Problem loading hg38

[Rohit Venkat]

Hello!

I'm running a local instance of the UCSC genome browser and have been happily using with the yeast genome. I recently decided to add the human genome to my local instance but have run into an issue in doing so. To retrace my steps, I downloaded the entire hg38 directory from hgdownload.cse.ucsc.edu/goldenPath/hg38/ using rsync and then ran the loadDb script from kentUtils to load hg38's database tables. Everything appears to have loaded successfully, and 

the Human species icon shows up on the Genome Portal page. However, when I click on the Human icon, the follow error message appears:

handleSetTaxId: error from server: Couldn't connect to database

hg38Patch2 on localhost as readonly.

Unknown database 'hg38Patch2'

I can't seem to figure out what I did wrong or why it's trying to find hg38Patch2 by default rather than hg38. Any help would be greatly appreciated!

Thanks,

Rohit

[Cath Tyner]

Hello Rohit,

Can you please connect to hgcentral in mysql and execute this command, and let us know the results?

delete from dbDb where taxId = 9606 and name not rlike '^hg[0-9][0-9]$';

Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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