[Bioperl-l] formatdb with the nr database

Hubert Prielinger hubert.prielinger at gmx.at
Mon Jan 23 19:15:45 EST 2006


Hi Nagesh,
thank you very much, I put my database into the data folder, run the 
program and got the following error message:

submit Sequence...just do it....
sh: /home/Hubert/blast/blast-2.2.13/bin/blastall: cannot execute binary file

------------- EXCEPTION  -------------
MSG: blastall call crashed: 32256 
/home/Hubert/blast/blast-2.2.13/bin/blastall -p  blastp  -d  "/nr"  -i  
/tmp/QTZfYMbgLM  -e  20000  -o  /tmp/v3YwWvONZ1  -v  1000  -b  1000

STACK Bio::Tools::Run::StandAloneBlast::_runblast 
/usr/lib/perl5/site_perl/5.8.6/Bio/Tools/Run/StandAloneBlast.pm:759
STACK Bio::Tools::Run::StandAloneBlast::_generic_local_blast 
/usr/lib/perl5/site_perl/5.8.6/Bio/Tools/Run/StandAloneBlast.pm:706
STACK Bio::Tools::Run::StandAloneBlast::blastall 
/usr/lib/perl5/site_perl/5.8.6/Bio/Tools/Run/StandAloneBlast.pm:557
STACK toplevel 
/home/Hubert/installed/eclipse/workspace/Database_Search/standalone_blast.pl:46

--------------------------------------

Why it did not find my binary file, but it is there

regards

Nagesh Chakka wrote:

>Hi,
>The following is from the StandAloneBlast.pm documentation
>" If the databases which will be searched by BLAST are located in the
>data subdirectory of the blast program directory (the default
>installation location), StandAloneBlast will find them; however, if the
>database files are located in any other location, environmental variable
>$BLASTDATADIR will need to be set to point to that directory."
>Please note that I have not used this module before.
>Nagesh
>
>
>
>On Mon, 2006-01-23 at 17:08 -0600, Hubert Prielinger wrote:
>  
>
>>Hi,
>>thank you very much for the help, another questions that raises up, do I 
>>have to write the path to the database files as well, I guess so, but 
>>how I do that, the same way I write the path to teh blast bin files?
>>Does anybody know how to set the Composition based statistics parameter?
>>there is my code:
>>
>>#!/usr/bin/perl -w
>>
>>use Bio::Tools::Run::StandAloneBlast;
>>use Bio::Seq;
>>use Bio::SeqIO;
>>use strict;
>>
>>BEGIN
>>{
>>    $ENV{PATH}=":/home/Hubert/blast/blast-2.2.13/bin/:";
>>}
>>
>>
>># parameters
>>my $expect_value = 20000;
>>#my $filter_query_sequence = 'F';
>>my $one_line_description = 1000;
>>my $alignments = 1000;
>># my $strands = 1;
>>my $count = 1;
>>
>>my @params = ('program' => 'blastp', 'database' => 'nr');
>>#my $progress_interval = 100;
>>
>>
>>my $seqio_obj = Bio::SeqIO->new(
>>  -file   => "Perm.txt",
>>  -format => "raw",
>>);
>>
>># create factory object and set parameters
>>my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
>>
>>$factory->e($expect_value);
>>#$factory->F($filter_query_sequence);
>>$factory->v($one_line_description);
>>$factory->b($alignments);
>>#$factory->S($strands);
>>
>>
>># get query
>>
>>while ( my $query = $seqio_obj->next_seq ) {
>>      my $blast_report = $factory->blastall($query);
>>      my $filename = "comp_$count.txt";
>>      my $factory->outfile($filename);
>>      print $query->seq;
>>      print "\n";
>> 
>>  $count++;
>>}
>>
>>thank you very much in advance
>>Hubert
>>
>>
>>
>>Nagesh Chakka wrote:
>>
>>    
>>
>>>Hi Hubert,
>>>I downloaded the nr.00.tar.gz file a week ago. I was able to get the 
>>>following files
>>>.phr, .pin, .pnd, .pni, .ppd, .ppi, .psd, .psi, .psq, .pal files. I 
>>>have no trouble in running standalone blast. You are not required to 
>>>run formardb on the downloaded blast databases and that may be the 
>>>reason why the sequences are not included as it will also reduce the 
>>>size of the file.
>>>Did you try to run a blast search, if so is it giving you any errors?
>>>Nagesh
>>>
>>>
>>>
>>>Hubert Prielinger wrote:
>>>
>>>      
>>>
>>>>Hi,
>>>>I have downloaded the nr database for doing a blast search locally, 
>>>>now I'm supposed to index the database with formatdb, but it doesn't 
>>>>work...
>>>>The online help says that you need a fasta file that is indexed to 
>>>>use for searching the database, but when I uncompressed the zip file, 
>>>>there were only .phr, .pnd, .pin, .pni, .ppd file....
>>>>Is there anybody who can tell me, how to use formatdb with the nr 
>>>>database...
>>>>
>>>>Help is very appreciated
>>>>Thank you very much in advance
>>>>
>>>>Hubert
>>>>
>>>>_______________________________________________
>>>>Bioperl-l mailing list
>>>>Bioperl-l at portal.open-bio.org
>>>>http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>>>        
>>>>
>>>
>>>
>>>      
>>>
>
>
>  
>



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