Missing tables after UCSC Genome Browser Upgrade

[McCully, Dwayne (NIH/NIAMS) [C]]

Hi Support,

 

Just completed an upgrade using the browserSetup.sh script and during testing I got the following error.

I have confirmed the tables are not in the database hg38 or hg19.

 

Dwayne

 

Dwayne McCully

NIAMS, NIH

Contractor

 

 

[Robert Kuhn]

Hello, Dwayne,

I am no longer on the Browser staff, but I still lurk on the mailing list as bit.  I can tell

you OMIM does not permit any third parties to download their data.  You need to go to

omim.org and download them there.

best wishes,

     --b0b kuhn

Robert Kuhn, PhD

Associate Director UCSC Genome Browser (retired)

dba Robert Kuhn Consulting -- bioinformatics training and consulting

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[Robert Kuhn]

Hello, Dwayne,

15 years ago we set up a system where we uploaded MySQL-formatted tables back to OMIM for mirrors to download from them. I believe they now do that themselves.

They require reqistration via:

https://omim.org/downloads

Please contact them there.  

I will let the Browser staff address the question about the script. Is it possible you are updating an installation that loaded the OMIM tables separately? 

Best regards,

   ..b0b

On Thu, Nov 30, 2023, 5:06 PM McCully, Dwayne (NIH/NIAMS) [C] <dmcc...@mail.nih.gov> wrote:

Thank you Robert for answering my e-mail!!

 

The UCSC Genome Browser group allowed an upgrade that required mirror managers to download

data from OMIM?   The error is indicating the data needs to be in a MariaDB table format for multiple genomes.   Will the omim.org site have this?

Will the message that your seeing in the below screen shot will affect the operations of the mirror site until fixed?

 

Sorry for all the questions but need to get the problem resolved.

 

Dwayne

 

Dwayne McCully

NIAMS, NIH

Contractor

 

From: Robert Kuhn <ku...@soe.ucsc.edu>

Sent: Thursday, November 30, 2023 7:38 PM
To: McCully, Dwayne (NIH/NIAMS) [C] <dmcc...@mail.nih.gov>
Cc: gen...@soe.ucsc.edu; genome-www <genom...@soe.ucsc.edu>; Mullacheri, Anilkumar (NIH/NIAMS) [C] <anilkumar....@nih.gov>; Winchester, Christine (NIH/NIAMS) [E] <christine....@nih.gov>; genome...@soe.ucsc.edu; Robert Kuhn <ku...@soe.ucsc.edu>
Subject: [EXTERNAL] Re: [genome] Missing tables after UCSC Genome Browser Upgrade

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.

 

[Maximilian Haeussler]

Hi Dwayne, 

OMIM tracks are not available on mirrors, you'll need to reach out to OMIM directly, they have a mysql dump in exactly the format for your UCSC mirror and can activate this special download once you have an OMIM username and contact them with a request for the UCSC sql files.

But this error is our fault, we made OMIM a default track without thinking of mirrors that don't have this track yet.

I now changed the update script to hide the OMIM track from the default track set, so this error shouldn't appear anymore.

Can you re-download the script and then run the update procedure again?

The commands should be something like the following:

wget https://raw.githubusercontent.com/ucscGenomeBrowser/kent/master/src/product/installer/browserSetup.sh

bash browserSetup.sh update

This should not only upgrade your CGIs but also hide the OMIM tracks so this error message won't appear anymore.

If this does not work or you have other questions, please do not hesitate to reach out to us. 

I agree that this error is a problem for mirrors and we will get your mirror working again ASAP.

best

Max

On Fri, Dec 1, 2023 at 2:06 AM 'McCully, Dwayne (NIH/NIAMS) [C]' via UCSC Genome Browser Confidential Support <genom...@soe.ucsc.edu> wrote:

Thank you Robert for answering my e-mail!!

 

The UCSC Genome Browser group allowed an upgrade that required mirror managers to download

data from OMIM?   The error is indicating the data needs to be in a MariaDB table format for multiple genomes.   Will the omim.org site have this?

Will the message that your seeing in the below screen shot will affect the operations of the mirror site until fixed?

 

Sorry for all the questions but need to get the problem resolved.

 

Dwayne

 

Dwayne McCully

NIAMS, NIH

Contractor

 

From: Robert Kuhn <ku...@soe.ucsc.edu>

Sent: Thursday, November 30, 2023 7:38 PM
To: McCully, Dwayne (NIH/NIAMS) [C] <dmcc...@mail.nih.gov>
Cc: gen...@soe.ucsc.edu; genome-www <genom...@soe.ucsc.edu>; Mullacheri, Anilkumar (NIH/NIAMS) [C] <anilkumar....@nih.gov>; Winchester, Christine (NIH/NIAMS) [E] <christine....@nih.gov>; genome...@soe.ucsc.edu; Robert Kuhn <ku...@soe.ucsc.edu>
Subject: [EXTERNAL] Re: [genome] Missing tables after UCSC Genome Browser Upgrade

 

Hello, Dwayne,

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.

 

[McCully, Dwayne (NIH/NIAMS) [C]]

Thank you Robert for answering my e-mail!!

 

The UCSC Genome Browser group allowed an upgrade that required mirror managers to download

data from OMIM?   The error is indicating the data needs to be in a MariaDB table format for multiple genomes.   Will the omim.org site have this?

Will the message that your seeing in the below screen shot will affect the operations of the mirror site until fixed?

 

Sorry for all the questions but need to get the problem resolved.

 

Dwayne

 

Dwayne McCully

NIAMS, NIH

Contractor

 

From: Robert Kuhn <ku...@soe.ucsc.edu>

Sent: Thursday, November 30, 2023 7:38 PM
To: McCully, Dwayne (NIH/NIAMS) [C] <dmcc...@mail.nih.gov>
Cc: gen...@soe.ucsc.edu; genome-www <genom...@soe.ucsc.edu>; Mullacheri, Anilkumar (NIH/NIAMS) [C] <anilkumar....@nih.gov>; Winchester, Christine (NIH/NIAMS) [E] <christine....@nih.gov>; genome...@soe.ucsc.edu; Robert Kuhn <ku...@soe.ucsc.edu>
Subject: [EXTERNAL] Re: [genome] Missing tables after UCSC Genome Browser Upgrade

 

Hello, Dwayne,

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.

 

[McCully, Dwayne (NIH/NIAMS) [C]]

Thank you Max for the update and new instructions!

 

After running the new browserSetup.sh it ran smoothly up to this point.

 

---------------------------------------------------------------------------------------------------------------------

sent 24 bytes  received 1,798 bytes  1,214.67 bytes/sec

total size is 46,015,696,612  speedup is 25,255,596.38

| Hiding some tracks by default and removing some tracks from searches

go

ERROR 1146 (42S02) at line 1: Table 'go.trackDb' doesn't exist

Exit error 1 occurred on line 1

The UCSC Genome Browser installation script exited with an error.

Please contact us at genome...@soe.ucsc.edu and send us an output log

of the command prefixed with "bash -x", e.g.

bash -x browserSetup.sh install 2>&1 > install.log

-------------------------------------------------------------------------------------------------------------------------

 

What would be my next step to fix?

 

Dwayne

[McCully, Dwayne (NIH/NIAMS) [C]]

Hi Robert,

 

We did not load the OMIM tables separately as this is the first time I’ve seen anything related to OMIM.

I will ask our federal staff about the registration with OMIM but this will take time due to the review of licensing requirements.

 

At the moment, Max is trying to resolve the OMIM issue short term with a new browserSetup.sh script.    

 

Dwayne