Question about update-sequence-db --ucsc

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jiecon...@gmail.com

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Jul 5, 2018, 9:26:06 AM7/5/18
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I have ran update-sequence-db --ucsc on Ubuntu 16.04, but I found that it can get any sequence data from UCSC, I looked into the log file, it said that there is no genomes found.

Here is the log file:

Jul 05, 2018 9:02:42 PM au.edu.uq.imb.memesuite.updatedb.UpdateSequenceDB getInitialisedDatabase
INFO: Creating a new sqlite database /home/jieconlin3/meme_db/ucsc1/fasta_db.sqlite
Jul 05, 2018 9:02:42 PM au.edu.uq.imb.memesuite.updatedb.UpdateSequenceDB setupTables
INFO: Creating database tables.
Jul 05, 2018 9:02:43 PM au.edu.uq.imb.memesuite.updatedb.UpdateSequenceDB setupTables
INFO: Creating category table
Jul 05, 2018 9:02:43 PM au.edu.uq.imb.memesuite.updatedb.UpdateSequenceDB setupTables
INFO: Creating listing table
Jul 05, 2018 9:02:43 PM au.edu.uq.imb.memesuite.updatedb.UpdateSequenceDB setupTables
INFO: Creating sequence table
Jul 05, 2018 9:02:43 PM au.edu.uq.imb.memesuite.updatedb.UpdateSequenceDB setupTables
INFO: Creating priors table
Jul 05, 2018 9:02:43 PM au.edu.uq.imb.memesuite.updatedb.UpdateSequenceDB setupTables
INFO: Declaring the schema version
Jul 05, 2018 9:02:43 PM au.edu.uq.imb.memesuite.updatedb.UpdateSequenceDB setupTables
INFO: Successfully created database tables.
Jul 05, 2018 9:02:43 PM au.edu.uq.imb.memesuite.updatedb.UpdateSequenceDB purge
INFO: Purged database entries for 0 missing files as well as 0 empty listings and 0 empty categories.  Also regenerated 0 background files.
Jul 05, 2018 9:02:43 PM au.edu.uq.imb.memesuite.updatedb.UpdateSequenceDB update
INFO: Started update of sequence databases in /home/jieconlin3/meme_db/ucsc1
Jul 05, 2018 9:02:43 PM au.edu.uq.imb.memesuite.updatedb.UCSCGenomeUpdater call
INFO: Starting UCSC update
Jul 05, 2018 9:02:44 PM au.edu.uq.imb.memesuite.updatedb.UCSCGenomeUpdater call
SEVERE: Failed parsing the genome releases from the FAQ... No genomes found!
Jul 05, 2018 9:02:44 PM au.edu.uq.imb.memesuite.updatedb.UpdateSequenceDB update
INFO: Finished update of sequence databases in /home/jieconlin3/meme_db/ucsc1

and when I ran update-sequence-db --ensembl, everything went right. 

Am I missing something?

CharlesEGrant

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Jul 5, 2018, 4:27:36 PM7/5/18
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Thanks for letting us know about the problem. We're always in a race to keep up with changes to the file systems of the original hosts of the databases. It looks like we've fallen behind on the UCSC genome database repository. We'll try to have a patch out in the next few weeks that will address this problem.
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