[Bioperl-l] formatdb with the nr database

Scott Markel smarkel at scitegic.com
Tue Jan 24 17:09:57 EST 2006


Hubert,

Since you can't run blastall on the command line, your initial
problem has nothing to do with BioPerl.  Once you get blastall
working on the command line, you'll know what directories and
environment variable settings to use when running via BioPerl.

What happens when you run the following?

   file /home/Hubert/blast/blast-2.2.13/bin/blastall

Is the executable the correct one for your operating system?

Scott

Hubert Prielinger wrote:

> Hi,
> thank you very much for the help, I have tried to run the blastall on 
> commandline, but I can't even execute the binary file, nevertheless the 
> blastall exe file have every permission...
> I always get the error message: blastall: cannot execute the binary file
> Need to be the exe file somewhere else, another path...now it is located 
> under /home/Hubert/blast/blast-2.2.13/bin
> 
> thanks
> Hubert
> 
> 
> 
> 
> 
> Scott Markel wrote:
> 
>> Hubert,
>>
>> If you look at the MSG line in the exception you can see
>> exactly what the command line was.  Nagesh is pointing out
>> that you used -d "/nr" and asking if that's what you want.
>> I suspect that the '/' shouldn't be there.
>>
>> Try invoking blastall directly from the command line.  All
>> BioPerl is doing is invoking BLAST on your behalf.  The
>> same command line that BioPerl uses should also work for
>> you on the command line.
>>
>> Scott
>>
>> Hubert Prielinger wrote:
>>
>>> hi,
>>> sorry, but what do you mean with is your blast database in /nr...
>>> my database is located in the path /home/Hubert/blast/blast-2.2.13/data
>>>
>>>
>>>
>>> Nagesh Chakka wrote:
>>>
>>>> Can you just run the blast from the command line.
>>>> Is your blast database in "/nr".
>>>>
>>>> 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
>>>>>>>>>       
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>     
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>  
>>>>>>
>>>>>
>>>>
>>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at portal.open-bio.org
>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>
> 
> 
> 
> 

-- 
Scott Markel, Ph.D.
Principal Bioinformatics Architect  email:  smarkel at scitegic.com
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