[Bioperl-l] blastall problem

[Chris Fields]

On Apr 5, 2007, at 4:09 PM, DeeGee wrote:

>
> Thanks again, Torsten. I tried (die "could not get seq" if not defined
> $queryin;) as you suggested, and now I get the following error  
> message:
>
> Software error:
> could not get seq at /usr/local/apache2/htdocs/remote_ncbi.pl line 50.
>
> Does this mean that next_seq() method in 'my $queryin =
> $Seq_in->next_seq();' has some problem? How can I fix it? I would  
> appreciate
> your help.
> Cheers!

This indicates there is likely some problem with your sequence file  
(either it isn't fasta or something else is wrong), but w/o actually  
seeing it we can't be sure.  I can't be sure but I don't think it is  
a next_seq() issue.  Also, if there are problems accessing the file  
the stream object should throw an error so I don't think it is that  
either...

chris

>
> Torsten Seemann wrote:
>>
>> 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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>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign