Assembly hub recent connection issues

[Hansen, Nancy (NIH/NHGRI) [E]]

Hello browser team!

We have an assembly hub at https://genome.ucsc.edu/cgi-bin/hgHubConnect?hgHub_do_redirect=on&hgHubConnect.remakeTrackHub=on&hgHub_do_firstDb=1&hubUrl=https://research.nhgri.nih.gov/CustomTracks/T2T_hubs/T2Tgenomes/hub.txt for which one of the genomes, T2T-CHM13v2.0, gives a connection error:

The strange thing is that the error is new, but none of the files on our assembly hub server have changed. Any insights into what might be going on? Thank you!

—Nancy

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*************************************

Nancy F. Hansen, PhD    nha...@mail.nih.gov

Staff Scientist, Genome Informatics Section

Center for Genomics and Data Science Research (CGDSR)

National Human Genome Research Institute (NHGRI)

National Institutes of Health (NIH)

49 Convent Drive, Rm 4A35

Bethesda, MD 20892

240-304-0362

 

 

[Matthew Speir]

Hello, Nancy.

Thank you for reporting this issue with your hubs.

We believe we've resolved the issue.

However, it did raise two bits of feedback for us:

1) Could you ensure that your hub isn't referencing the same trackDb.txt from several assemblies? The Genome Browser caches trackDb configurations on our server, but these can get confused when the same trackDb.txt is referenced by different hubs. This could be resolved by either duplicating the trackDb where needed or by symlinking the trackDb where needed.

2) It may be a good idea to point your hub at our GenArk repository, which I believe contains many (or all) of these genome assemblies? You can see which genomes we have by searching for the GCA or GCF identifier here: https://genome.ucsc.edu/assemblySearch.html. Any that are missing can be requested. We have documentation for creating hubs on GenArk genomes here: https://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#GenArkTrackHubs.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Matthew Speir

UCSC Genome Browser, User Support

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