hg19 genome loading problem

[Dominika]

Hi,

Now, today, I have problem with connection to the igv genom server and hg19 genome loading. My IGV doesn't work. Please help.

[sania Rauf]

Is there anyone who can help me to learn IGV in detail for WES data?

On Thu, Jul 10, 2025, 1:27 PM DUYGU GAMZE ARACI <gamzed...@gmail.com> wrote:

I do also have the same problem for today. I hope that they'll resolve it soon.

10 Temmuz 2025 Perşembe tarihinde saat 11:21:07 UTC+3 itibarıyla Dominika şunları yazdı:

Hi,

Now, today, I have problem with connection to the igv genom server and hg19 genome loading. My IGV doesn't work. Please help.

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[Ezgi DAŞKIN]

I also received the same error for mm10 

  "Unexpected error: org.broad.igv.exceptions.HttpResponseException: Access forbidden.See igv.log for more details"    

[Dario Cocciadiferro]

  Same here. The genome 'Human hg19' could not be read.     

[Miloslav Švub]

Error loading genome: hg19

Dne čtvrtek 10. července 2025 v 11:26:30 UTC+2 uživatel Dario Cocciadiferro napsal:

[María José Ariza Corbo]

I'm having exactly the same problem today. Thank you.

[igv-help]

Hi all,

Are you running older versions of IGV? If you are running a version older than 2.19.0, please try the following:

- install the latest IGV from https://igv.org/doc/desktop/#DownloadPage

- remove (or rename) the genomes subfolder from the igv folder (in your user home). 

- run IGV again

[Miloslav Švub]

I downloaded hg19 locally to my PC and it helped. Until now I was using the remote annotations.

Dne čtvrtek 10. července 2025 v 14:50:33 UTC+2 uživatel igv-help napsal:

[David Pisapia]

getting the same error.  running v2.19.4

[hoai tran]

I have the same error for mm10

[David Pisapia]

ok, I deleted that genomes folder, and IGV is working again. thanks

On Thursday, July 10, 2025 at 8:50:33 AM UTC-4 igv-help wrote:

[igv-help]

For everyone having this error,  please try loading your genome again from the Genomes menu.  

[Mark Routbort]

We don't have the option to switch to the latest version of IGV immediately as we are a clinical lab and use automated session files as well which will need to be updated.

The breaking point for us seems to be the access forbidden on the legacy Genome Server http://igv.broadinstitute.org/genomes/genomes.txt

For our users we could host this file or a modified version of it locally, and point to it using our very old version of IGV (2.4).  Is it possible to get this file?

Mark

[hoai tran]

It is working again! Thank you!

[igv-help]

Hi Mark,  the permissions problem should be resolved.   However, to future proof your application it would be a good ideal to host what you need locally.    If you let us know what genome assemblies we use we can prepare some files and/or instructions for you.

[igv-help]

Correction, genome assemblies you use.

[Εμμανουέλα Λιναρδακη]

Hi! We have the same issue as well today! Any help would be greatly appreciated!

[Mark Routbort]

Many thanks, we are back in business with even our old version of IGV working.

We just use hg19 and then some custom dynamically loaded reference transcriptomes/fasta files.

We have hosted a .genome file locally in the past.  Looks like the formats of some things have been updated and the main thing we need to do is validate a more recent version of IGV and make sure our session files work with it.

Mark

[igv-help]

Hi Mark,

.genome files are still supported,  newer versions of IGV use a .json format.     You can remain on 2.4 but I would recommend you host all needed files locally.  

As you probably know a ".genome" file is just a zip archive.  The steps to creating a locally hosted version (including sequence) follow

(0) download the genomes.txt file from https://raw.githubusercontent.com/igvteam/igv-data/refs/heads/main/genomes/legacy/genomes.txt

(1) download the .genome file of interest, or just copy it from your "igv/genomes" folder

(2) unzip the genome file to a tmp directory.      "unzip hg19.genome"

(3) examine the "property.txt" file.   The "sequenceLocation" property has the URL to the fasta file.   Download this and upload it to your local server.  Also transfer the fasta index, which will have the same URL + ".fai" extension.   For example "https://igv.org/genomes/data/hg19/hg19.fasta.fai"

(4) update the sequenceLocation in property.txt to the new location

(5) rm the original "hg19.genome" file

(6) zip all files to create a new "hg19.genome" file ->   "zip hg19.genome *"

(7) upload the new hg19.genome file

(8) edit "genomes.txt",  replace the url to hg19.genome with the new location.  Note this is a tab delimited format, the genome url is the middle column.   You might also want to remove the other entries

(9) instruction your users to update the genomes.txt url in the "Advanced" tab of user preferences

I do not have any hardware that can even run version 2.4,  so I can't test this for you, but if you have any issues post them here.