try adding --skip-reorder to the mpiformatdb command line
by default, mpiformatdb 1.4.0 tries to reorder the queries so the
resulting fragments end up as evenly sized as possible. There were a
few bugs in the reordering code that was released as 1.4.0 (since fixed
in CVS, I think). The reordering may be disabled by default in future
releases since it can take significantly longer to format the database
with reordering-- the entire fasta is read, then written out to a temp
file with reordered sequence entries, then the temp file is fed to
formatdb...
-Aaron
Waibhav Tembe wrote:
Hello List,
I am trying split the nt database from NCBI using mpiformatdb program.
As a test case, first I tried nt.00.fasta (nt db is split into 4 small
dbs nt00...nt03).
I got the following error message for several sequences and the
program fails to create index at the end.
[formatdb] WARNING: Sequence number 1053529
(gi|3077651|emb|Z95929.1|SCZ95929), 19 illegal characters were
removed: 4 Es, 1 F, 4 Is, 1 J, 2 Os, 7 Ps
When I used nt.03.fasta, everything was fine.
How do I fix this? Do I have to preprocess nt.00.fasta before feeding
to mpiformatdb?
Thanks.
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