Slow loading from localhost

[Kieran Pechter]

Hello,

My group uses localhost links to open locations in IGV; the link is generated by our analysis software and opens a browser window, IGV then loads the appropriate location via port 60151. We have used this for years with no issues, but in the past month or so, while using IGV 2.19.7, we have encountered intermittent slowness in the link loading. The browser window opens but the loading indicator spins for several minutes before finally loading in IGV. The problem will go on for a while and then suddenly the links will start loading immediately, then the problem will come back. It happens to our on site and remote (VPN) team members, and as of today we are seeing the same problem in 2.19.8. 

I am trying to determine if this is a problem with our internet service or if it has to do with IGV itself. Notably, we do not have these issues with other linkouts, including one that operates on a different localhost port. I'm attaching my log file.

Thanks in advance for any help you can provide!

Kieran

[Bryan G]

We are having a similar issue.

[igv-help]

In which of the steps below is the slowness?  Loading the annotation (a local file in your case),  initial load of the cram file, or the "goto locus" step?  

C:\Users\pechterk\igv\genomes\hg38.json INFO [Jun 24,2026 09:12] [TrackLoader] Loading resource: C:\Users\pechterk\igv\genomes\hg38\ncbiRefSeq.txt.gz INFO [Jun 24,2026 09:12] [TrackLoader] Loading resource: Z:\cons\WGS\run\WDL\2026\26-WGSN93\26U-GD-04582_RGPEX\cram\26U-GD-04582_RGPEX.cram INFO [Jun 24,2026 09:12] [TrackLoader] Loading resource: Z:\cons\WGS\run\WDL\2026\26-WGSN93\26U-GD-04582_RGPEX\cram\26U-GD-04622_GSFAM.cram INFO [Jun 24,2026 09:12] [TrackLoader] Loading resource: Z:\cons\WGS\run\WDL\2026\26-WGSN93\26U-GD-04582_RGPEX\cram\26U-GD-04623_GSFAM.cram INFO [Jun 24,2026 09:16] [CommandListener] GET /goto?locus=19:4513032-4513032 HTTP/1.1

[igv-help]

Also, could you try these steps manually from the IGV UI? 

[Kieran Pechter]

It should be the goto locus step, which is coming from http.

The other parts do not exhibit any lag; they are done manually using the UI.

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[James Robinson]

And do you see the same delay when entering the locus manually through the UI?   Also, is your hg38.json file customized,  or is the standard download?   If the latter, try refreshing it from the "Genomes" menu (select it again).    If it's customized I might need to see it.

On Wed, Jun 24, 2026 at 8:48 AM Kieran Pechter <kpec...@gmail.com> wrote:

It should be the goto locus step, which is coming from http.

The other parts do not exhibit any lag; they are done manually using the UI.

On Wed, Jun 24, 2026, 11:45 AM igv-help <igv-...@googlegroups.com> wrote:

In which of the steps below is the slowness?  Loading the annotation (a local file in your case),  initial load of the cram file, or the "goto locus" step?  

C:\Users\pechterk\igv\genomes\hg38.json INFO [Jun 24,2026 09:12] [TrackLoader] Loading resource: C:\Users\pechterk\igv\genomes\hg38\ncbiRefSeq.txt.gz INFO [Jun 24,2026 09:12] [TrackLoader] Loading resource: Z:\cons\WGS\run\WDL\2026\26-WGSN93\26U-GD-04582_RGPEX\cram\26U-GD-04582_RGPEX.cram INFO [Jun 24,2026 09:12] [TrackLoader] Loading resource: Z:\cons\WGS\run\WDL\2026\26-WGSN93\26U-GD-04582_RGPEX\cram\26U-GD-04622_GSFAM.cram INFO [Jun 24,2026 09:12] [TrackLoader] Loading resource: Z:\cons\WGS\run\WDL\2026\26-WGSN93\26U-GD-04582_RGPEX\cram\26U-GD-04623_GSFAM.cram INFO [Jun 24,2026 09:16] [CommandListener] GET /goto?locus=19:4513032-4513032 HTTP/1.1

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[James Robinson]

And, for the best performance check "Download sequence" when you select the genome.  You'll need to be patient on the initial download, and it will of course take disk space, but it will be fast and you will be mostly immune from network issues.

 Screenshot 2026-06-24 at 8.52.08 AM.png

[Kieran Pechter]

Thank you! I actually downloaded the genome I use the most (Human GRCh38/hg38) because of the recent issue with UCSC. It unfortunately had no impact on this issue.

We do not see any delay when opening the locus manually through the UI. That has been our workaround when we encounter this issue.

For the hg38 json file, I do not think it is customized but am attaching it here just in case!

[James Robinson]

Hi, I can't reproduce this.  Try opening the "developer tools" in your browser.   This will let you see the network interaction to localhost to some extent.   In Chrome it looks like this.   There is a timing tab, but in my case it doesn't show much as I can't reproduce the problem.  

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[AP]

We had similar issues with either IGV 2.16 or 2.19.  We first made sure local host is configured on the windows machines. 127.0.0.1 in hosts file was commented out for us.

After this Firefox based localhost:60151 worked just fine. But not for chrome and Edge users.

 Surprisingly, we were able to resolve for this users  by switching to  incognito mode (on chrome) and InPrivate mode on Edge. 

Hope it helps.

[James Robinson]

A possibly related issue I have become aware of,  if you are accessing the port through javascript it might stop working altogether soon, due to new browser security rules.   However it should just stop working, not work but slowly.

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