Genome browser V439 - debugging issue with hs1 assembly hub hub:/gbdb/hs1/hubs

[Weinberger, Volker]

Hi,

 

I need some advice for debugging issues with assembly hub hub:/gbdb/hs1/hubs  in V439.

 

We’ve made sure the content os /gbdb/hs1 is properly synced to local filesystem and up-to-date. Assumption is that the hub is based on /gbdb/hs1/hubs/public/hub.txt dated Sep 22 06:35

 

hub:/gbdb/mpxvRivers/hubs seems to be working fine.

 

For hs1, we almost see no tracks at all.

 

Is there any debugging / checking tool for this type of local-fs hub ? Anything else to look for e.g. in logs to get hints about what might be wrong ?

 

I did note that on the public MYSQL server there’s a database hs1 with a few tables, which we did not get for download.  Is that an issue? However, the mpxvRivers database is also missing and it doesn’t seem to matter.

 

 

 

 

 

Thanks,

Volker

 

 

 

 

[Gerardo Perez]

Hello, Volker.

Thank you for your interest in the Genome Browser.

Our engineer shares that there is an error in the hubStatus table for the hs1 hub:

hgsql hgcentral -Ne "select * from hubStatus where hubUrl='/gbdb/hs1/hubs/public/hub.txt'"

You can fix the issue by running the following command:

hgsql -Ne "update hubStatus set errorMessage='' where hubUrl='/gbdb/hs1/hubs/public/hub.txt'" hgcentral

Let us know if you experience any further issues, or have any questions.

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.

Gerardo Perez
UCSC Genomics Institute

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