Nowlan Freese added a comment - 14/Jan/20 9:21 AM Nowlan Freese <nfreese@uncc.edu> Mon, Jan 13, 2020 at 9:24 AM To: pablo.tapia.o@gmail.com Cc: Ann Loraine <Ann.Loraine@uncc.edu> Hi Pablo, Thank you for letting us know about this issue. Please reset your IGB preferences to see if that resolves the issue. To reset preferences to default in IGB: Click on File Select Preferences... In the Preferences window, select the Other Options tab Click Reset Preferences to Defaults This will cause IGB to close. When you start IGB, it will have the default settings and hopefully the server issues will be resolved. If you continue to have issues, please send me the Console logs so I can try to diagnose the problem. To copy the Console logs in IGB: Click on Help Select Show Console In the Console window, click Copy All To Clipboard Paste the Console logs as a reply to this email Best, Nowlan IGB Support Pablo Tapia O. <pablo.tapia.o@gmail.com> Mon, Jan 13, 2020 at 9:34 AM To: Nowlan Freese <nfreese@uncc.edu> Cc: Ann Loraine <Ann.Loraine@uncc.edu> Dear Nowlan, thanks for your reply. Unfortunately, the problems persist. I send the console logs 11:31:06.895 INFO com.affymetrix.igb.update.Activator - No update notifications found 11:31:08.970 INFO c.a.i.b.action.BookmarkActionManager - Loading bookmarks from file C:\Users\pablo\AppData\Roaming\IGB\bookmarks.html 11:31:08.977 INFO c.a.i.b.action.BookmarkActionManager - Saving bookmarks to file C:\Users\pablo\AppData\Roaming\IGB\bookmarks.html~ 11:31:09.046 INFO o.l.i.appstore.IgbAppServerLauncher - setPlugingManagerService START 11:31:09.047 INFO o.l.i.appstore.IgbAppServerLauncher - setPluginManagerService DONE 11:31:09.048 INFO o.l.i.appstore.IgbAppServerLauncher - activate START 11:31:09.049 INFO o.l.i.appstore.IgbAppServerLauncher - org.lorainelab.igb.plugin.manager.service.impl.PluginManagerServiceImpl@74d46040 11:31:09.052 INFO o.l.i.appstore.IgbAppServerLauncher - activate DONE 11:31:09.055 INFO o.l.i.appstore.IgbAppServerLauncher - Started REST endpoint. 11:31:09.192 INFO com.affymetrix.igb.Activator - IGB Started 11:31:09.328 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.framework 11:31:09.333 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: affymetrix-common 11:31:09.334 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: annotation-tab 11:31:09.334 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: apollo-library 11:31:09.335 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: appstore 11:31:09.335 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.bai 11:31:09.335 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.bam 11:31:09.335 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.bed 11:31:09.336 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: bigBedHandler 11:31:09.336 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: bigWigHandler 11:31:09.337 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.broad.igv.bigwig 11:31:09.337 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: bookmark 11:31:09.337 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.cache 11:31:09.337 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.cache-api 11:31:09.337 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.codec 11:31:09.337 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.compress 11:31:09.338 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.csv 11:31:09.338 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.commons-fileupload 11:31:09.338 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.io 11:31:09.338 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.jexl 11:31:09.339 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.lang3 11:31:09.339 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.logging 11:31:09.340 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.pool 11:31:09.340 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: console-tab 11:31:09.340 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: context-menu-service 11:31:09.340 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: das 11:31:09.340 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: das2 11:31:09.340 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.external-sort 11:31:09.340 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: externalView 11:31:09.341 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.feedback 11:31:09.342 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: frameManager 11:31:09.342 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: genometry 11:31:09.342 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.affymetrix.genoviz 11:31:09.343 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: graphTab 11:31:09.343 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.google.gson 11:31:09.343 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.google.guava 11:31:09.343 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: heatmap-editor 11:31:09.343 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: htsjdk-igb 11:31:09.344 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb 11:31:09.344 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-genoviz-extensions 11:31:09.344 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-javafx-util 11:31:09.344 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-preferences 11:31:09.344 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-services 11:31:09.344 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igbScript 11:31:09.344 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igbSwingExt 11:31:09.345 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: image-exporter 11:31:09.345 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.fasterxml.jackson.core.jackson-annotations 11:31:09.345 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.fasterxml.jackson.core.jackson-core 11:31:09.345 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.fasterxml.jackson.core.jackson-databind 11:31:09.345 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.jidesoft.ultimate 11:31:09.345 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: keyWordSearch 11:31:09.346 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: keybinding-registry 11:31:09.346 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: ch.qos.logback.classic 11:31:09.347 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: ch.qos.logback.core 11:31:09.347 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.logging-config 11:31:09.348 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.narrowpeak 11:31:09.348 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: ncbiBlast 11:31:09.348 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.bundlerepository 11:31:09.348 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.configadmin 11:31:09.348 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.dependencymanager 11:31:09.349 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.eventadmin 11:31:09.350 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.http.bundle 11:31:09.350 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.http.jetty 11:31:09.350 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.http.servlet-api 11:31:09.350 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.scr 11:31:09.350 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.webconsole 11:31:09.350 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.error.reporter.api 11:31:09.351 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.error.reporter.manager 11:31:09.351 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.menu.api 11:31:09.351 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.remote.services.commons 11:31:09.351 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.remote.services.discovery.provider.configured 11:31:09.351 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.remote.services.distribution.provider.http 11:31:09.351 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.remote.services.topology.manager 11:31:09.351 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: osgi.cmpn 11:31:09.351 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.osgi.service.remoteserviceadmin 11:31:09.352 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: paired-data-preprocessor 11:31:09.352 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.plugins-manager 11:31:09.352 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: propertyView 11:31:09.353 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: quickload 11:31:09.353 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: restrictionSites 11:31:09.353 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: searchModelIdOrProps 11:31:09.354 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: searchView 11:31:09.354 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: sequenceViewer 11:31:09.354 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: session-manager 11:31:09.354 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: shared-lib-wrapper 11:31:09.355 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: slf4j.api 11:31:09.355 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: survey 11:31:09.355 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: synonym-lookup 11:31:09.356 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: thresholding 11:31:09.356 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: track-operations-panel 11:31:09.356 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: update 11:31:09.357 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: weblinks 11:31:09.357 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: window-service 11:31:09.357 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.tukaani.xz 11:31:09.357 [main] INFO com.affymetrix.main.OSGiHandler - OSGi is started with org.apache.felix.framework version 5.2.0 Regards Pablo [Quoted text hidden] Nowlan Freese <nfreese@uncc.edu> Mon, Jan 13, 2020 at 10:44 AM To: "Pablo Tapia O." <pablo.tapia.o@gmail.com> Cc: Ann Loraine <Ann.Loraine@uncc.edu> Hi Pablo, Thank you for sending the logs, this is very helpful. I have a few more questions: -Can you confirm which version of IGB you are using? In IGB select Help > About Integrated Genome Browser. The version number should be at the top (something like 9.1.2). -Can you connect to this website - http://lorainelab-quickload.scidas.org/quickload/ - through your web browser? You should see a page like this: Screen Shot 2020-01-13 at 10.40.48 AM.png [Quoted text hidden] Pablo Tapia O. <pablo.tapia.o@gmail.com> Mon, Jan 13, 2020 at 10:57 AM To: Nowlan Freese <nfreese@uncc.edu> Cc: Ann Loraine <Ann.Loraine@uncc.edu> Hi Nowlan: Yes, the version of IGB is 9.1.2 Yes, I can connect with the website indicated with my web browser (Firefox) Thanks for your help Regards Pablo Saludos Pablo El lun., 13 ene. 2020 a las 12:44, Nowlan Freese (<nfreese@uncc.edu>) escribió: > > Hi Pablo, > > Thank you for sending the logs, this is very helpful. > > I have a few more questions: > > -Can you confirm which version of IGB you are using? In IGB select Help > About Integrated Genome Browser. The version number should be at the top (something like 9.1.2). > > -Can you connect to this website - http://lorainelab-quickload.scidas.org/quickload/ - through your web browser? You should see a page like this: > > > [Quoted text hidden] Nowlan Freese <nfreese@uncc.edu> Mon, Jan 13, 2020 at 12:00 PM To: "Pablo Tapia O." <pablo.tapia.o@gmail.com> Cc: Ann Loraine <Ann.Loraine@uncc.edu> I would like you to try one more thing to confirm that the issue is not related to the IGB settings. Follow the same steps to reset the settings in IGB: Click on File Select Preferences... In the Preferences window, select the Other Options tab Click Reset Preferences to Defaults While IGB is closed: Using File Explorer on your computer: Navigate to C:\Users\pablo\AppData\Roaming\ Delete the IGB folder This folder contains additional temporary settings used by IGB that could be interfering with the network connection. [Quoted text hidden] Pablo Tapia O. <pablo.tapia.o@gmail.com> Mon, Jan 13, 2020 at 12:26 PM To: Nowlan Freese <nfreese@uncc.edu> Cc: Ann Loraine <Ann.Loraine@uncc.edu> Hi Nowlan: I did what you told me (reset and delete the folder) and started the program again. However, the same error message continues. Regards Pablo [Quoted text hidden] Nowlan Freese <nfreese@uncc.edu> Mon, Jan 13, 2020 at 3:18 PM To: "Pablo Tapia O." <pablo.tapia.o@gmail.com> Cc: Ann Loraine <Ann.Loraine@uncc.edu> Hi Pablo, I would like to see if your IGB can connect to the internet. On the home screen of IGB: Click File Select Open URL... In the Open URL window enter http://igbquickload.org/quickload/A_thaliana_Jun_2009/Araport11.bed.gz Click OK If IGB can connect to the web, it should load the file. If IGB cannot connect to the web, then there should be an UNABLE TO FIND URL popup. This is what my screen looks like when the file loads successfully: Screen Shot 2020-01-13 at 3.12.41 PM.png Another option may be to refresh the servers and see what happens. In IGB: Click on the Data Access tab (usually in the lower left of the IGB main screen) Click on Configure (usually in the lower left, next to Available Data) The Data Sources panel window should appear Click on the refresh button for a server and see what happens This is what my Data Sources panel looks like (red arrow points at the refresh buttons): Screen Shot 2020-01-13 at 2.13.17 PM.png The last IGB thing we could try would be to install an older version of IGB to make sure it's not a version issue. You can go to https://sourceforge.net/projects/genoviz/files/IGB%209.0.2/ and download the Windows 64bit version ( https://sourceforge.net/projects/genoviz/files/IGB%209.0.2/IGB_windows-x64_9_0_2.exe/download ). This can then be installed over top of the most recent version of IGB to see if it solves the problem. If the Quickload servers are not responding it could be due to an issue with the IGB settings (should not be the issue since we reset the settings), the IGB servers themselves (should not be the issue as you can see the IGB server page), or there is something on your computer/network that is blocking IGB's access to the internet. If none of the above works, it may be worth looking to see if there is a Windows setting that is blocking IGB's access to the web. Thank you for helping us resolve this issue! Best, Nowlan [Quoted text hidden] Pablo Tapia O. <pablo.tapia.o@gmail.com> Tue, Jan 14, 2020 at 9:01 AM To: Nowlan Freese <nfreese@uncc.edu> Cc: Ann Loraine <Ann.Loraine@uncc.edu> Hi Nowlan: Indeed, my IGV internet connection is blocked. Probably windows, but I still can't find the cause. Thanks so much for everything Saludos Pablo Saludos Pablo El lun., 13 ene. 2020 a las 17:18, Nowlan Freese (<nfreese@uncc.edu>) escribió: > > Hi Pablo, > > I would like to see if your IGB can connect to the internet. > > On the home screen of IGB: > Click File > Select Open URL... > In the Open URL window enter http://igbquickload.org/quickload/A_thaliana_Jun_2009/Araport11.bed.gz > Click OK > > If IGB can connect to the web, it should load the file. If IGB cannot connect to the web, then there should be an UNABLE TO FIND URL popup. > This is what my screen looks like when the file loads successfully: > > > Another option may be to refresh the servers and see what happens. > > In IGB: > Click on the Data Access tab (usually in the lower left of the IGB main screen) > Click on Configure (usually in the lower left, next to Available Data) > The Data Sources panel window should appear > Click on the refresh button for a server and see what happens > > This is what my Data Sources panel looks like (red arrow points at the refresh buttons): > >

Nowlan Freese added a comment - 14/Jan/20 9:29 AM Thoughts: As the user has the most recent version of IGB, reset preferences to default and removed the IGB folder, I do not think the issue is directly related to IGB. Their IGB acts as though it cannot connect to the internet at all, but the user can connect to the Quickload site in their browser. Most likely something on the user's computer is preventing IGB from connecting to the internet. It could be some kind of security option, but this would be difficult for the IGB team to diagnose. Unless further information becomes available, there does not appear to be a path forward.