Access forbidden when trying to load T2T CHM13-v1.1 and T2T CHM13-v2.0/hs1

[cheehongsg]

Unsure if this is the correct place to report..

When running IGV Desktop v2.18.2 and 2.16.2, there is no problem loading genome hg19 and hg38. I will get error message "Access forbidden" when I try T2T CHM13-v1.1 or T2T CHM13-v2.0/hs1 Is this a setup issue on IGV's Amazon infrastructure? Have been such for >20 min.

Cheers, Chee

console log below:

INFO [Sep 03,2024 12:15] [Main] Startup  IGV Version 2.18.2 08/21/2024 12:06 PM
INFO [Sep 03,2024 12:15] [Main] Java 17.0.9 (build 17.0.9+9) 2023-10-17
INFO [Sep 03,2024 12:15] [Main] Java Vendor: Eclipse Adoptium https://adoptium.net/
INFO [Sep 03,2024 12:15] [Main] JVM: OpenJDK 64-Bit Server VM Temurin-17.0.9+9   
INFO [Sep 03,2024 12:15] [Main] OS: Mac OS X 14.6.1 x86_64
INFO [Sep 03,2024 12:15] [Main] IGV Directory: /Users/cheehong/igv
INFO [Sep 03,2024 12:15] [CommandListener] Listening on port 60151
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
INFO [Sep 03,2024 12:15] [GenomeManager] Loading genome: https://igv-genepattern-org.s3.amazonaws.com/genomes/hg38/hg38.json
INFO [Sep 03,2024 12:15] [TrackLoader] Loading resource:  https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ncbiRefSeq.txt.gz
INFO [Sep 03,2024 12:15] [GenomeManager] Loading genome: https://igv.org/genomes/json/hs1.json
SEVERE [Sep 03,2024 12:15] [MessageUtils] Error loading genome Human (T2T CHM13-v2.0/hs1)
SEVERE [Sep 03,2024 12:15] [MessageUtils] org.broad.igv.exceptions.HttpResponseException: Access forbidden <br> 
    at org.igv/org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:882)
    at org.igv/org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:665)
    at org.igv/org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:661)
    at org.igv/org.broad.igv.util.HttpUtils.openConnectionStream(HttpUtils.java:368)
    at org.igv/org.broad.igv.util.HttpUtils.openConnectionStream(HttpUtils.java:362)
    at org.igv/org.broad.igv.util.ParsingUtils.openInputStreamGZ(ParsingUtils.java:128)
    at org.igv/org.broad.igv.util.ParsingUtils.openInputStream(ParsingUtils.java:103)
    at org.igv/org.broad.igv.util.ParsingUtils.openBufferedReader(ParsingUtils.java:86)
    at org.igv/org.broad.igv.feature.genome.fasta.FastaIndex.parseIndexFile(FastaIndex.java:88)
    at org.igv/org.broad.igv.feature.genome.fasta.FastaIndex.<init>(FastaIndex.java:55)
    at org.igv/org.broad.igv.feature.genome.Genome.<init>(Genome.java:145)
    at org.igv/org.broad.igv.feature.genome.load.JsonGenomeLoader.loadGenome(JsonGenomeLoader.java:52)
    at org.igv/org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:197)
    at org.igv/org.broad.igv.ui.commandbar.GenomeComboBox.lambda$loadGenomeFromServer$1(GenomeComboBox.java:237)
    at org.igv/org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:73)
    at org.igv/org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:43)
    at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.base/java.lang.Thread.run(Unknown Source)

[helgathorv]

Thanks for letting us know. There are issues with our AWS buckets where some of the genomes are stored. We are working on resolving this.

[jrobinso]

@cheehongsg Could you try refreshing your genome? You can do this from the Genomes > Select Hosted Genome... menu. That should resolve the problem with the T2T genome, still working through others. Let us know if it does not.

The webapp should also be fixed for this genome.

[cheehongsg]

Thanks. T2T-CHM13v2.0 works for Desktop and WebApp. T2T CHM13-v1.1 still gives "Access forbidden".

[jrobinso]

Right, I was referring to v2.0. There aren't quick solutions for all genomes, v1.1 being one of those.

[cheehongsg]

No problem. I am working with v2.0. Thanks for getting the resources back online.

[lbergelson]

@jrobinso I'm seeing https://s3.amazonaws.com/igv.org.genomes/hg38/hg38_annotations.xml Access forbidden When opening the "load from server" menu.

[jrobinso]

@lbergelson There will be problems with "load from server" for sure, or anything that references "igv.org.genomes". I'm concentrating on the essential genome reference files for now.

[jrobinso]

@lbergelson load from server for hg38 is fixed.

[zhanglw05]

@jrobinso , Hi, we are using igv web version. getting this error recently. Access forbidden: https://s3.amazonaws.com/igv.org.genomes/hg38/refGene.sorted.txt.gz.tbi: https://s3.amazonaws.com/igv.org.genomes/hg38/refGene.sorted.txt.gz. Will this be resolved soon or we should think other solutions, like hosting ourselves.

[mwalker174]

Hi, I'm also seeing a problem with Google oAuth:

echo Using bundled JDK.
WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
WARNING: package com.sun.java.swing.plaf.windows not in java.desktop
WARNING: package sun.awt.windows not in java.desktop
WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
openjdk version "17.0.9" 2023-10-17
OpenJDK Runtime Environment Temurin-17.0.9+9 (build 17.0.9+9)
OpenJDK 64-Bit Server VM Temurin-17.0.9+9 (build 17.0.9+9, mixed mode)
INFO [Sep 04,2024 11:10] [Main] Startup  IGV Version 2.18.2 08/21/2024 12:06 PM
INFO [Sep 04,2024 11:10] [Main] Java 17.0.9 (build 17.0.9+9) 2023-10-17
INFO [Sep 04,2024 11:10] [Main] Java Vendor: Eclipse Adoptium https://adoptium.net/
INFO [Sep 04,2024 11:10] [Main] JVM: OpenJDK 64-Bit Server VM Temurin-17.0.9+9
INFO [Sep 04,2024 11:10] [Main] OS: Mac OS X 14.5 x86_64
INFO [Sep 04,2024 11:10] [Main] IGV Directory: /Users/markw/igv
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
INFO [Sep 04,2024 11:10] [CommandListener] Listening on port 60151
INFO [Sep 04,2024 11:10] [GenomeManager] Loading genome: /Users/markw/igv/genomes/hg38_1kg.json
WARNING [Sep 04,2024 11:10] [LoadFromServerAction] No data found for current genome.
INFO [Sep 04,2024 11:10] [TrackLoader] Loading resource:  https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ncbiRefSeq.txt.gz
INFO [Sep 04,2024 11:10] [OAuthUtils] Loading Google oAuth properties
SEVERE [Sep 04,2024 11:10] [OAuthUtils] Error loading Google oAuth properties
SEVERE [Sep 04,2024 11:10] [OAuthUtils] java.io.IOException: Server returned HTTP response code: 403 for URL: https://s3.amazonaws.com/igv.org.app/desktop_google
    at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source)
    at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
    at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(Unknown Source)
    at org.igv/org.broad.igv.oauth.OAuthUtils.openInputStream(OAuthUtils.java:265)
    at org.igv/org.broad.igv.oauth.OAuthUtils.loadAsString(OAuthUtils.java:171)
    at org.igv/org.broad.igv.oauth.OAuthUtils.loadDefaultOauthProperties(OAuthUtils.java:145)
    at org.igv/org.broad.igv.oauth.OAuthUtils.getGoogleProvider(OAuthUtils.java:126)
    at org.igv/org.broad.igv.ui.IGVMenuBar$27.menuSelected(IGVMenuBar.java:1080)
    at java.desktop/javax.swing.JMenu.fireMenuSelected(Unknown Source)
    at java.desktop/javax.swing.JMenu$MenuChangeListener.stateChanged(Unknown Source)
    at java.desktop/javax.swing.DefaultButtonModel.fireStateChanged(Unknown Source)
    at java.desktop/javax.swing.DefaultButtonModel.setSelected(Unknown Source)
    at java.desktop/javax.swing.JMenu.setSelected(Unknown Source)
    at java.desktop/com.apple.laf.ScreenMenu$2.run(Unknown Source)
    at java.desktop/java.awt.event.InvocationEvent.dispatch(Unknown Source)
    at java.desktop/java.awt.EventQueue.dispatchEventImpl(Unknown Source)
    at java.desktop/java.awt.EventQueue$4.run(Unknown Source)
    at java.desktop/java.awt.EventQueue$4.run(Unknown Source)
    at java.base/java.security.AccessController.doPrivileged(Unknown Source)
    at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
    at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
    at java.desktop/java.awt.EventQueue$5.run(Unknown Source)
    at java.desktop/java.awt.EventQueue$5.run(Unknown Source)
    at java.base/java.security.AccessController.doPrivileged(Unknown Source)
    at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
    at java.desktop/java.awt.EventQueue.dispatchEvent(Unknown Source)
    at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
    at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
    at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
    at java.desktop/java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    at java.desktop/java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    at java.desktop/java.awt.EventDispatchThread.run(Unknown Source)

SEVERE [Sep 04,2024 11:10] [MessageUtils] Error loading Google oAuth properties
SEVERE [Sep 04,2024 11:10] [MessageUtils] java.io.IOException: Server returned HTTP response code: 403 for URL: https://s3.amazonaws.com/igv.org.app/desktop_google
    at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source)
    at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
    at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(Unknown Source)
    at org.igv/org.broad.igv.oauth.OAuthUtils.openInputStream(OAuthUtils.java:265)
    at org.igv/org.broad.igv.oauth.OAuthUtils.loadAsString(OAuthUtils.java:171)
    at org.igv/org.broad.igv.oauth.OAuthUtils.loadDefaultOauthProperties(OAuthUtils.java:145)
    at org.igv/org.broad.igv.oauth.OAuthUtils.getGoogleProvider(OAuthUtils.java:126)
    at org.igv/org.broad.igv.ui.IGVMenuBar$27.menuSelected(IGVMenuBar.java:1080)
    at java.desktop/javax.swing.JMenu.fireMenuSelected(Unknown Source)
    at java.desktop/javax.swing.JMenu$MenuChangeListener.stateChanged(Unknown Source)
    at java.desktop/javax.swing.DefaultButtonModel.fireStateChanged(Unknown Source)
    at java.desktop/javax.swing.DefaultButtonModel.setSelected(Unknown Source)
    at java.desktop/javax.swing.JMenu.setSelected(Unknown Source)
    at java.desktop/com.apple.laf.ScreenMenu$2.run(Unknown Source)
    at java.desktop/java.awt.event.InvocationEvent.dispatch(Unknown Source)
    at java.desktop/java.awt.EventQueue.dispatchEventImpl(Unknown Source)
    at java.desktop/java.awt.EventQueue$4.run(Unknown Source)
    at java.desktop/java.awt.EventQueue$4.run(Unknown Source)
    at java.base/java.security.AccessController.doPrivileged(Unknown Source)
    at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
    at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
    at java.desktop/java.awt.EventQueue$5.run(Unknown Source)
    at java.desktop/java.awt.EventQueue$5.run(Unknown Source)
    at java.base/java.security.AccessController.doPrivileged(Unknown Source)
    at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
    at java.desktop/java.awt.EventQueue.dispatchEvent(Unknown Source)
    at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
    at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
    at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
    at java.desktop/java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    at java.desktop/java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    at java.desktop/java.awt.EventDispatchThread.run(Unknown Source)

SEVERE [Sep 04,2024 11:10] [MessageUtils] Error loading Google oAuth properties

[helgathorv]

@mwalker174 The Google access is also due to the issues with some of our AWS buckets and we are working on resolving them. In the meantime, try the following workaround: From the menu select View > Preferences > Advanced and enter the following for the "OAuth provisioning URL": https://igv.org/services/desktop_google

Let us know if that doesn't work for you.

[helgathorv]

@zhanglw05 The hg38 genome works for me now at igv.org/app. Try clearing the browser cache and selecting a different genome and then back to hg38. Note that not all the genomes currently work.

[zhanglw05]

@helgathorv , thank you. it is working for us now.