Problem in uploading hg37/hg19

[sania Rauf]

Dear Team

I tried to upload Hg37 but its keep saying " The genome 'Human (GRCh37/hg19)' could not be read. "is there any problem in server? because even i cannot upload my bam files to read on IGV

Kind regards

Sania

[igv-help]

Are you still having this problem? Everything seems to be ok on our end.

Helga

[Paul Avalos]

Hello, I am not the original poster but we are having a similar/same issue

We are currently using IGV 2.12.3. When opening the Desktop app, we receive "Error loading genome: hg19". Pressing OK gives us " Unexpected error:null. See igv.log for more details". I do not know where to find igv.log

Clicking on Hg19 from the top left gives "The genome [Hg19] could not be read. Would you like to remove the selected entry?".

I have also tried Going to Genomes>Select Hosted Genomes and receive the error " Warning: could not connect to the genome server (https:\\s3.amazonaws.com/igv.org.genomes/genomes.tsv) Or locally defined genomes will be available." This opens to a "Hosted Genomes" window that is blank with nothing to select. I'm not sure if this is related.

Thank you,

Paul

[igv-help]

Hi Paul,

The Amazon host that supported older versions of IGV (> 5 years old) is being decommissioned.   To fix this problem you need to edit your preferences.   Specifically select "View > Preferences > Advanced tab".   There is a field on this tab for the "Genome Server URL".   Replace the entry there with the following

https://igv.org/genomes/genomes.tsv

You might run into other issues,  I will help you work around them, but this is the first step.

-- Jim

[Natasha Chavez]

Hi, I'm not the original posted but we are having similar issues. 

1) Browser IGV in non functional for us 

2) Desktop IGV for users who updated to the newer versions are loading h19 but not loading hg38 

We would appreciate any insight. 

Thanks, 

Natasha 

[Adam Clayton]

I'm seeing the same outage where UCSC hosted genomes aren't loading. I suspect a UCSC outage?

-Adam

[James Robinson]

For users who cannot load hg38 in the latest version what error are they seeing?   If you can send us the igv log that might be helpful.   It is located in an "igv" folder in their home directory with the name "igv0.log", "igv0.log.1", or similar.   You can email it to igv-...@broadinstitute.org.

Also, in the "igv" folder is a subfolder called "genomes".    Check for the presence of a file called "hg38.json".   If present please send us a copy.   

Finally,  if you save the attached "hg38.json" file in the "igv/genomes" folder it might resolve the issue you are seeing.   This file will work for the latest release (2.19.X)

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[Natasha Chavez]

Emily and Jaimie would you be able to add on? 

Natasha Chavez

Manager, CLS - Carrier Screening

nch...@natera.com

mobile: 408.427.1101

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[Adam Clayton]

Sorry my issue was separate from this where the UCSC genomes weren't loading. My work around was actually setting up a local version of the hg19 files, which is working.

-Adam

[Jaimie Schweiger]

Well, now it seems like it's not loading HG19 either and I just got these messages:

 

My URL is already updated in the Advanced preferences, I did not edit anything there. 

I do have both json but that doesn't seem to matter 

--

Jaimie Schweiger, MLS(ASCP)

Senior MLS Data Reviewer, Carrier Screening

jschw...@natera.com

Phone: 650.249.2203

[Jaimie Schweiger]

Just got this

Which then removed Hg19 from the drop down. Tried to manually import it again and now I get this:

 

[igv-help]

I  suspect your institution is blocking access to our github URLs.   To confirm that I need to see your igv log and the "hg19.json" or "hg38.json" in your igv/genomes folder.   You can email this to igv-...@broadinstitute.org.    I can provide a workaround but need to see what's in those files first.

As mentioned above you can email these files to igv-...@broadinstitute.org

[Natasha Chavez]

Thanks for the information. +Jaimie Schweiger +Emily Onyema +Davis Chettupuzha looks like you might have gotten looped out 

To view this discussion visit https://groups.google.com/d/msgid/igv-help/92c1b0ae-ebaa-4a43-83fc-8999c905aaaen%40googlegroups.com.

--

[Jaimie Schweiger]

and igv log 

On Mon, Jun 1, 2026 at 4:27 PM Jaimie Schweiger <jschw...@natera.com> wrote:

These are my hg19 and hg38 json

[Jaimie Schweiger]

These are my hg19 and hg38 json

[igv-help]

@Jaimie The json files look fine, and unfortunately there is nothing informative in the log.    This is a long thread with multiple issues, some unrelated to the problem you are seeing.  So for clarity when did this problem first appear?    

As an experiment let's try the following

1. From the Genomes > Load from URL menu load the fasta directly with this URL:   https://igv.org/genomes/data/hg38/hg38.fa

2. Load the annotation file from File > Load from URL > File URL:  https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ncbiRefSeq.txt.gz

Let us know if this works.   

As another experiment you might try the current release, 2.19.7.    While it might not be possible to update immediately the result might give us more information.

Finally you might try deleting or renaming the entire "igv" folder while IGV is shutdown,  then restart.   This clears all cached items.

-- Jim

[Natasha Chavez]

+Emily Onyema +Jaimie Schweiger 

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