Opened 3 years ago

Last modified 15 months ago

#7387 reopened enhancement

BLAST of Uniref50, UniRef90, UniRef100 appears to be using old databases from 2012 — at Version 14

Reported by: Tom Goddard Owned by: Zach Pearson
Priority: high Milestone:
Component: Sequence Version:
Keywords: Cc: Elaine Meng, Eric Pettersen, Greg Couch, Scooter
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Elaine Meng)

Not sure if these are the uniref databases being used by blast protein. They are from 2012. The UniRef100 file is 8 Gbytes, while the current UniRef100 is 83 Gbytes. So these old databases only have 1/10 of the sequences. They should be updated.

Change History (14)

comment:1 by Tom Goddard, 3 years ago

Forgot to include the path to the 2012 databases on plato

/databases/mol/blast/db_uniref

comment:2 by Eric Pettersen, 3 years ago

Cc: Greg Couch Scooter Morris added

The line in periodic.conf that would update the UniRef databases seems to be commented out:

# 0 6 28 * * su sacsdb -c "/usr/local/etc/periodic/scripts/get_uniref_blast.py |& /usr/bin/Mail -s 'UniRef update' scooter@…"

comment:3 by Elaine Meng, 3 years ago

same issue as #7458?

comment:4 by Zach Pearson, 3 years ago

Cc: Zach Pearson added; Scooter Morris removed
Owner: changed from Zach Pearson to Scooter Morris

comment:5 by Zach Pearson, 3 years ago

My user account is not allowed to write files in that directory. Additionally, that script doesn't exist(!)

Reassigning to Scooter.

in reply to:  6 ; comment:6 by Tom Goddard, 3 years ago 

The uniref databases can be downloaded by ftp here, uniref100, uniref90 and uniref50 are each a single large gziped fasta file.  Then a simple makeblastdb command makes the database files.  The database directory is owned by sacsdb with group sacs and is not writable by group sacs.

$ ls -ld /databases/mol/blast/db_uniref
drwxr-xr-x. 2 sacsdb sacs 42 Jul 28  2012 /databases/mol/blast/db_uniref

comment:7 by Elaine Meng, 3 years ago

Priority: moderate → high

comment:8 by Elaine Meng, 3 years ago

Milestone: → 1.5

comment:9 by Greg Couch, 3 years ago

Newer data, from 16 June 2021, is in /wynton/group/databases/UniProt/uniref/uniref{100,50,90}.

comment:10 by Greg Couch, 3 years ago

Milestone: 1.5 → 1.6

Give Scooter more time.

comment:11 by Tom Goddard, 3 years ago

Cc: Zach Pearson removed
Owner: changed from Scooter Morris to Zach Pearson

comment:12 by Zach Pearson, 3 years ago

I've re-created the missing get_uniref_blast script and am testing it now.

comment:13 by Zach Pearson, 3 years ago

Milestone: 1.6

comment:14 by Elaine Meng, 18 months ago

Description: modified (diff)

Still hoping for updates. :-)

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