[Bioperl-l] formatdb with the nr database
Hubert Prielinger
hubert.prielinger at gmx.at
Tue Jan 24 21:15:38 UTC 2006
hi alex,
I have done, as you recommended and got the following output:
[Hubert at ppc7 ~]$ file /home/Hubert/blast/blast-2.2.13/bin/blastall
/home/Hubert/blast/blast-2.2.13/bin/blastall: ELF 64-bit LSB executable,
AMD x86-64, version 1 (SYSV), for GNU/Linux 2.4.1, dynamically linked
(uses shared libs), for GNU/Linux 2.4.1, not stripped
[Hubert at ppc7 ~]$
does it mean, that it is compatible with the operating system
thanks for help
Hubert
Alexander Kozik wrote:
> try Unix command "file", for example:
>
>
> bash-2.03$ file /usr/local/genome/bin/blastall
>
> /usr/local/genome/bin/blastall: ELF 64-bit MSB executable SPARCV9
> Version 1, UltraSPARC1 Extensions Required, dynamically linked, stripped
>
> bash-2.03$
>
> it will tell if it's compatible with the operating system
>
> -Alex
>
> 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/standalo
>>>>>>ne_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
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>>>>http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>>
>>>>
>>>>
>>
>>
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