Failure to connect to hgdownload.soe.ucsc.edu

[Cully, Todd]

Hello

Our users are currently experiencing an intermittent issue when accessing resources hosted on hgdownload.soe.ucsc.edu.

We have performed troubleshooting on our end and, based on our findings, the connection appears to be timing out when attempting to reach your server. Users have tested with different browsers, restarted their systems, and confirmed that the issue persists intermittently.

In some cases, simply refreshing the browser tab allows the page to load successfully, while at other times the request times out.

Could you please review your logs and let us know if there are any known service issues, rate-limiting policies, or other factors that might be contributing to this behavior?

 

Thanks,

 

Todd Cully | LIS Administrator

Caris Life Sciences

4415 Cotton Center Blvd, Suite 100, Phoenix, AZ 85040

Mobile: 480-772-1544

CarisLifeSciences.com

 

 

This email message and any attachment thereto is for the sole use of the intended recipient(s) and may contain confidential information. If you are not the intended recipient, please contact the sender by reply email and permanently delete this email, any attachment(s) and all copies made of the original message or attachment(s). Any unauthorized review, use, disclosure or distribution is prohibited.

 

 

[Hiram Clawson]

Good Afternoon Todd:

Do you have any information on the types of requests or which files are
attempted access at the site that may be failing ? I realize an intermittent
outage is difficult to pin down, but if you have any examples at all,
this may provide clues. At the moment, we are unaware of any unusual
difficulties with the download system.

--Hiram

On 8/2/26 11:29 AM, 'Cully, Todd' via UCSC Genome Browser Public Support wrote:
> Hello
>
> Our users are currently experiencing an intermittent issue when accessing resources hosted on hgdownload.soe.ucsc.edu.
> We have performed troubleshooting on our end and, based on our findings, the connection appears to be timing out when attempting to reach your server. Users have tested with different browsers, restarted their systems, and confirmed that the issue persists intermittently.
> In some cases, simply refreshing the browser tab allows the page to load successfully, while at other times the request times out.
> Could you please review your logs and let us know if there are any known service issues, rate-limiting policies, or other factors that might be contributing to this behavior?
>
> Thanks,
>
> Todd Cully | LIS Administrator
> Caris Life Sciences
> 4415 Cotton Center Blvd, Suite 100, Phoenix, AZ 85040
> Mobile: 480-772-1544

> CarisLifeSciences.com<http://www.CarisLifeSciences.com>

[Maximilian Haeussler]

Hi Todd, 

this report is very interesting. We've recently tightened the connection timeouts on our servers due to denial of service attacks. This may or may not be related to what you're seeing. Users that open connections but do not send data at sufficient bandwidth for a few seconds will see dropped connections.

Do you know if the problems that your users report could be related to something special about your network, maybe you're using a proxy server, or your users go through a stateful firewall system that takes more than a second to inspect certain connection requests? Or maybe your users connect through a VPN or something else that could slow down some requests, but not others? Maybe the problem only appears on https but not http?

Can you reproduce the problems from a phone (=totally different network) or is there another type of network, e.g. wired versus wifi laptops in your organisation?

thanks

Max

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[Maximilian Haeussler]

Hi Todd again,

also, I wonder which files your users are trying to access? And do you happen to know your IP network? If you can send it to us, we can look into our log files and see if we can see something in the Apache logs. 

You can send your IP network to genom...@soe.ucsc.edu, unlike this email address, it is not a public list and only read by our team.

best

Max

[McMahon, Robert]

Santosh,

 

Can you provide the details here for Maximillian and Hiram?

 

 

Gentlemen,

 

The problem we had was intermittent, we did look at various aspects of this issue including Specific Browser, Network, and other potential configurations.

We did traceroutes and could not find anything that specifically cleared the problem.

We made no change on our side. Sometimes we could connect, sometimes we could not. The issue appeared to clear hours later. Obviously with an intermittent issue it was hard to track down.

Santosh can give you specific details they have requested for in previous emails….see attached.

That might lead us to a thread we can pull on.

 

 

Robert McMahon | Director IT Resiliency Operations

Caris Life Sciences

Irving (Lab): 3600 West Royal Lane, Irving, TX 75063

Mobile: 469-822-6501

CarisLifeSciences.com

 

This email message and any attachment thereto is for the sole use of the intended recipient(s) and may contain confidential information. If you are not the intended recipient, please contact the sender by reply email and permanently delete this email, any attachment(s) and all copies made of the original message or attachment(s). Any unauthorized review, use, disclosure or distribution is prohibited.

 

From: Maximilian Haeussler <mhae...@ucsc.edu>
Sent: Monday, 3 August, 2026 06:42
To: Hiram Clawson <hi...@soe.ucsc.edu>
Cc: Cully, Todd <tcu...@carisls.com>; gen...@soe.ucsc.edu; Markgraf, Christian <cmar...@carisls.com>; Nystel, Van <vny...@carisls.com>; McMahon, Robert <rmcm...@carisls.com>; Singh, Santosh <ssi...@carisls.com>
Subject: Re: [genome] Failure to connect to hgdownload.soe.ucsc.edu

 

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---

[Singh, Santosh]

Hi Max,

As Robert mentioned problem was intermittent. We were seeing (failed) net::ERR_TIMED_OUT error. I tried today couple of times and did not get any error.

We also tried this url https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit directly from bowser and sometimes it worked and sometimes gave timeout error.

Thanks,

Santosh Singh

[Hiram Clawson]

Good Morning Santosh:

This is a curious file to use as an example.
What do you mean you tried it directly from the 'browser' ?
Your web browser or to the UCSC genome browser ?

This is a binary file, and it isn't clear what would happen
if you used that URL in a web browser. If you were lucky, your web
browser would download the file to your computer.

And if you meant to the UCSC genome browser, how does that
reference function ?

--Hiram

On 8/3/26 7:31 AM, 'Singh, Santosh' via UCSC Genome Browser Public Support wrote:
> We also tried this url https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit directly from browser and sometimes it worked and sometimes gave timeout error.

[Singh, Santosh]

We tried in chrome browser like 

Yes, when it worked then it was downloading otherwise erroring out rest of the time.

Thanks,

Santosh

From: Hiram Clawson <hcla...@ucsc.edu>
Date: Monday, August 3, 2026 at 11:16 AM
To: Singh, Santosh <ssi...@carisls.com>; McMahon, Robert <rmcm...@carisls.com>; Maximilian Haeussler <mhae...@ucsc.edu>; Hiram Clawson <hi...@soe.ucsc.edu>
Cc: Cully, Todd <tcu...@carisls.com>; gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>; Markgraf, Christian <cmar...@carisls.com>; Nystel, Van <vny...@carisls.com>
Subject: Re: [genome] Failure to connect to hgdownload.soe.ucsc.edu

External Email   Please do not click any links or open any attachments unless you trust the sender and know the contents are safe.   

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[Nancy Hansen]

Hi all--sorry to piggy-back on this thread but I think a problem I've been experiencing may be related. I'm adding a new genome to our assembly hub at https://genome.ucsc.edu/cgi-bin/hgGateway?hgHub_do_redirect=on&hgHubConnect.remakeTrackHub=on&hgHub_do_firstDb=1&hubUrl=https://research.nhgri.nih.gov/CustomTracks/T2T_hubs/T2Tgenomes/hub.txt and for the HG002v1.1.MAT/PAT assemblies (which have far more tracks than the newer ones) the page is intermittently failing to load:


It's true we do have slow connections, so I'm wondering if the new timeouts are crippling us? If that's the case, I can have larger tracks default to hidden, but I wanted to confirm that's the problem before doing it.

Thanks!

--Nancy