Hi Chris,
The mpiformatdb releases shipped with older versions of mpiblast, e.g.
before 1.3.0, construct a single volume at a time. It should be fine to
use databases formatted with the older mpiformatdb in conjunction with
newer mpiblast releases. One caveat is that the older mpiformatdb may
not create the .mbf file in the shared storage directory. The file is
simply a listing of all the fragments that were created and could
probably be easily constructed with a wrapper script. The other major
caveat is that the older mpiformatdb can't guarantee a given number of
fragments.
If that route isn't appealing for whatever reason, an alternative would
be to "roll your own" mpiformatdb-like script that first splits up the
fasta into many small FastAs, formats each separately with ncbi
formatdb, then creates the appropriate alias file and .mbf file.
Just out of curiousity, how many fragments are being created for this
large database? mpiformatdb simultaneously opens somewhere between 4
and 7 files per fragment.
-Aaron
Christopher Dwan wrote:
When I format a large target, I notice that mpiformatdb writes all of
the volumes at once, and writes the index files at the very end.
I'm continuing to wrestle with some SAN / filesystem problems, and
concurrent writes seems to be the weak point. I'm wondering if
there's a way to write one volume at a time.
Here's my mpiformatdb command:
/common/bin/mpiformatdb --skip-reorder --config-file=/common/etc/
mpiblast.conf --nfrags=16 --quiet -p F -i /common/data/nt -o T &
Thanks.
-Chris Dwan
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