IGV 2.18.4 does not load Whole Transcriptome Bams via pre-signed urls

[fidibidi]

Recently upgraded IGV from 2.17.4 to 2.18.4. With this update, we noticed that IGV session made with whole transcriptome bam files, would not load correctly.

They would load initially, but any subsequent moves to other regions would cause the loading to stop, and just show empty tracks.

This issue does not appear when using 2.17.4.

I've included a RNA bam file for you to use and see if you encounter this same issue. I was unable to to determine the cause of this issue.

initial load into 2.18

scrolling a little ways

Reference files/data:

2.18.4 Log:
INFO [Oct 30,2024 15:02] [Main] Startup IGV Version 2.18.4 10/03/2024 09:12 AM
INFO [Oct 30,2024 15:02] [Main] Java 17.0.9 (build 17.0.9+9) 2023-10-17
INFO [Oct 30,2024 15:02] [Main] Java Vendor: Eclipse Adoptium https://adoptium.net/
INFO [Oct 30,2024 15:02] [Main] JVM: OpenJDK 64-Bit Server VM Temurin-17.0.9+9
INFO [Oct 30,2024 15:02] [Main] OS: Windows 11 10.0 amd64
INFO [Oct 30,2024 15:02] [Main] IGV Directory: C:\Users\me\igv
INFO [Oct 30,2024 15:02] [OAuthUtils] Loading Google oAuth properties
INFO [Oct 30,2024 15:02] [CommandListener] Listening on port 60151
INFO [Oct 30,2024 15:02] [AmazonUtils] AWS default credentials found. AWS support enabled.
INFO [Oct 30,2024 15:02] [GenomeManager] Loading genome: https://igv-genepattern-org.s3.amazonaws.com/genomes/hg38/hg38.json
INFO [Oct 30,2024 15:03] [TrackLoader] Loading resource: {removed for privacy}
INFO [Oct 30,2024 15:05] [TrackLoader] Loading resource: {removed for privacy}
INFO [Oct 30,2024 15:05] [TrackLoader] Loading resource: {removed for privacy}
INFO [Oct 30,2024 15:05] [TrackLoader] Loading resource: {removed for privacy}
INFO [Oct 30,2024 15:05] [TrackLoader] Loading resource: {removed for privacy}
INFO [Oct 30,2024 15:05] [TrackLoader] Loading resource: {removed for privacy}

2.17.4
INFO [Oct 30,2024 15:09] [Main] Startup IGV Version 2.17.4 03/26/2024 12:38 PM
INFO [Oct 30,2024 15:09] [Main] Java 17.0.9 (build 17.0.9+9) 2023-10-17
INFO [Oct 30,2024 15:09] [Main] Java Vendor: Eclipse Adoptium https://adoptium.net/
INFO [Oct 30,2024 15:09] [Main] JVM: OpenJDK 64-Bit Server VM Temurin-17.0.9+9
INFO [Oct 30,2024 15:09] [Main] OS: Windows 11 10.0 amd64
INFO [Oct 30,2024 15:09] [Main] IGV Directory: C:\Users\me\igv
INFO [Oct 30,2024 15:09] [AmazonUtils] AWS default credentials found. AWS support enabled.
INFO [Oct 30,2024 15:09] [CommandListener] Listening on port 60151
INFO [Oct 30,2024 15:09] [GenomeManager] Loading genome: https://igv.org/genomes/json/hg38.json
INFO [Oct 30,2024 15:09] [TrackLoader] Loading resource: {removed for privacy}
INFO [Oct 30,2024 15:09] [TrackLoader] Loading resource: {removed for privacy}
INFO [Oct 30,2024 15:09] [TrackLoader] Loading resource: {removed for privacy} Expires=1730736710
INFO [Oct 30,2024 15:09] [TrackLoader] Loading resource: {removed for privacy} Expires=1730736710
INFO [Oct 30,2024 15:09] [TrackLoader] Loading resource: {removed for privacy}
INFO [Oct 30,2024 15:09] [TrackLoader] Loading resource: {removed for privacy}

Bam:
https://praxisgenomics-patient-prod.s3.us-east-1.amazonaws.com/share/share.bam?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIASEJWMTN76OTW345Z%2F20241119%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20241119T185843Z&X-Amz-Expires=604800&X-Amz-SignedHeaders=host&X-Amz-Signature=1fe2edb58014001d33002a3c93bca7eda8253a94d24adcf8ddf0babc4eb77f56

Bai:
https://praxisgenomics-patient-prod.s3.us-east-1.amazonaws.com/share/share.bam.bai?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIASEJWMTN76OTW345Z%2F20241119%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20241119T185841Z&X-Amz-Expires=604800&X-Amz-SignedHeaders=host&X-Amz-Signature=ee4ab02c3b0ab642036d7d71e9a13a228788d764d0223d26dc370754c046eeae

[jrobinso]

I can navigate around with that bam and see alignments, but I don't see any at the specific locus in your second screenshot (chrX:88,682,177-88,682,216). There doesn't seem to be anything there. This is true regardless of IGV version I use.

Could you give me more specific steps to reproduce?

[fidibidi]

Hi Jim,

Thanks for looking into this, it does seem like the version is not the issue... at least sort of? This issue has been more complicated and confusing than I realized. For some additional context, here is a brief history of me trying to figure out whats been going on.

Initially started when Lab Director was unable to load xml sessions that contained Transcriptome pURL bam files; he was able to open WGS pURL bams no issue.

The screenshot below is me trying to open the pre-signed URL I shared with you; then navigating to gene ABCA1.
I've waited for ~15 minutes before taking the image.

On this computer, I tried to uninstall/reinstall, different versions, but they always resulted in this same outcome... nothing loading.

What was extra confusing is that we tested using IGV on computers in the lab, on the same network, and they were able to load the pURL RNA bam.

With this ongoing... we decided it was time anyway to upgrade the LabDirector computer, hoping this fresh install would potentially resolve any lingering configurations that might have been the cause of our woes.

YET STILL: on this brand new computer, when I try to load the RNA pURL using 2.18.4, it doesn't appear load.

It only loaded when I installed version 2.17.4, and tried again.

(You can see in the image above it loads, but there is a strange artifact on the alignment track? )

So to be honest, I'm still at a loss for why this issue is so chronic and seemingly only affecting our Lab Directors computers. The only thing that carried over from his old computer was the Microsoft 365 User... but I don't really know how to troubleshoot further...

[jrobinso]

I'm afraid I don't have any good ideas. I see aws credentials are loaded. These shouldn't be needed for signed URLs. You might try renaming ~/.aws/credentials to ~/.aws/credentials.bak just as a test. I would be really surprised if that had any effect at all.

I'm not sure IGV on this computer is working properly for 2.17.4 either. This is what I see for gene ABCA1 with 2.18.4. It took around 7 seconds to fully load.

[fidibidi]

Wanted to update this:

A fresh install of windows with no association Microsoft user, has NOT resolved the issue on the laptop...

Tried with Java and with Java seperate; behaviour has remained the same.

Here are the device specs:

Lenovo X1 Extreme
Device name LAPTOP-1RI2RCS7
Processor Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz 2.59 GHz
Installed RAM 64.0 GB (63.7 GB usable)
Device ID 7FFD8A0C-59BD-4E21-B4AF-CBB74C4C6209
Product ID 00330-52460-12827-AAOEM
System type 64-bit operating system, x64-based processor

Edition Windows 10 Pro
Version 22H2
Installed on ‎11/‎19/‎2024
OS build 19045.5131
Serial number R90WXXQF
Experience Windows Feature Experience Pack 1000.19060.1000.0

[jrobinso]

I really don't have any ideas, well save one. Have you tried deleting the users "igv" folder? It should be located under the user home directory. Scrolling through this thread I don't see this specifically mentioned. Deleting (or better renaming) the "igv" folder will completely clear igv's cached files and user preferences.