Unable to load Genome

[deepa paul]

Dear Team,

I am unable to load genomes in IGV. Kindly advice on how to rectify this issue.

Thank you,

Deepa

[JoyitaB]

Hi, I'm too facing issues with loading genome in the IGV desktop application. I'm using IGV 2.19.6 version. 

Please help to resolve this issue. Thanks!

[JoyitaB]

To add to my previous post, I'm from India and I'm using Windows OS. I have tried loading RefSeq by opening available datasets and also tried by loading from the URL. 

IGV is just remaining blank. I have tried using previous versions too, but still remained same. Please suggest to resolve this issue. 

[igv-help]

There are questions from 2 people on this thread.

To Deepa: 

If this is still an issue for you, please let us know more about your problem. We cannot know what might be going on unless you describe the problem. The more details the better, including the version of IGV you are using, exactly what you are seeing, and the precise steps to reproduce the problem. Screenshots can also be helpful. Sometimes the IGV log has information that is useful for our debugging; you can find it in the folder named "igv" in your user home. It is will be named igv0.log or something similar.

To JoyitaB:

I'm not sure what you are trying to do. A RefSeq track is typically loaded by default for the most common reference genomes. You shouldn't need to load it yourself. You will need to zoom in to see the details of the gene annotations. If you still think it is a problem, feel free to send more details, including the precise steps to reproduce the problem; screenshot(s); info from the IGV log file named igv0.log (or something similar) in the "igv" folder in your home folder.

Helga

[Minh-Duc Nguyen]

Hi everyone,

I am having the same issue when using the web app version of IGV (igv.org/app). The error I got was:

Error accessing resource: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ncbiRefSeq.txt.gz Status: 0

Some members of my team also ran into this issue while others did not. So I think this is a network issue?

Please let me know if you need further information. Thanks for your time!

Minh-Duc

Vào lúc 03:51:22 UTC+7 ngày Thứ Sáu, 19 tháng 9, 2025, igv-help đã viết:

[Jeff Koble]

Hi,

I am also getting what seems to be a connection error despite my internet being fine.

I tried selecting Genomes -> Select hosted Genome -> human (hg38)

Using version 2.16.2 and I was able to upload this genome yesterday.

Error message below.

Unexpected error: null 

See ig.log for more details

igv.log message below

INFO [Sep 22,2025 09:36] [GenomeManager] Loading genome: https://raw.githubusercontent.com/igvteam/igv-data/refs/heads/main/genomes/legacy/json/hg38.json
SEVERE [Sep 22,2025 09:37] [LongRunningTask] Exception running task
SEVERE [Sep 22,2025 09:37] [LongRunningTask] java.lang.NullPointerException
at org.igv/org.broad.igv.feature.genome.load.JsonGenomeLoader.loadGenome(JsonGenomeLoader.java:167)
at org.igv/org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:197)
at org.igv/org.broad.igv.ui.commandbar.GenomeComboBox.lambda$loadGenomeFromServer$1(GenomeComboBox.java:260)
at org.igv/org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)

Thanks,

Jeff 

[igv-help]

Hi Minh-Duc,

It's working for me right now. IGV-Web retrieves that file directly from the site of the UCSC Genome Browser database. I wonder if there was a brief outage there when you were trying to use IGV. If you continue to experience the problem In IGV, can you try entering that link directly into your web browser to see if it is only a problem with IGV or if it is a general issue with connecting to that URL.

Helga

[igv-help]

Hi Jeff,

I ran the version of IGV you are running and I was able to load hg38 without issue.  

As I mentioned to the other user in this thread,  IGV retrieves genome-related files directly from the site of the UCSC Genome Browser database. I wonder if there was an outage there when you were trying to use IGV. In the hg38.json genome definition file that IGV retrieves  from our GitHub site (see URL in the log message you posted) you can see exactly which files are used for the genome. If you are still experiencing problems in IGV, check to see if those genome files are in general accessible through a web browser.

If it's only an issue with accessing the files through IGV, you could try renaming or deleting the "genome" folder in the "igv" folder where the log file is. 

Also, note that IGV 2.16.2 is more than 2 years old. I recommend updating to a newer version.

Helga