I am using the nt database with mpiblast from Rocks (oct 2006). I have no
problem with any of the NCBI databases, but uniprot has been giving me fits
with mpiformatdb. There is a serious problem there and I am trying
workarounds. No problems with formatdb in either case.
David Lapointe, Ph.D.
Manager - Research Computing
UMass Medical School
Worcester MA 01655
508-856-7600
________________________________
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Daniel Xavier de
Sousa
Sent: Wednesday, June 06, 2007 5:39 PM
To: [email protected]
Subject: [Mpiblast-users] Res: ERROR IN mpiFORMATDB?
Hi,
There are some days I have sent the email about difficult of use mpiFormatdb
for nt database. My apologies for Mike Cariaso that help me, but the error
keep.
Please, Any one have used mpiformat to nt? Anybody have had problem with this
database?
Thanks,
Daniel
*****************************************************************
* Daniel Xavier de Sousa *
* Mestrando em Informática - PUC-Rio *
* E-MAIL : dsousaARROBAinf.puc-rio.br *
* Fone : +55 21 35271500 - 4543 *
****************************************************************
----- Mensagem original ----
De: Mike Cariaso <[EMAIL PROTECTED]>
Para: [email protected]
Enviadas: Terça-feira, 29 de Maio de 2007 16:44:22
Assunto: Re: [Mpiblast-users] ERROR IN mpiFORMATDB?
Not a solution, but a next step. Cut your fasta into 2 parts, and see which
reproduces the error. Repeat this a few more times until you can get a smaller
file that reproduces the error.
--
Mike Cariaso * Bioinformatics Software * http://www.cariaso.com
----- Original Message ----
From: Daniel Xavier de Sousa <[EMAIL PROTECTED]>
To: [email protected]
Sent: Tuesday, May 29, 2007 11:08:56 AM
Subject: [Mpiblast-users] ERROR IN mpiFORMATDB?
Hi for all,
Please, I have a problem with mpiblast, in mpiFormatdb.
When I process mpiFORMATDB with nt database, I get this out error:
=> [formatdb] ERROR: Failed to create index. Possibly a gi included more
than once in the database.
When I executed just formatdb (from ncbi) there wasn't error message.
I have confirmed and there aren't repted GI numbers in nt database.
Please, anyone have one suggestion?
Thank you so much.
Daniel
*****************************************************************
* Daniel Xavier de Sousa *
* Mestrando em Informática - PUC-Rio *
* E-MAIL : dsousaARROBAinf.puc-rio.br *
* Fone : +55 21 35271500 - 4543 *
****************************************************************
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