"The genome mm10 could not be read. Would you like to remove this entry?"

[Adrian Arrieta]

Restarted computer and IGV browser, and re-added the genome. Same error. Just me or is something happening on the server side?

[igv-help]

What version of IGV are you using?

[Adrian Arrieta]

Using this version:

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[James Robinson]

Could you clear the genomes in your genomes folder and try it again?    The "genomes" folder is in the "IGV" folder, which itself is under your home directory.   You can delete everything in there.

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[Adrian Arrieta]

Cleared and re-added. Was able to add Rn6, Rn7, mm9 without trouble.

To view this discussion visit https://groups.google.com/d/msgid/igv-help/CACOP%2BptiZaRp6_0%3Du%2B42jasUHJ3Dvu8DsYpdgi17%2Bc3LJ6bAgQ%40mail.gmail.com.

[Adrian Arrieta]

Installed newest version of IGV, didn't help either.

[Adrian Arrieta]

From IGV Log:

SEVERE [May 28,2026 06:17] [MessageUtils] The genome 'Mouse (GRCm38/mm10)' could not be read.
SEVERE [May 28,2026 06:17] [MessageUtils] java.lang.RuntimeException: org.broad.igv.exceptions.HttpResponseException: Access forbidden <br>
at org.igv/org.broad.igv.feature.genome.CytobandMap.<init>(CytobandMap.java:20)
at org.igv/org.broad.igv.feature.genome.Genome.<init>(Genome.java:200)
at org.igv/org.broad.igv.feature.genome.load.JsonGenomeLoader.loadGenome(JsonGenomeLoader.java:42)
at org.igv/org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:169)
at org.igv/org.broad.igv.feature.genome.GenomeManager.loadGenomeById(GenomeManager.java:142)
at org.igv/org.broad.igv.ui.commandbar.GenomeComboBox$GenomeBoxActionListener.lambda$actionPerformed$0(GenomeComboBox.java:97)
at org.igv/org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:73)
at org.igv/org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:43)
at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)
Caused by: org.broad.igv.exceptions.HttpResponseException: Access forbidden <br>
at org.igv/org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:876)
at org.igv/org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:658)
at org.igv/org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:654)
at org.igv/org.broad.igv.util.HttpUtils.openConnectionStream(HttpUtils.java:361)
at org.igv/org.broad.igv.util.HttpUtils.openConnectionStream(HttpUtils.java:355)
at org.igv/org.broad.igv.util.ParsingUtils.openInputStreamGZ(ParsingUtils.java:126)
at org.igv/org.broad.igv.util.ParsingUtils.openInputStream(ParsingUtils.java:98)
at org.igv/org.broad.igv.util.ParsingUtils.openBufferedReader(ParsingUtils.java:81)
at org.igv/org.broad.igv.feature.genome.CytobandMap.init(CytobandMap.java:29)
at org.igv/org.broad.igv.feature.genome.CytobandMap.<init>(CytobandMap.java:18)
... 11 more

[igv-help]

I'm stumped on this one.   Are you able to access  https://hgdownload.soe.ucsc.edu/hubs/GCF/000/001/635/GCF_000001635.26/bbi/GCF_000001635.26_GRCm38.p6.cytoBand.bb

[和也阿部]

I am experiencing the same issue on Mac.

I deleted the IGV cache, reinstalled IGV, and restarted my computer, but mm10 still cannot be loaded.
I also get the following error:

“Unexpected error: org.broad.igv.exceptions.HttpResponseException: Access forbidden”

Interestingly, mm9 can still be downloaded without problems.

So this may be an issue on the server side for the mm10 resource.

2026年5月28日木曜日 9:23:41 UTC-4 Adrian Arrieta:

[igv-help]

Can you access https://hgdownload.soe.ucsc.edu/hubs/GCF/000/001/635/GCF_000001635.26/bbi/GCF_000001635.26_GRCm38.p6.cytoBand.bb?

[Riitta Lindström]

We have the same issue, trying to access 

https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/genes/refGene.hg19.bed.gz
http://igv.broadinstitute.org/annotations/hg19/genes/refGene.hg19.bed.gz

Getting this kind of error:

This XML file does not appear to have any style information associated with it. The document tree is shown below.

<Error>

<Code>AccessDenied</Code>

<Message>Access Denied</Message>

<RequestId>DZPHE4TTH2T1BYH0</RequestId>

<HostId>sp8oh1vTXOlS0sH9ID9CoTASjSnFFR+ObJoSxGycQesLXY/NvSg0NDvOBeSdTQzC3Ko1tUX+r0a+2jU3d/VUVXHMIMJGMP4s</HostId>

</Error>

We had the same issuee July 10th 2025 related to this thread: 

https://groups.google.com/g/igv-help/c/q8LkqfNvxkM/m/PxUJDghCBgAJ

We use embedded web browser IGV and version is 2.3.5, MacOS. However, I'm not able to access these neither of these links with Windows laptop (Firefox or Chrome browser), either.

[igv-help]

If using an embedded web component updatin your  "genomes.json" file should resolve the problem.   I don't know enough about your setup to give specific advise but this is the current genomes: "https://igv.org/genomes/genomes3.json",

genomes: "https://igv.org/genomes/genomes3.json",

[Adrian Arrieta]

Current json file attached.

To view this discussion visit https://groups.google.com/d/msgid/igv-help/b62b4a56-3853-4350-899c-c286f8fb47e6n%40googlegroups.com.

[igv-help]

Where is that json file coming from?  This is not going to work

  "cytobandURL": "https://s3.amazonaws.com/igv.broadinstitute.org/annotations/mm10/cytoBandIdeo.txt.gz",

I think you indicated you cleared your genome cache, if so I don't know where you are getting this reference.   The current definition is

"cytobandURL": "https://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/cytoBand.txt.gz",

I would really like to understand how you are getting an old json definition after clearing your cache.   If you select "View > Preferences > Advanced" tab what does it have for the Genome Server URL?

[Adrian Arrieta]

It came directly from my computer?

To view this discussion visit https://groups.google.com/d/msgid/igv-help/0e8a3012-94f8-4240-9e7e-697bf7117069n%40googlegroups.com.

[igv-help]

Right, but the question is how did it get there?  If you load from the IGV genomes menu for any release since 2.15 you should get this

https://raw.githubusercontent.com/igvteam/igv-data/refs/heads/main/genomes/json/mm10.json

[Adrian Arrieta]

To start, I'll re-install IGV. Keep you posted.

To view this discussion visit https://groups.google.com/d/msgid/igv-help/99f18b1d-f4db-4802-8290-74a37f06a4fan%40googlegroups.com.

[James Robinson]

Reinstalling IGV is not necessary, and won't remove your existing mm10.json.   All you need to do is redownload it from "Genomes > Download Hosted Genome".   Alternatively you can just replace your existing mm10.json with the one I linked to.

To view this discussion visit https://groups.google.com/d/msgid/igv-help/CAHU%3D3rr7NM4OxZckPHtHijk9nS9dwtVRnVqYwqEm%2Bkv5b3n0WA%40mail.gmail.com.

[Riitta Lindström]

The problem is that https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/genes/refGene.hg19.bed.gz has been publicly available, it has been for ages (also working yesterday), but it is not publicly available anymore. Last year when we experienced the exact same issue (also then we got the Forbidden Access when our IGV tried to call this URL), we did not change anything in our end and our issue resolved when you fixed the permission issue in your end. We use this URL to get Genes track in IGV.

Last year igv-help responded in message https://groups.google.com/g/igv-help/c/q8LkqfNvxkM/m/U_JHJkNaBgAJ : 
"the permissions problem should be resolved" 

Could you have another look on the permissions of this URL if it has changed and if the permissions could be restored? Thank you in advance.

[igv-help]

Hosting that file and others on Amazon is not free,  in fact it's a substantial cost.  For several years we have been transitioning away from Amazon storage.   Releases of IGV since 2.15 should be be reliant on these files,  although cached genomes sometimes need to be cleared.   For older releases I am available to provide workarounds, which in most cases are fairly simple.    

[igv-help]

Typo there,  it should read "...2.15 should NOT be reliant."

[igv-help]

This thread was opened specifically for mm10,  so I want to bring the topic back to that.   This should be resolved now for IGV versions 2.14 - 2.19,  but you will need to redownload the mm10 genome from the "Genomes" menu, in 2.15 the menu item is "Select Genome From Host".    Other versions might have different wording,  but in all cases you need to download from the "Genomes" menu and not the pulldown genome widget.   After successful download you can use the pulldown widget.    The "Genomes" menu item downloads a fresh copy, the pulldown widget just loads the local copy previously downloaded.

[Teri]

Note: I did get it to work (my solution is at the end).

I have been having the same issue. I used mm10 in IGV early this week and it was fine and then yesterday when I open IGV the mm10 would not load. The hg19, mm39 & C.elegans load just fine, but hg38 also errors. If I look at the json for the genomes that load vs the ones that did not, the only noticeable difference is the cytobands url is hgdownload for those that load and amazon for those that don't. I am running Ubuntu. 

For mm10, I checked the json and it is the same as Adrian's. I replaced it with the one that was posted by igv-help and tried to load genome from file selecting the new json but nothing happened. 

I was running IGV version 2.12, so I updated to 2.16 and tried to open mm10 and got the same error as before. I checked the json and it had reverted back to the original version. If I alter the json, it will always revert back to the json Adrian showed if I load mm10 by selecting it from the dropdown menu in the main viewer. 

If I remove mm10 from the list and then click more to select the genome from the available genomes, the json will revert to the one Adrian showed and mm10 will not load.

If I delete all the genomes in the igv/genomes/ and then select mm10 from the dropdown menu > Mouse mm10, the json that is downloaded is the one Adrian showed.

If I delete all the genomes in igv/genomes and the 'select hosted genome' from the Genomes menu and pick mm10, it downloads the json Adrian showed.

And because this was asked earlier:

View>preferences>advanced: the genome server URL is https://s3.amazonaws.com/igv.org.genomes/genomes.tsv 

But I did get it to work eventually. I made a copy of the mm10.json (the one Adrian showed) and replaced only the cytobands line with cytobands line from json igv-help linked. And then I use 'load genome from file' and selected the new mm10_altered.json. And it now works fine again.

[igv-help]

Messages are crossing.  This is fixed now see above message.

To fix version 2.12 - 2.13 you need to change your Genome Server URL in advanced preferences to https://igv.org/genomes/genomes.tsv.