09:45:44.980 INFO o.l.i.appstore.IgbAppServerLauncher - setPlugingManagerService START 09:45:44.981 INFO o.l.i.appstore.IgbAppServerLauncher - setPluginManagerService DONE 09:45:44.981 INFO o.l.i.appstore.IgbAppServerLauncher - activate START 09:45:44.981 INFO o.l.i.appstore.IgbAppServerLauncher - org.lorainelab.igb.plugin.manager.service.impl.PluginManagerServiceImpl@6c8f76a3 09:45:44.981 INFO o.l.i.appstore.IgbAppServerLauncher - activate DONE 09:45:45.225 INFO c.a.i.b.action.BookmarkActionManager - Loading bookmarks from file /Users/pkulzer/.igb/bookmarks.html 09:45:45.226 INFO c.a.i.b.action.BookmarkActionManager - Saving bookmarks to file /Users/pkulzer/.igb/bookmarks.html~ 09:45:45.798 INFO c.a.igb.util.IGBTrustManager - Trusted Certificates:CN=*.bioviz.org; CN=Sectigo RSA Domain Validation Secure Server CA,O=Sectigo Limited,L=Salford,ST=Greater Manchester,C=GB; CN=USERTrust RSA Certification Authority,O=The USERTRUST Network,L=Jersey City,ST=New Jersey,C=US 09:45:45.866 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. 09:45:45.888 INFO c.a.igb.util.IGBTrustManager - Trusted Certificates:CN=genome.ucsc.edu,O=University of California\, Santa Cruz,ST=California,C=US; CN=AAA Certificate Services,O=Comodo CA Limited,L=Salford,ST=Greater Manchester,C=GB; CN=USERTrust RSA Certification Authority,O=The USERTRUST Network,L=Jersey City,ST=New Jersey,C=US; CN=InCommon RSA Server CA,OU=InCommon,O=Internet2,L=Ann Arbor,ST=MI,C=US 09:45:46.413 INFO com.affymetrix.igb.Activator - IGB Started 09:45:46.433 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.framework 09:45:46.434 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.sun.xml.fastinfoset.FastInfoset 09:45:46.434 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: affymetrix-common 09:45:46.434 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: annotation-tab 09:45:46.434 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: apollo-library 09:45:46.434 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: appstore 09:45:46.434 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.bai 09:45:46.435 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.bam 09:45:46.435 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.bed 09:45:46.435 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: bigBedHandler 09:45:46.435 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: bigWigHandler 09:45:46.435 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.broad.igv.bigwig 09:45:46.435 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: bookmark 09:45:46.435 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.cache 09:45:46.435 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.cache-api 09:45:46.435 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.commons-codec 09:45:46.435 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.commons-compress 09:45:46.435 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.commons-csv 09:45:46.436 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.commons-fileupload 09:45:46.436 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.commons-io 09:45:46.436 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.jexl 09:45:46.436 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.lang3 09:45:46.436 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.logging 09:45:46.436 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.pool 09:45:46.436 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: console-tab 09:45:46.436 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: context-menu-service 09:45:46.436 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: das 09:45:46.436 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.external-sort 09:45:46.436 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: externalView 09:45:46.436 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.google.guava.failureaccess 09:45:46.436 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.feedback 09:45:46.436 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: frameManager 09:45:46.436 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: genometry 09:45:46.436 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.genotyping 09:45:46.436 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.affymetrix.genoviz 09:45:46.436 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: graphTab 09:45:46.436 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.google.gson 09:45:46.437 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.google.guava 09:45:46.437 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: heatmap-editor 09:45:46.437 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: htsjdk-igb 09:45:46.437 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb 09:45:46.437 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-genoviz-extensions 09:45:46.437 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-javafx-util 09:45:46.437 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-preferences 09:45:46.437 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-services 09:45:46.437 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igbScript 09:45:46.437 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igbSwingExt 09:45:46.437 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: image-exporter 09:45:46.437 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.sun.istack.commons-runtime 09:45:46.437 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: jakarta.activation-api 09:45:46.437 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: jakarta.xml.bind-api 09:45:46.437 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.glassfish.jaxb.core 09:45:46.437 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.glassfish.jaxb.runtime 09:45:46.437 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.jidesoft.ultimate.jakarta 09:45:46.437 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: keyWordSearch 09:45:46.437 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: keybinding-registry 09:45:46.437 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: ch.qos.logback.classic 09:45:46.437 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: ch.qos.logback.core 09:45:46.437 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.logging-config 09:45:46.437 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.narrowpeak 09:45:46.438 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: ncbiBlast 09:45:46.438 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.bundlerepository 09:45:46.438 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.configadmin 09:45:46.438 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.eventadmin 09:45:46.438 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: null 09:45:46.438 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.http.jetty 09:45:46.438 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.http.servlet-api 09:45:46.438 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.scr 09:45:46.438 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.webconsole 09:45:46.438 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.menu.api 09:45:46.438 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.osgi.service.component 09:45:46.438 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.osgi.service.log 09:45:46.438 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.osgi.util.function 09:45:46.438 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.osgi.util.promise 09:45:46.438 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.glassfish.hk2.osgi-resource-locator 09:45:46.438 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: paired-data-preprocessor 09:45:46.438 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.plugins-manager 09:45:46.438 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: propertyView 09:45:46.438 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: quickload 09:45:46.438 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: restrictionSites 09:45:46.439 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: searchModelIdOrProps 09:45:46.439 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: searchView 09:45:46.439 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: sequenceViewer 09:45:46.439 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: session-manager 09:45:46.439 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: shared-lib-wrapper 09:45:46.439 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: slf4j.api 09:45:46.439 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: survey 09:45:46.439 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: synonym-lookup 09:45:46.439 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: thresholding 09:45:46.439 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: track-operations-panel 09:45:46.439 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: null 09:45:46.439 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: update 09:45:46.439 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: weblinks 09:45:46.439 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: window-service 09:45:46.439 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.tukaani.xz 09:45:46.439 [main] INFO com.affymetrix.main.OSGiHandler - OSGi is started with org.apache.felix.framework version 7.0.5 09:45:46.517 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://lorainelab-quickload.scidas.org/bar/ 09:45:46.704 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 09:45:46.782 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://lorainelab-quickload.scidas.org/bar/species.txt 09:45:46.787 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://lorainelab-quickload.scidas.org/chipseq/ 09:45:46.993 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 09:45:47.071 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://lorainelab-quickload.scidas.org/chipseq/species.txt 09:45:47.077 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server https://bioviz.org/quickload/genome-in-a-bottle/ 09:45:47.437 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 09:45:47.533 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 09:45:47.537 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://www.igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/ 09:45:47.610 WARN o.l.i.quickload.util.QuickloadUtils - Could not read contents.txt from: http://www.igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/contents.txt 09:45:47.611 WARN o.l.i.q.QuickloadDataProvider - Missing required quickload file, or could not reach source. This quickloak source will be disabled for this session. 09:45:47.681 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://www.igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/synonyms.txt 09:45:47.761 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://www.igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/species.txt 09:45:47.762 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server https://data.bioviz.org/rnaseq/S_lycopersicum_Sep_2019/PGRP1939255/ 09:45:47.925 WARN o.l.i.quickload.util.QuickloadUtils - Could not read contents.txt from: https://data.bioviz.org/rnaseq/S_lycopersicum_Sep_2019/PGRP1939255/contents.txt 09:45:47.926 WARN o.l.i.q.QuickloadDataProvider - Missing required quickload file, or could not reach source. This quickloak source will be disabled for this session. 09:45:48.042 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from https://data.bioviz.org/rnaseq/S_lycopersicum_Sep_2019/PGRP1939255/synonyms.txt 09:45:48.155 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: https://data.bioviz.org/rnaseq/S_lycopersicum_Sep_2019/PGRP1939255/species.txt 09:45:48.156 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server https://translate.bioviz.org/api/?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/birds/hub.txt&filePath=/ 09:45:49.245 INFO c.a.igb.util.IGBTrustManager - Trusted Certificates:CN=*.bioviz.org; CN=Sectigo RSA Domain Validation Secure Server CA,O=Sectigo Limited,L=Salford,ST=Greater Manchester,C=GB; CN=USERTrust RSA Certification Authority,O=The USERTRUST Network,L=Jersey City,ST=New Jersey,C=US 09:45:53.521 INFO o.l.i.appstore.IgbAppServerLauncher - Started REST endpoint. 09:46:00.652 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 09:46:00.653 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: genome H_sapiens_Dec_2013 09:46:07.725 INFO c.a.igb.view.load.GeneralLoadUtils - Loaded RefSeq Curated in 657.7 ms 09:46:08.085 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957124_Adrenal_gland.scaled.bedgraph.gz 09:46:10.383 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957125_Brain_Cerebellum.scaled.bedgraph.gz 09:46:12.627 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957183_Brain_Whole.scaled.bedgraph.gz 09:46:14.909 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957186_Brain_Fetal.scaled.bedgraph.gz 09:46:17.233 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957188_Liver_Fetal.scaled.bedgraph.gz 09:46:19.500 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957191_Heart.scaled.bedgraph.gz 09:46:21.771 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957192_Kidney.scaled.bedgraph.gz 09:46:24.102 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957193_Liver.scaled.bedgraph.gz 09:46:26.373 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957195_Lung.scaled.bedgraph.gz 09:46:28.771 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957197_Placenta.scaled.bedgraph.gz 09:46:31.107 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957198_Prostate.scaled.bedgraph.gz 09:46:33.367 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957200_Salivary_Gland.scaled.bedgraph.gz 09:46:35.798 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957201_Skeletal_Muscle.scaled.bedgraph.gz 09:46:38.197 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957202_Small_Intestine.scaled.bedgraph.gz 09:46:40.602 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957203_Spleen.scaled.bedgraph.gz 09:46:42.878 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957205_Stomach.scaled.bedgraph.gz 09:46:45.345 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957206_Thymus.scaled.bedgraph.gz 09:46:47.841 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957207_Thyroid.scaled.bedgraph.gz 09:46:50.105 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957208_Trachea.scaled.bedgraph.gz 09:46:52.521 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957209_Uterus.scaled.bedgraph.gz 09:46:54.791 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 09:46:55.800 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 09:46:56.806 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: goto chr1:206,940,473-206,940,546 09:46:57.818 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: refresh 09:46:58.825 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: goto chr1:206,940,481-206,940,589 09:46:59.833 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957124_Adrenal_gland.scaled.bedgraph.gz 09:47:00.844 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957125_Brain_Cerebellum.scaled.bedgraph.gz 09:47:01.874 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957193_Liver.scaled.bedgraph.gz 09:47:02.924 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957191_Heart.scaled.bedgraph.gz 09:47:03.976 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957183_Brain_Whole.scaled.bedgraph.gz 09:47:05.025 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957201_Skeletal_Muscle.scaled.bedgraph.gz 09:47:06.062 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957197_Placenta.scaled.bedgraph.gz 09:47:07.104 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957198_Prostate.scaled.bedgraph.gz 09:47:08.150 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957206_Thymus.scaled.bedgraph.gz 09:47:09.192 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957203_Spleen.scaled.bedgraph.gz 09:47:10.227 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957209_Uterus.scaled.bedgraph.gz 09:47:11.262 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: loadsequence 09:47:11.595 INFO com.affymetrix.igb.IGB - Completed loading sequence for chr1 : 206,940,481 - 206,940,589 from IGB Quickload http://lorainelab-quickload.scidas.org/quickload/ 09:47:12.273 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 09:47:14.307 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 09:47:15.313 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 09:47:16.321 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: refresh 09:47:17.332 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957188_Liver_Fetal.scaled.bedgraph.gz 09:47:18.350 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: hidetrack http://igbquickload.org/rnaseq/H_sapiens_Dec_2013/SRP056969/SRR1957186_Brain_Fetal.scaled.bedgraph.gz 09:47:19.360 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: snapshotwholeFrame 09:47:19.360 INFO com.gene.igbscript.IGBScriptEngine - Exporting file H_sapiens_Dec_20131709218039360.gif in mode: wholeFrame to H_sapiens_Dec_20131709218039360.gif 09:47:19.360 ERROR com.gene.igbscript.IGBScriptEngine - image file extension {0} is not supported 09:47:20.366 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: snapshotmainViewWithLabels RNASeq_AdultTissueExpData.svg 09:47:20.368 INFO com.gene.igbscript.IGBScriptEngine - Exporting file RNASeq_AdultTissueExpData.svg in mode: mainViewWithLabels to /Users/pkulzer/Downloads/RNASeq_AdultTissueExpData.svg 09:47:21.626 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: genome A_thaliana_Jun_2009 09:47:23.991 INFO c.a.igb.view.load.GeneralLoadUtils - Loaded Araport in 177.4 ms 09:47:24.820 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: load ~/A_thaliana_Jun_2009_Chr1.bam 09:47:25.835 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: snapshotmainview ~/A_thaliana_testimage.jpeg 09:47:25.836 INFO com.gene.igbscript.IGBScriptEngine - Exporting file A_thaliana_testimage.jpeg in mode: mainView to /Users/pkulzer/A_thaliana_testimage.jpeg