[Bioperl-l] formatdb with the nr database

Hubert Prielinger hubert.prielinger at gmx.at
Tue Jan 24 15:49:07 EST 2006


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
>>>>>>>>
>>>>>>>> _______________________________________________
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>>>>>>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>>       
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>     
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>  
>>>>>
>>>>
>>>
>>>
>>
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