Hi for all,
I have had some errors with nt and mpiFormatdb. Last time I changed the
database to nr, and the error is keeping. The error is
below:
PLEASE, ANYBODY HAVE SOME IDEA?
THANKS
...
[formatdb] WARNING: Sequence number 4435752 (gi|82539641|ref|XP_724193.1|), 21
illegal characters were removed:
18 Os, 3 -s
[formatdb] WARNING: Sequence number 4438435 (gi|83286073|ref|XP_730001.1|), 5
illegal characters were removed:
1 J, 4 Os
[formatdb] WARNING: Sequence number 4439491 (gi|82793428|ref|XP_728036.1|), 149
illegal characters were removed:
125 Os, 24 -s
[formatdb] WARNING: Sequence number 4440410 (gi|85092826|ref|XP_959564.1|), 6
illegal characters were removed:
5 Os, 1 -
[formatdb] ERROR: Failed to create index. Possibly a gi included more than
once in the database.
Removed /tmp/reorderTzk79D
There was an error executing formatdb. Check formatdb.log
*****************************************************************
* Daniel Xavier de Sousa *
* Mestrando em Informática - PUC-Rio *
* E-MAIL : dsousaARROBAinf.puc-rio.br *
* Fone : +55 21 35271500 - 4543 *
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----- Mensagem original ----
De: Daniel Xavier de Sousa <[EMAIL PROTECTED]>
Para: [email protected]
Enviadas: Quarta-feira, 30 de Maio de 2007 12:15:09
Assunto: Res: [Mpiblast-users] ERROR IN mpiFORMATDB?
Hi Mike,
I have cut nt(fasta) into 24 parts and executed with mpiFormatdb, and I didn't
see error, or, the mpiformatdb didn't send error.
What can I do?
I think that there aren't gi repeated.
Thanks
*****************************************************************
* 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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