IGV not working

[loklam2024]

Hi, my IGV desktop not working. I am getting 'connect timed out' messages:

or other messages:

Please can you help?

[maximilianh]

This may have to do with downtime of the UCSC download server. Or the move of the S3 bucket ? Either way, it’ll take us a few hours to look into it, as the US West is not awake yet for a while. It should work again as soon as they’re up, so in 5-6 hours.

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On Wed, Jun 24, 2026 at 11:05 loklam2024 ***@***.***> wrote: *loklam2024* created an issue (igvteam/igv#1840) <#1840> Hi, my IGV desktop not working. I am getting 'connect timed out' messages: image.png (view on web) <https://github.com/user-attachments/assets/992091f4-c2a2-4bb9-8a04-1c51c38e12be> or other messages: image.png (view on web) <https://github.com/user-attachments/assets/e1324bba-bf42-46bf-87d9-f80bb80e429e> Please can you help? — Reply to this email directly, view it on GitHub <#1840?email_source=notifications&email_token=AACL4TJNDZII4NKDIC4PYA35BOKVPA5CNFSL4Z3JMQ5C6L3HNF2C22DVMIXUS43TOVSS6NBXGMZTGMRZHE4TDJTSMVQXG33OVJZXKYTTMNZGSYTFMSSWK5TFNZ2KYZTPN52GK4S7MNWGSY3L>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AACL4TPQVE5TOFXX3QY4IXL5BOKVPAVCNFSNUABDKJSXA33TNF2G64TZHMZTIMJWGU3TQO2JONZXKZJ3GQ3TGMZTGI4TSOJRUF3AE> . Triage notifications, keep track of coding agent tasks and review pull requests on the go with GitHub Mobile for iOS <https://github.com/notifications/mobile/ios/AACL4TIPOB7YHOHHFIX2IQ35BOKVPA5CNFSL4Z3JMQ5C6L3HNF2C22DVMIXUS43TOVSS6NBXGMZTGMRZHE4TDJTSMVQXG33OVJZXKYTTMNZGSYTFMSSWK5TFNZ2KUZTPN52GK4S7NFXXG> and Android <https://github.com/notifications/mobile/android/AACL4TKHGJNRCEM32IXU6F35BOKVPA5CNFSL4Z3JMQ5C6L3HNF2C22DVMIXUS43TOVSS6NBXGMZTGMRZHE4TDJTSMVQXG33OVJZXKYTTMNZGSYTFMSSWK5TFNZ2K4ZTPN52GK4S7MFXGI4TPNFSA>. Download it today! You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[jrobinso]

@loklam2024 There's not enough information to isolate the problems. What version of IGV are you using? Could you zip and attach your igv log file, it's located in an "igv" folder and probably has a name like "igv0.log". Also, I suggest you refresh you genome file definition by loading/selecting it again from the "Genomes" menu (note, not the pulldown widget, the menu).

@maximilianh Was there an outtage? I have an igv-help ticket about slowness loading crams, which is probably from loading the 2bit sequence to decode them.

[maximilianh]

There still is on outage, at least for me, hgdownload.gi.ucsc.edu is not reachable, it looks like it's being targeted by a SYN DOS attack, why anyone would target our download server is a mystery to me. We need to block these requests in the firewall.

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On Wed, Jun 24, 2026 at 9:02 AM Jim Robinson ***@***.***> wrote: *jrobinso* left a comment (igvteam/igv#1840) <#1840 (comment)> @loklam2024 <https://github.com/loklam2024> There's not enough information to isolate the problems. What version of IGV are you using? Could you zip and attach your igv log file, it's located in an "igv" folder and probably has a name like "igv0.log". Also, I suggest you refresh you genome file definition by loading/selecting it again from the "Genomes" menu (note, not the pulldown widget, the menu). @maximilianh <https://github.com/maximilianh> Was there an outtage? I have an igv-help ticket about slowness loading crams, which is probably from loading the 2bit sequence to decode them. — Reply to this email directly, view it on GitHub <#1840?email_source=notifications&email_token=AACL4TI6DIWJGN33LSR3IED5BP3RDA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTINZZGEZDKOBYGAZ2M4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJLDGN5XXIZLSL5RWY2LDNM#issuecomment-4791258803>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AACL4TKXGZ2YUXWCS2TPB235BP3RDAVCNFSNUABDKJSXA33TNF2G64TZHMZTIMJWGU3TQO2JONZXKZJ3GQ3TGMZTGI4TSOJRUF3AE> . Triage notifications, keep track of coding agent tasks and review pull requests on the go with GitHub Mobile for iOS <https://github.com/notifications/mobile/ios/AACL4TKBF74QM7SWWFFICQD5BP3RDA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTINZZGEZDKOBYGAZ2M4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJKTGN5XXIZLSL5UW64Y> and Android <https://github.com/notifications/mobile/android/AACL4TKXFADFRY6URWBXP5T5BP3RDA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTINZZGEZDKOBYGAZ2M4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJLTGN5XXIZLSL5QW4ZDSN5UWI>. Download it today! You are receiving this because you were mentioned.Message ID: ***@***.***>

[loklam2024]

@loklam2024 There's not enough information to isolate the problems. What version of IGV are you using? Could you zip and attach your igv log file, it's located in an "igv" folder and probably has a name like "igv0.log". Also, I suggest you refresh you genome file definition by loading/selecting it again from the "Genomes" menu (note, not the pulldown widget, the menu).

@maximilianh Was there an outtage? I have an igv-help ticket about slowness loading crams, which is probably from loading the 2bit sequence to decode them.

Hi, I'm using 2.19.1. I can't find the igv0.log files I'm afraid. Still not loading/working.

[jrobinso]

We use these URLs for hg38 (+ a few more). They are working for me.

https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ncbiRefSeq.txt.gz
https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit

[jrobinso]

@loklam2024 Have you looked in your home directory for an "igv" folder? Also, did you try refreshing your genome from the Genomes menu as suggested? And which genome are you using?