assembly hub

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GIOVANNA MIGLIORELLI

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Jul 26, 2021, 1:06:02 PMJul 26
to gen...@soe.ucsc.edu
Dear Support,
I am trying to display my assembly hum hosted on cyverse on the UCSC browser. I applied the procedure you provided but I encountered some issues. Do you have additional documentation for errors like the following one?
Can you try and display my hub if I share the link?
Do you think hosting the hub at my institution instead of cyverse may help?

Thanks  a lot,
Giovanna 

unable to fetch 8192 bytes from https://data.cyverse.org/dav-anon/iplant/home/gmuser/HUB/equCab3/equCab3.2bit @248201216 (got 0 bytes)


Startup (bottleneck 0 ms) : 6280 millis
Get cart of 38 for user:394052585_qUJW1dyXg8CqCRfThakbAQ6umaSA session:271352007_Akk8RyBMqYVpZ32fmBpzsYI4XZxB: 0 millis
Time to write and close cart: 33409 millis
Overall total time: 39689 millis



Dan Schmelter

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Jul 30, 2021, 7:09:26 PMJul 30
to GIOVANNA MIGLIORELLI, UCSC Genome Browser Support

Hello Giovanna,

Thanks for writing to the Genome Browser and for your patience with this response time.

After looking into your track hub, I believe that error you referenced was a temporary issue with CyVerse. It resolved itself after reloading. I validated that your 2bit file was valid and that the server is set up to accept byte-range requests. CyVerse sometimes gets their servers overloaded and will generate these types of errors, but generally is reliable. An institutional server may be better, but it depends on your institution.

Unfortunately, there are other errors in your data file configuration that appear. You should be able to see them here:

http://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://data.cyverse.org/dav-anon/iplant/home/gmuser/HUB/hub.txt&genome=hub_2964811_equCab3&position=lastDbPos

The bigBed tracks have errors because of trackDb.ra errors. The URL referenced in the "GenescerSim" track is not actually at that location. The following path does not exist:

https://data.cyverse.org/dav-anon/iplant/home/gmuser/HUB/liftoverbed/Genes/cerSim/equCab3.bb

For the halSnake tracks, you have a similar issue with referencing the wrong file. I see the following line:

bigDataUrl https://data.cyverse.org/dav-anon/iplant/home/gmuser/HUB/lod.txt

which references a file that is not an actual hal file. You may instead want to reference the file directly:

https://data.cyverse.org/dav-anon/iplant/home/gmuser/HUB/lod/rhino_lod_111559.hal

I hope this was helpful. If you have any more questions, please reply-all to gen...@soe.ucsc.edu. All messages sent to that address are publicly archived. If your question includes sensitive data, please reply-all to genom...@soe.ucsc.edu.

All the best,

Daniel Schmelter
UCSC Genome Browser


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