Complete loss of access to hg38 and hg19 reference genomes affecting all users

[BPenn]

I am using 2.18.2. Today when I try to load hg38 or hg19, I get an unexpected error.

My entire team is seeing the same thing.  Upgrading to 2.19 did not solve the problem.

[igv-help]

Thanks for letting us know. IGV retrieves the reference genome and the annotation tracks from the UCSC site at https://hgdownload.soe.ucsc.edu and it appears to be down. They usually address issues like that quickly.

In the meantime, we do have a copy of the reference genome that will be loaded if you use the attached genome json files. You load them via Genomes > Load Genome from File.  They will not load the refseq track, but hopefully this will be helpful until the UCSC site is back up.

[BPenn]

Thanks for the quick response. Nothing happens when I load the genome from the attached file i.e I can't see any tracks or look up chromosomal locations.

[igv-help]

As I mentioned, this only loads the reference genome itself, not the refseq annotation track that is usually loaded by default with the reference genome. It allows you though to load any data files and annotations either local or from the internet (just not from UCSC while their site is down). Not sure what you mean by not being able to look up chromosomal locations.  Entering eg EGFR in the search box or entering a genomic locus works for me.

[BPenn]

You are right, I can now see the sequence, enter a genomic locus etc, but no transcripts.

I found the response from UCSC:

https://groups.google.com/a/soe.ucsc.edu/g/genome/c/REsxI1Q6gG8

Is there a way to use this second server instead in IGV?

https://hgdownload2.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit

[Adam Clayton]

I have the same question. It looks like IGV is referencing the server  https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit in this link https://igv.org/genomes/json/hg19.json but I don't see how to change anything in that link locally. Any tips on how to access the hgdownload2 UCSC server would be great.

[igv-help]

Thanks for the info about the alternate UCSC site.

Attached are updated .json files that use it instead for hg38 and hg19. 

FYI, If you need other genomes, you can find the list of where all of IGV .json genome files are here: https://igv.org/genomes/genomes.tsv

Then you can download the .json of interest and update it as needed.

[BPenn]

 Thank you! I can only see the RefSeq select track and not the RefSeq Curated track, but it worked.

[igv-help]

It appears as though the main UCSC site is back up.