Daniel Xavier de Sousa | 6 Oct 16:02 2010
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(no subject)

http://muremyku.tripod.com/gigigy.html slhoppy body can be revitablized

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Daniel Xavier de Sousa | 24 Jul 16:33 2007
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Time of mpiBLAST

Hi for all,

I have run the mpiblast with 8 workstations with same line command:

mpirun -np 10 mpiblast -p blastn -d nt -i net_1000_nucl.seq -o out_mpiblast_net_1000_nucl_nt2.seq

The first time with 25 fragments and another time with 96 fragments.
With 25 fragments the mpiblast have get 138360 seconds. With 96 fragments the mpiblast have get 129060 seconds.

I have run without a shared filesystem.

My question is: It is normal this difference of time with 25 and 96 fragments?
I was hopping faster with 96 fragments than 25 fragments.

Thanks



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Jeremy Archuleta | 10 Jul 23:30 2007
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mpiBLAST User mailing list moved


Hello all,

This email is to inform everyone that the mailing lists for the  
mpiBLAST project have been moved to the mpiblast.org domain. The new  
"users" mailing list is "users@..." and
information  
about the new mailing lists can be found at http://www.mpiblast.org/ 
Support/Lists

At the above link, you'll notice that there are several more lists  
available too which perhaps you will want to join as well. The aim of  
the multiple lists is to compartmentalize the discussions about  
mpiBLAST into more focused topics and in turn catalyze mpiBLAST  
development.

We're sorry for this inconvenience and appreciate your patience  
during this transition and hope to retain your support for mpiBLAST.
-J

This will be the last email to this Sourceforge mailing list. All  
future mpiBLAST "user" emails should be directed to  
"users@...".

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Amy Lee | 10 Jun 14:54 2007
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Help: About .ncbirc file

Hello,

I'm a college student, I built a Linux cluster for Bio-informatics 
Department,  and I use MpiBLAST in this machines. I have some problems 
about the .ncbirc file.

I wanna know something about this, where should I put .ncbirc in? The 
MpiBLAST binary directory or home directory or else?

Thanks in advance!

Amy Lee

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Daniel Xavier de Sousa | 6 Jun 23:38 2007
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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

 
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* 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: Mike Cariaso <cariaso-/E1597aS9LQAvxtiuMwx3w@public.gmane.org>
Para: mpiblast-users-5NWGOfrQmneRv+LV9MX5ug@public.gmane.orge.net
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 <danielucg-/E1597aS9LRfJ/NunPodnw@public.gmane.org>
To: mpiblast-users <at> lists.sourceforge.net
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


 
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* Mestrando em Informática - PUC-Rio *
* E-MAIL : dsousaARROBAinf.puc-rio.br *
* Fone : +55 21 35271500 - 4543 *
****************************************************************

 

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Daniel Xavier de Sousa | 31 May 14:23 2007
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ERROR with NR in mpiFORMATDB too ?

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

 
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* Daniel Xavier de Sousa *
* Mestrando em Informática - PUC-Rio *
* E-MAIL : dsousaARROBAinf.puc-rio.br *
* Fone : +55 21 35271500 - 4543 *
****************************************************************


----- Mensagem original ----
De: Daniel Xavier de Sousa <danielucg-/E1597aS9LRfJ/NunPodnw@public.gmane.org>
Para: mpiblast-users <at> lists.sourceforge.net
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 <cariaso <at> yahoo.com>
Para: mpiblast-users-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
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 <danielucg-/E1597aS9LRfJ/NunPodnw@public.gmane.org>
To: mpiblast-users-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
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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Daniel Xavier de Sousa | 30 May 17:15 2007
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Res: 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 <cariaso-/E1597aS9LQAvxtiuMwx3w@public.gmane.org>
Para: mpiblast-users-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
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 <danielucg-/E1597aS9LRfJ/NunPodnw@public.gmane.org>
To: mpiblast-users-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
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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Daniel Xavier de Sousa | 29 May 17:08 2007
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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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Daniel Xavier de Sousa | 21 May 16:40 2007
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Res: MPIFORMATDB

Hi,

But when I executed just FOTMATDB, whitout mpiBLAST, craw formatdb from ncbi. These erros don't happened.
So I think, there is some problem with mpiFormatdb.

What do you think about?

Thanks
Daniel

 
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* 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 <cariaso-/E1597aS9LQAvxtiuMwx3w@public.gmane.org>
Para: mpiblast-users-5NWGOfrQmneRv+LV9MX5ug@public.gmane.orge.net
Enviadas: Segunda-feira, 21 de Maio de 2007 9:54:15
Assunto: Re: [Mpiblast-users] MPIFORMATDB

As you state in your email:
     [formatdb] ERROR: Failed to create index.  Possibly a gi included more than once in the database.


while untested, a command such as

grep '^>' fastafile.txt | cat -d'|' -f2 | sort | uniq -c | sort -n | grep -v " 1 "

may allow you to determine which GI is occuring more than once. Remove this GI from your fasta file





I've previously used this code to skip duplicate GIs. A small amount of modification will be necessary.

use strict;
use Getopt::Long;
use Data::Dumper;
use Bio::SeqIO;
use FileHandle;

use figur_config qw($PRIMARY_TMPDIR);
my ($quick_run, $help);
my %optControl = (
          'quick'            => \$quick_run,
          'help'             => \$help,
          );
my $res = GetOptions(%optControl);

if ($help) {
    print usage();
    exit;
}

my $infn = $ARGV[0] || '-';
my $outfn = $ARGV[1] || '-';

my $inh = FileHandle->new($infn) or warn ("$!:$infn");
my $outh = FileHandle->new('>'.$outfn) or warn ("$!:$outfn");


my $seenvec = '';

my $line;
my $show = 1;
while ($line = <$inh>) {
    if ($line =~ /^>/) {
    my ($gi) = $line =~ /gi\|(\d+)/;

    if (0==vec($seenvec, $gi, 1)) {
        $show = 1;
        vec($seenvec, $gi, 1) = 1;
    } else {
        $show = 0;
        print STDERR "skip $line";
    }

    }
    if ($show) {
    print $outh $line;
    }
}






Since nt is so large, you may also want to consider adding the switch --skip-reorder to your mpiformatdb call.
Does anyone else feel this should become a default?





 
--
Mike Cariaso * Bioinformatics Software * http://www.cariaso.com


----- Original Message ----
From: Daniel Xavier de Sousa <danielucg-/E1597aS9LRfJ/NunPodnw@public.gmane.org>
To: mpiBlast <mpiblast-users <at> lists.sourceforge.net>
Sent: Monday, May 21, 2007 8:34:10 AM
Subject: [Mpiblast-users] MPIFORMATDB

Hi,

I have a problem with MPIFORMATDB.

I have put this command: ./mpiformatdb -N 24 -i nt -p F

And the program returned this out:

/////////////////////////////////////////////////////////////////////////////// OUT OF MPIBLAST
nt: Value too large for defined data type
Reading input file
0%Done, read 263843064 lines
Temp name base: /tmp/reorderXXXXXX
Got temp name: /tmp/reorderb0538C
Reordering 5214551 sequence entries
2.58%

...

[formatdb] WARNING: Sequence number 5051632 (gi|4704323|dbj|AB013452.1|), 15 illegal characters were removed:
2 Es, 1 F, 4 Is, 3 Ls, 3 Os, 2 Ps

[formatdb] WARNING: Sequence number 5052135 (gi|640099|pdb|172D|D), 32 illegal characters were removed:
4 Es, 3 Fs, 9 Is, 3 Ls, 7 Os, 3 Ps, 3 -s

[formatdb] WARNING: Sequence number 5052365 (gi|999772), 31 illegal characters were removed:
5 Es, 1 F, 9 Is, 6 Ls, 5 Os, 5 Ps

[formatdb] ERROR: Failed to create index.  Possibly a gi included more than once in the database.

Removed /tmp/reorder9UjHhX
There was an error executing formatdb.  Check formatdb.log
///////////////////////////////////////////////////////////////////////////////

To test I broke the nt file in 24 parts and executed each one and I did'nt find nothing of error.This error is happening because de size of NT to be 20 GB?
What I have to do for resolve this error?

Thanks
Daniel Sousa
*****************************************************************
* Daniel Xavier de Sousa *
* Mestrando em Informática - PUC-Rio *
* E-MAIL : dsousaARROBAinf.puc-rio.br *
* Fone : +55 21 35271500 - 4543 *
****************************************************************


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Daniel Xavier de Sousa | 21 May 14:34 2007
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MPIFORMATDB

Hi,

I have a problem with MPIFORMATDB.

I have put this command: ./mpiformatdb -N 24 -i nt -p F

And the program returned this out:

/////////////////////////////////////////////////////////////////////////////// OUT OF MPIBLAST
nt: Value too large for defined data type
Reading input file
0%Done, read 263843064 lines
Temp name base: /tmp/reorderXXXXXX
Got temp name: /tmp/reorderb0538C
Reordering 5214551 sequence entries
2.58%

...

[formatdb] WARNING: Sequence number 5051632 (gi|4704323|dbj|AB013452.1|), 15 illegal characters were removed:
2 Es, 1 F, 4 Is, 3 Ls, 3 Os, 2 Ps

[formatdb] WARNING: Sequence number 5052135 (gi|640099|pdb|172D|D), 32 illegal characters were removed:
4 Es, 3 Fs, 9 Is, 3 Ls, 7 Os, 3 Ps, 3 -s

[formatdb] WARNING: Sequence number 5052365 (gi|999772), 31 illegal characters were removed:
5 Es, 1 F, 9 Is, 6 Ls, 5 Os, 5 Ps

[formatdb] ERROR: Failed to create index.  Possibly a gi included more than once in the database.

Removed /tmp/reorder9UjHhX
There was an error executing formatdb.  Check formatdb.log
///////////////////////////////////////////////////////////////////////////////

To test I broke the nt file in 24 parts and executed each one and I did'nt find nothing of error.This error is happening because de size of NT to be 20 GB?
What I have to do for resolve this error?

Thanks
Daniel Sousa
*****************************************************************
* Daniel Xavier de Sousa *
* Mestrando em Informática - PUC-Rio *
* E-MAIL : dsousaARROBAinf.puc-rio.br *
* Fone : +55 21 35271500 - 4543 *
****************************************************************


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Ray Muirhead | 12 May 14:07 2007
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Running mpiBLAST on Microsoft Windows Compute Cluster Server 2003 with MS MPI

Hi there,

May I ask if anyone has experience with running mpiBLAST on Microsoft
Windows Compute Cluster Server 2003, either with the MS MPI
implementation or MPICH2?  Are there any potential problems that might
occur with such a configuration?

Thank you for your time.

Kind Regards,
Ray Muirhead

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Gmane