Team Sporadically Unable to Load Ref Genomes Past 3 Days - Absolutely Cannot Today

[Stephen Michel]

First noticed Wednesday, 8/5, me and my team were having difficulties loading hg19 and hg38.

I've confirmed my genome server URL is https://igv.org/genomes/genomes.tsv

Ultimately the most common feedback I've received when IGV fails to load the reference genome is this:

We've randomly been able to load at different times the past few days, but haven't had any success today.

IGV Version 2.16.1 04/19/2023 02:19AM

Windows 11 10.0 amd64

Example log output when reference genome fails to load:

INFO [Aug 07,2026 09:38] [GenomeManager] Loading genome: C:\Users\smichel3\igv\genomes\hg19.json
SEVERE [Aug 07,2026 09:38] [GenomeComboBox] java.lang.NullPointerException: Cannot invoke "java.io.BufferedReader.close()" because "br" is null
        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.feature.genome.GenomeManager.loadGenomeById(GenomeManager.java:175)
        at org.igv/org.broad.igv.ui.commandbar.GenomeComboBox$GenomeBoxActionListener$1.run(GenomeComboBox.java:123)
        at org.igv/org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
        at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
        at java.base/java.lang.Thread.run(Thread.java:1583)

[igv-help]

Thanks for letting us know. We're looking into it.

[igv-help]

Hi, could you try re-downloading your genome from the Genomes menu and let us know if it improves?    For IGV 2.16 you do this with the "Select Hosted Genome.." option,  then select the genome of interest and click "OK".

[Stephen Michel]

Hello,

I just booted up v2.16.1 and didn't even need to go that far. Human (GRCh37/hg19) loaded upon booting. 

Switching between hg19 to hg38 and back to hg19 caused no issues, so it appears to be working okay thus far.

[James Robinson]

The problem seems to be intermittent.   If it recurs try the steps suggested.   

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[Stephen Michel]

Fair enough. I will keep you in the loop. It is worth saying that I had attempted the outlined steps above unsuccessfully earlier today and on previous days, in the event that no changes have been made on your end.

[robin...@gmail.com]

I updated  the genome jsons for hg19 and hg38 earlier today.   

[robin...@gmail.com]

Could I ask where you are located?  We're trying to determine if physical distance from UCSC (Santa Cruz) CA, USA is a factor

[Stephen Michel]

Minneapolis, MN