ERROR: Unsupported type 'bigbed' in hub

[Ann Black-Ziegelbein]

Hi,

 

I was hoping for some guidance on what I might be doing wrong.  I have created a custom track hub, and I am trying to add a bigBed file to it (an annotated bed file I converted using the bedToBigBed tool). 

Whenever I try to load my custom track hub, I get the following error: ERROR: Unsupported type 'bigbed' in hub 

I can directly load my bigBed file as a custom track, and prior to adding the bigBed track to my custom hub, the hub was loading fine.  I am trying to figure out what is wrong with my bigBed track that the UCSC browser doesn't like?

Here is the custom track hub I am trying to load:

https://raw.githubusercontent.com/annblackz/DFNB31_UCSC_Hub/master/hub.txt 

Thanks so much for your time,

Ann Black-Ziegelbein

[Brian Lee]

Dear Ann,

Thank you for using the UCSC Genome Browser and taking the time to build a Track Hub to visualize your data and the question about the "type bigbed' error message.

Likely the message is coming due to a lower-cased "bed" and if you change it to "type bigBed" the hub should work. We use a format called "camel-case" (https://en.wikipedia.org/wiki/Camel_case) where we capitalize the beginning of new words, but the very first letter is lower-case. For example, we have other file formats such as the narrow peak format that we call "type bigNarrowPeak" in our code where the N and P are capitalized.

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further public questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee

UC Santa Cruz Genomics Institute

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[Ann Black-Ziegelbein]

Hi Brian,

Thanks so much.  That is what I thought and when I fixed the case, the error persisted.  However, later in the day the error went away and my hub loaded ....  Is there some type of cached period where the cache does not get refreshed and stuck with my old copy of trackDb.txt on the UCSC server side?  I have hit a very similar problem with a new custom hub I have created.  I had a typo in my trackDb.txt file, corrected it, but UCSC does not seem to pick up the fixed file.  I thought it may have been a browser cache issue, but changing browsers gives me the same error (changed from Chrome to Firefox).  I also tried to drop the connection to the hub and connect to it fresh (didn't work).  Is there some hack to force a re-load of the tracksDb.txt file?

Thanks so much,

Ann 

[Luis Nassar]

Hello Ann,

Regarding the browser caching hubs, hub files are cached and checked every 300s for changes, even if you disconnect and reconnect a hub. If you hit the 'Retry' button when you try the 'Add Hub' button it should force a reload.

If you encountered a wait time longer than this, it may have been a bug. If so please send us a link to the track hub and any specific steps you undertook so we can try to recreate it.

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.

Lou Nassar

UCSC Genomics Institute

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