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ComparativeGenomicsToolkit / hal

Hierarchical Alignment Format
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UCSC genome browser fails to display an assembly hub due to a hal get blocks error #209

Open ybukhman opened 3 years ago

ybukhman commented 3 years ago

Hello,

here are the steps to reproduce the problem:

Assembly hub URL: http://genome.ucsc.edu/cgi-bin/hgHubConnect?hgHub_do_redirect=on&hgHubConnect.remakeTrackHub=on&hgHub_do_firstDb=1&hubUrl=http://www.morgridge.net/dmz/ybukhman/NILERAT/4_rodents_hub/hub.txt

Using A.niloticus genome as the reference, try displaying the following coordinates: NW_023044993.1:34870742-34927456.

A screen shot of the error: 4-rodents assembly hub display error

Commands used to generate the hub:

export alignment=4_rodents
hal2assemblyHub.py jobstore ${alignment}.hal ${alignment}_hub --lod \
--alignability --gcContent --hub ${alignment} --shortLabel ${alignment} \
|& tee hal2assemblyHub.out

Cactus version 1.2.3 (hal2assemblyHub.py does not work in 1.3.0: see https://github.com/ComparativeGenomicsToolkit/cactus/issues/463)

Thanks.

Yury

alexgilgal commented 3 years ago

Hi, I have exactly the same error. I have been trying to tune the lod options when generating the hub, like the --lodScale. So far I have not solved this problem. Anyone has reached to some solution, or has a sugestion? Thanks a lot.