[Bioperl-l] blastall problem

Torsten Seemann torsten.seemann at infotech.monash.edu.au
Wed Apr 4 22:57:09 EDT 2007


DeeGee,

Please add the following lines to help deduce the problem:

> my $Seq_in = Bio::SeqIO->new (-file => 'result/fasta.faa', '-format' =>
> 'Fasta');

die "could not open fasta" if not defined $Seq_in;

> my $queryin = $Seq_in->next_seq();

die "could not get seq" if not defined $queryin;

Does anything happen now?

...

Some other comments:

> my $factory = Bio::Tools::Run::StandAloneBlast->new('program'  => 'blastp',
> STACK Bio::Tools::Run::StandAloneBlast::blastpgp

I'm not sure why it is in the blastpgp() method when you chose
$factory->blastall() ?

>                                                  _READMETHOD => 'Blast'

I don't think this is required anymore in modern Bioperl. Are you
using 1.5.x or bioperl-live ?

> when i paste the protein sequence into the textarea of my html page and
> STACK toplevel /usr/local/apache2/htdocs/remote_ncbi.pl:50

So this is a CGI script?
Does the script run as user 'apache' or 'httpd', or as yourself via SuEXEC?
Does 'apache' have permissions to READ/WRITE the result/ directory?

--Torsten


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