IGB app takes very long time to open in Mac

[Lakshmi Mahendrawada]

Hi,

I am using IGB on Mac ventura 13.5 (M1 chip).  I could install IGB and it works, but it takes about 10 minutes to launch the application. Please let me know if there is a way to fix this issue. Thank you!

Best,

Lakshmi

[Ann Loraine]

Thanks for your question.

I think the problem may be due to a problem with one of the data sources IGB contacts when it first starts up. 

if this continues to happen, I recommend opening up the IGB Data Sources Preference window and de-activating the UCSC DAS Data source.

We learned recently that there was a change to the UCSC DAS data source that "breaks" IGB's ability to query and display data from just that source. I'm not sure, but that could be the root cause for the slow-down you're observing.

To de-activate the UCSC DAS data source:

• Start IGB
• Once IGB starts, choose File > Preferences > Data Sources
• You will see a table with many Data Sources listed. De-select the one named "UCSC"

Also, if any of the rows have a red or yellow background, that means that the Data Source is not properly responding during your current IGB session. 

The only data source you'll want to keep active is the data source named "IGB Quickload." This is the data source IGB uses to display the various genome assemblies for organisms shown on the IGB Home screen. 

All the other data sources can be de-activated and IGB will still work fine. The other data sets are serving data sets like RNA-Seq or ChIP-Seq data. If you don't need any of those data sets, then you can safely de-activate them.

Please let us know if this helps, or not.

Thank you for using IGB and for your question!

-Ann

[Lakshmi Mahendrawada]

Hi Ann,

Thank you for getting back to me. I have now deselected all data sources except IGB Quickload. But it still takes long time to open.

-Lakshmi

[Ann Loraine]

Thanks for trying my previous suggestion. Yes, it looks like either the "main" IGB Quickload site is super-slow, or there's another problem.

If you could send me IGB's logging messages, that might help us figure out what's going on.

To do this:

* Start IGB again. 

* Click the lower tabbed panel labeled "Log" to view all the various logging messages IGB prints while it's running. 

* Click the bottom left button labeled "Copy All To Clipboard" 

* Paste the copied content from the previous step an ordinary file - a Word document or TextEdit document would be fine. 

* Review the pasted content and delete anything that you need to keep confidential.

Then please either email the document to me as an attachment, or just reply to this post and attach the file to your reply.

Hopefully the logs will contain something that lets us diagnose - and fix! - the problem.

Last but not least, please let me know what version of IGB you are running.

[Lakshmi Mahendrawada]

I replied via email. Guess it didn't reach you.

I am using IGB version - 9.1.10

Here are the logging messages. Time matches with the time app opened.

15:22:25.918 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
15:22:26.327 INFO  com.affymetrix.igb.Activator - IGB Started
15:22:26.782 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.framework
15:22:26.782 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: affymetrix-common
15:22:26.782 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: annotation-tab
15:22:26.782 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: apollo-library
15:22:26.782 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: appstore
15:22:26.782 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.bai
15:22:26.782 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.bam
15:22:26.782 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.bed
15:22:26.782 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: bigBedHandler
15:22:26.783 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: bigWigHandler
15:22:26.783 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.broad.igv.bigwig
15:22:26.783 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: bookmark
15:22:26.783 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.cache
15:22:26.783 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.cache-api
15:22:26.783 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.codec
15:22:26.783 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.compress
15:22:26.783 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.csv
15:22:26.783 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.commons-fileupload
15:22:26.783 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.io
15:22:26.783 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.jexl
15:22:26.783 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.lang3
15:22:26.784 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.logging
15:22:26.784 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.pool
15:22:26.784 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: console-tab
15:22:26.785 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: context-menu-service
15:22:26.785 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: das
15:22:26.785 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.external-sort
15:22:26.785 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: externalView
15:22:26.785 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.feedback
15:22:26.785 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: frameManager
15:22:26.785 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: genometry
15:22:26.785 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.genotyping
15:22:26.785 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: com.affymetrix.genoviz
15:22:26.785 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: graphTab
15:22:26.785 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: com.google.gson
15:22:26.786 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: com.google.guava
15:22:26.786 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: heatmap-editor
15:22:26.786 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: htsjdk-igb
15:22:26.786 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: igb
15:22:26.786 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: igb-genoviz-extensions
15:22:26.786 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: igb-javafx-util
15:22:26.786 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: igb-preferences
15:22:26.786 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: igb-services
15:22:26.786 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: igbScript
15:22:26.786 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: igbSwingExt
15:22:26.786 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: image-exporter
15:22:26.786 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: com.fasterxml.jackson.core.jackson-annotations
15:22:26.786 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: com.fasterxml.jackson.core.jackson-core
15:22:26.786 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: com.fasterxml.jackson.core.jackson-databind
15:22:26.786 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: com.jidesoft.ultimate
15:22:26.786 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: keyWordSearch
15:22:26.787 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: keybinding-registry
15:22:26.787 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: ch.qos.logback.classic
15:22:26.787 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: ch.qos.logback.core
15:22:26.787 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.logging-config
15:22:26.787 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.narrowpeak
15:22:26.788 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: ncbiBlast
15:22:26.788 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.bundlerepository
15:22:26.788 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.configadmin
15:22:26.788 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.dependencymanager
15:22:26.788 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.eventadmin
15:22:26.788 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.http.bundle
15:22:26.788 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.http.jetty
15:22:26.788 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.http.servlet-api
15:22:26.788 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.scr
15:22:26.788 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.webconsole
15:22:26.788 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.error.reporter.api
15:22:26.788 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.error.reporter.manager
15:22:26.788 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.menu.api
15:22:26.788 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.remote.services.commons
15:22:26.788 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.remote.services.discovery.provider.configured
15:22:26.788 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.remote.services.distribution.provider.http
15:22:26.788 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.remote.services.topology.manager
15:22:26.788 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: osgi.cmpn
15:22:26.789 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.osgi.service.remoteserviceadmin
15:22:26.789 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: paired-data-preprocessor
15:22:26.789 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.plugins-manager
15:22:26.789 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: propertyView
15:22:26.789 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: quickload
15:22:26.789 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: restrictionSites
15:22:26.789 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: searchModelIdOrProps
15:22:26.789 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: searchView
15:22:26.789 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: sequenceViewer
15:22:26.789 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: session-manager
15:22:26.789 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: shared-lib-wrapper
15:22:26.789 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: slf4j.api
15:22:26.789 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: survey
15:22:26.789 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: synonym-lookup
15:22:26.789 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: thresholding
15:22:26.789 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: track-operations-panel
15:22:26.789 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: update
15:22:26.790 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: weblinks
15:22:26.790 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: window-service
15:22:26.790 [main] INFO  com.affymetrix.main.OSGiHandler - Starting Bundle: org.tukaani.xz
15:22:26.790 [main] INFO  com.affymetrix.main.OSGiHandler - OSGi is started with org.apache.felix.framework version 5.2.0

[Nowlan Freese]

Hi Lakshmi,

We are preparing a major update to IGB that may fix this issue. We will be releasing the new update sometime in January. If you would like to try the in development version now, I have included the link below. Let me know if this helps!

Link to in development version of IGB: https://bitbucket.org/nfreese/nowlanfork-igb/downloads/IGB-macos-universal-main-JDK21-with-javafx-no-theme.dmg