbquickload.org/blueberry/synonyms.txt 10:22:09.336 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://igbquickload.org/blueberry/species.txt 10:22:09.369 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://igbquickload.org/soyseq/ 10:22:09.705 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://igbquickload.org/soyseq/synonyms.txt 10:22:09.786 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://igbquickload.org/soyseq/species.txt 10:22:09.797 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://lorainelab-quickload.scidas.org/bar/ 10:22:09.833 INFO o.l.i.appstore.IgbAppServerLauncher - setPlugingManagerService START 10:22:09.833 INFO o.l.i.appstore.IgbAppServerLauncher - setPluginManagerService DONE 10:22:09.833 INFO o.l.i.appstore.IgbAppServerLauncher - activate START 10:22:09.834 INFO o.l.i.appstore.IgbAppServerLauncher - org.lorainelab.igb.plugin.manager.service.impl.PluginManagerServiceImpl@5792ede0 10:22:09.837 INFO o.l.i.appstore.IgbAppServerLauncher - activate DONE 10:22:09.986 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 10:22:10.063 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://lorainelab-quickload.scidas.org/bar/species.txt 10:22:10.071 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://lorainelab-quickload.scidas.org/dnaseq/ 10:22:10.263 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://lorainelab-quickload.scidas.org/dnaseq/synonyms.txt 10:22:10.498 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://lorainelab-quickload.scidas.org/dnaseq/species.txt [Fatal Error] :1:50: White spaces are required between publicId and systemId. 10:22:10.617 INFO com.affymetrix.igb.update.Activator - No update notifications found 10:22:11.486 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://lorainelab-quickload.scidas.org/chipseq/ 10:22:11.703 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 10:22:11.782 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://lorainelab-quickload.scidas.org/chipseq/species.txt 10:22:12.163 INFO o.l.i.appstore.IgbAppServerLauncher - Started REST endpoint. 10:22:12.527 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. [Fatal Error] :1:50: White spaces are required between publicId and systemId. com.affymetrix.igb.survey.Activator - Exception in Activator.registerService() -> White spaces are required between publicId and systemId. org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 50; White spaces are required between publicId and systemId. at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(DOMParser.java:257) at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(DocumentBuilderImpl.java:339) at javax.xml.parsers.DocumentBuilder.parse(DocumentBuilder.java:121) at com.affymetrix.igb.survey.SurveyParser.parse(SurveyParser.java:40) at com.affymetrix.igb.survey.Activator.getServices(Activator.java:59) at com.affymetrix.igb.survey.Activator.getServices(Activator.java:40) at org.lorainelab.igb.services.XServiceRegistrar.getServices(XServiceRegistrar.java:26) at org.lorainelab.igb.services.SimpleServiceRegistrar.registerService(SimpleServiceRegistrar.java:19) at org.lorainelab.igb.services.XServiceRegistrar.access$001(XServiceRegistrar.java:13) at org.lorainelab.igb.services.XServiceRegistrar$1.addingService(XServiceRegistrar.java:47) at org.osgi.util.tracker.ServiceTracker$Tracked.customizerAdding(ServiceTracker.java:941) at org.osgi.util.tracker.ServiceTracker$Tracked.customizerAdding(ServiceTracker.java:870) at org.osgi.util.tracker.AbstractTracked.trackAdding(AbstractTracked.java:256) at org.osgi.util.tracker.AbstractTracked.track(AbstractTracked.java:229) at org.osgi.util.tracker.ServiceTracker$Tracked.serviceChanged(ServiceTracker.java:901) 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.framework.BundleContextImpl.registerService(BundleContextImpl.java:355) at com.affymetrix.igb.Activator$1.initializeWindowService(Activator.java:143) at com.affymetrix.igb.Activator$1.addingService(Activator.java:134) at org.osgi.util.tracker.ServiceTracker$Tracked.customizerAdding(ServiceTracker.java:941) at org.osgi.util.tracker.ServiceTracker$Tracked.customizerAdding(ServiceTracker.java:870) at org.osgi.util.tracker.AbstractTracked.trackAdding(AbstractTracked.java:256) at org.osgi.util.tracker.AbstractTracked.track(AbstractTracked.java:229) at org.osgi.util.tracker.ServiceTracker$Tracked.serviceChanged(ServiceTracker.java:901) 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.(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) 10:22:14.398 INFO com.affymetrix.igb.Activator - IGB Started 10:22:15.396 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.framework 10:22:15.402 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: affymetrix-common 10:22:15.403 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: annotation-tab 10:22:15.403 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: apollo-library 10:22:15.404 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: appstore 10:22:15.404 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.bai 10:22:15.404 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.bam 10:22:15.404 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.bed 10:22:15.404 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: bigBedHandler 10:22:15.404 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: bigWigHandler 10:22:15.404 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.broad.igv.bigwig 10:22:15.405 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: bookmark 10:22:15.405 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.cache 10:22:15.405 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.cache-api 10:22:15.405 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.codec 10:22:15.405 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.compress 10:22:15.405 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.csv 10:22:15.405 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.commons-fileupload 10:22:15.405 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.io 10:22:15.405 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.jexl 10:22:15.406 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.lang3 10:22:15.406 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.logging 10:22:15.406 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.pool 10:22:15.406 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: console-tab 10:22:15.406 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: context-menu-service 10:22:15.406 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: das 10:22:15.406 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: das2 10:22:15.406 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.external-sort 10:22:15.406 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: externalView 10:22:15.406 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.feedback 10:22:15.406 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: frameManager 10:22:15.406 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: genometry 10:22:15.406 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.genotyping 10:22:15.406 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.affymetrix.genoviz 10:22:15.406 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: graphTab 10:22:15.407 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.google.gson 10:22:15.407 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.google.guava 10:22:15.407 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: heatmap-editor 10:22:15.407 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: htsjdk-igb 10:22:15.407 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb 10:22:15.407 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-genoviz-extensions 10:22:15.408 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-javafx-util 10:22:15.408 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-preferences 10:22:15.408 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-services 10:22:15.408 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igbScript 10:22:15.408 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igbSwingExt 10:22:15.408 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: image-exporter 10:22:15.408 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.fasterxml.jackson.core.jackson-annotations 10:22:15.408 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.fasterxml.jackson.core.jackson-core 10:22:15.408 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.fasterxml.jackson.core.jackson-databind 10:22:15.408 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.jidesoft.ultimate 10:22:15.408 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: keyWordSearch 10:22:15.408 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: keybinding-registry 10:22:15.408 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: ch.qos.logback.classic 10:22:15.408 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: ch.qos.logback.core 10:22:15.408 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.logging-config 10:22:15.408 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.narrowpeak 10:22:15.408 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: ncbiBlast 10:22:15.408 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.bundlerepository 10:22:15.408 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.configadmin 10:22:15.408 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.dependencymanager 10:22:15.408 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.eventadmin 10:22:15.409 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.http.bundle 10:22:15.409 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.http.jetty 10:22:15.409 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.http.servlet-api 10:22:15.409 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.scr 10:22:15.409 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.webconsole 10:22:15.409 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.error.reporter.api 10:22:15.409 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.error.reporter.manager 10:22:15.410 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.menu.api 10:22:15.412 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.remote.services.commons 10:22:15.412 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.remote.services.discovery.provider.configured 10:22:15.412 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.remote.services.distribution.provider.http 10:22:15.413 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.remote.services.topology.manager 10:22:15.413 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: osgi.cmpn 10:22:15.413 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.osgi.service.remoteserviceadmin 10:22:15.417 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: paired-data-preprocessor 10:22:15.422 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.plugins-manager 10:22:15.424 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: propertyView 10:22:15.424 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: quickload 10:22:15.424 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: restrictionSites 10:22:15.424 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: searchModelIdOrProps 10:22:15.424 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: searchView 10:22:15.424 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: sequenceViewer 10:22:15.425 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: session-manager 10:22:15.425 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: shared-lib-wrapper 10:22:15.425 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: slf4j.api 10:22:15.425 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: survey 10:22:15.425 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: synonym-lookup 10:22:15.425 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: thresholding 10:22:15.425 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: track-operations-panel 10:22:15.426 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: update 10:22:15.426 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: weblinks 10:22:15.426 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: window-service 10:22:15.426 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.tukaani.xz 10:22:15.426 [main] INFO com.affymetrix.main.OSGiHandler - OSGi is started with org.apache.felix.framework version 5.2.0 10:22:25.006 INFO com.gene.igbscript.IGBScriptEngine - Running script# Stress Testing # select and open the human genome genome H_sapiens_Dec_2013 # Add all of the RNA-Seq scaled coverage graphs (20 total) to the IGB Data Management Table load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957124_Adrenal_gland.scaled.bedgraph.gz load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957125_Brain_Cerebellum.scaled.bedgraph.gz load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957183_Brain_Whole.scaled.bedgraph.gz load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957186_Brain_Fetal.scaled.bedgraph.gz load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957188_Liver_Fetal.scaled.bedgraph.gz load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957191_Heart.scaled.bedgraph.gz load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957192_Kidney.scaled.bedgraph.gz load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957193_Liver.scaled.bedgraph.gz load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957195_Lung.scaled.bedgraph.gz load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957197_Placenta.scaled.bedgraph.gz load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957198_Prostate.scaled.bedgraph.gz load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957200_Salivary_Gland.scaled.bedgraph.gz load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957201_Skeletal_Muscle.scaled.bedgraph.gz load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957202_Small_Intestine.scaled.bedgraph.gz load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957203_Spleen.scaled.bedgraph.gz load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957205_Stomach.scaled.bedgraph.gz load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957206_Thymus.scaled.bedgraph.gz load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957207_Thyroid.scaled.bedgraph.gz load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957208_Trachea.scaled.bedgraph.gz load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957209_Uterus.scaled.bedgraph.gz # prevent the fetal datasets from loading just yet loadmode NO_LOAD http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957186_Brain_Fetal.scaled.bedgraph.gz loadmode NO_LOAD http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957188_Liver_Fetal.scaled.bedgraph.gz # go to a gene you'd like to investigate # commas are optional goto chr1:206,940,473-206,940,546 # load data in IGB refresh # zoom out a little bit to see where interesting gene expression is happening goto chr1:206,940,481-206,940,589 # hide tracks that aren't interesting at that gene hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957124_Adrenal_gland.scaled.bedgraph.gz hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957125_Brain_Cerebellum.scaled.bedgraph.gz hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957193_Liver.scaled.bedgraph.gz hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957191_Heart.scaled.bedgraph.gz hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957183_Brain_Whole.scaled.bedgraph.gz hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957201_Skeletal_Muscle.scaled.bedgraph.gz hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957197_Placenta.scaled.bedgraph.gz hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957198_Prostate.scaled.bedgraph.gz hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957206_Thymus.scaled.bedgraph.gz hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957203_Spleen.scaled.bedgraph.gz hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957209_Uterus.scaled.bedgraph.gz # load sequence in IGB loadsequence # remove certain datasets from IGB unload http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957192_Kidney.scaled.bedgraph.gz, http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957195_Lung.scaled.bedgraph.gz, http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957207_Thyroid.scaled.bedgraph.gz # now that you've pared down the adult datasets, load the fetal datasets loadmode REGION_IN_VIEW http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957186_Brain_Fetal.scaled.bedgraph.gz loadmode REGION_IN_VIEW http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957188_Liver_Fetal.scaled.bedgraph.gz refresh # neither seem interesting, so hide these, too hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957188_Liver_Fetal.scaled.bedgraph.gz hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957186_Brain_Fetal.scaled.bedgraph.gz # take a snapshot of the whole frame without specifying a file name # this should default to ".png" snapshotwholeFrame # then, take a snapshot of the main view with labels and save it with a specific file name in svg format snapshotmainViewWithLabels RNASeq_AdultTissueExpData.svg # select and open the A_thaliana genome genome A_thaliana_Jun_2009 # load in a local bam file load ~/A_thaliana_Jun_2009_Chr1.bam # take a snapshot and save it as a jpeg snapshotmainview ~/A_thaliana_testimage.jpeg 10:22:25.018 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: genome H_sapiens_Dec_2013 10:22:27.363 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957124_Adrenal_gland.scaled.bedgraph.gz 10:22:28.767 INFO c.a.igb.view.load.GeneralLoadUtils - Loaded RefSeq Curated in 2.418 s 10:22:30.196 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957125_Brain_Cerebellum.scaled.bedgraph.gz 10:22:32.695 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957183_Brain_Whole.scaled.bedgraph.gz 10:22:35.208 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957186_Brain_Fetal.scaled.bedgraph.gz 10:22:37.946 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957188_Liver_Fetal.scaled.bedgraph.gz 10:22:40.515 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957191_Heart.scaled.bedgraph.gz 10:22:43.028 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957192_Kidney.scaled.bedgraph.gz 10:22:45.548 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957193_Liver.scaled.bedgraph.gz 10:22:48.082 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957195_Lung.scaled.bedgraph.gz 10:22:50.528 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957197_Placenta.scaled.bedgraph.gz 10:22:53.174 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957198_Prostate.scaled.bedgraph.gz 10:22:55.666 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957200_Salivary_Gland.scaled.bedgraph.gz 10:22:58.125 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957201_Skeletal_Muscle.scaled.bedgraph.gz 10:23:01.074 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957202_Small_Intestine.scaled.bedgraph.gz 10:23:03.605 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957203_Spleen.scaled.bedgraph.gz 10:23:06.150 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957205_Stomach.scaled.bedgraph.gz 10:23:08.577 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957206_Thymus.scaled.bedgraph.gz 10:23:11.101 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957207_Thyroid.scaled.bedgraph.gz 10:23:13.691 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957208_Trachea.scaled.bedgraph.gz 10:23:16.188 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957209_Uterus.scaled.bedgraph.gz 10:23:18.600 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: loadmode NO_LOAD http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957186_Brain_Fetal.scaled.bedgraph.gz 10:23:19.627 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: loadmode NO_LOAD http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957188_Liver_Fetal.scaled.bedgraph.gz 10:23:20.642 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: goto chr1:206,940,473-206,940,546 10:23:21.689 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: refresh 10:23:22.723 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: goto chr1:206,940,481-206,940,589 10:23:23.794 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957124_Adrenal_gland.scaled.bedgraph.gz 10:23:24.813 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957125_Brain_Cerebellum.scaled.bedgraph.gz 10:23:25.856 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957193_Liver.scaled.bedgraph.gz 10:23:26.901 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957191_Heart.scaled.bedgraph.gz 10:23:27.943 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957183_Brain_Whole.scaled.bedgraph.gz 10:23:28.978 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957201_Skeletal_Muscle.scaled.bedgraph.gz 10:23:30.019 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957197_Placenta.scaled.bedgraph.gz 10:23:31.061 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957198_Prostate.scaled.bedgraph.gz 10:23:32.101 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957206_Thymus.scaled.bedgraph.gz 10:23:33.143 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957203_Spleen.scaled.bedgraph.gz 10:23:34.239 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957209_Uterus.scaled.bedgraph.gz 10:23:35.297 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: loadsequence 10:23:35.604 INFO com.affymetrix.igb.IGB - Completed loading sequence for chr1 : 206,940,480 - 206,940,588 from IGB Quickload http://igbquickload.org/quickload/ 10:23:36.320 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: unload http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957192_Kidney.scaled.bedgraph.gz, http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957195_Lung.scaled.bedgraph.gz, http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957207_Thyroid.scaled.bedgraph.gz 10:23:38.392 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: loadmode REGION_IN_VIEW http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957186_Brain_Fetal.scaled.bedgraph.gz 10:23:39.399 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: loadmode REGION_IN_VIEW http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957188_Liver_Fetal.scaled.bedgraph.gz 10:23:40.412 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: refresh 10:23:41.432 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957188_Liver_Fetal.scaled.bedgraph.gz 10:23:42.464 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957186_Brain_Fetal.scaled.bedgraph.gz 10:23:43.486 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: snapshotwholeFrame 10:23:43.493 INFO com.gene.igbscript.IGBScriptEngine - Exporting file H_sapiens_Dec_20131709220223493.gif in mode: wholeFrame to H_sapiens_Dec_20131709220223493.gif 10:23:43.494 ERROR com.gene.igbscript.IGBScriptEngine - image file extension {0} is not supported 10:23:44.501 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: snapshotmainViewWithLabels RNASeq_AdultTissueExpData.svg 10:23:44.509 INFO com.gene.igbscript.IGBScriptEngine - Exporting file RNASeq_AdultTissueExpData.svg in mode: mainViewWithLabels to /Users/pkulzer/Downloads/RNASeq_AdultTissueExpData.svg 10:23:46.209 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: genome A_thaliana_Jun_2009 10:23:48.868 INFO c.a.igb.view.load.GeneralLoadUtils - Loaded Araport in 325.7 ms 10:23:49.550 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load ~/A_thaliana_Jun_2009_Chr1.bam 10:23:50.611 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: snapshotmainview ~/A_thaliana_testimage.jpeg 10:23:50.618 INFO com.gene.igbscript.IGBScriptEngine - Exporting file A_thaliana_testimage.jpeg in mode: mainView to /Users/pkulzer/A_thaliana_testimage.jpeg