[Bioperl-l] formatdb with the nr database

Scott Markel smarkel at scitegic.com
Mon Jan 23 20:47:38 EST 2006


Hubert,

Does your blastall file have execute permission turned on?

Scott

Hubert Prielinger wrote:

> 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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> 

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Scott Markel, Ph.D.
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