[Bioperl-l] error while remote blast against swissprot db

DeeGee gdorjee at hotmail.com
Mon Apr 16 15:10:01 EDT 2007


hi Chris,
thanks for your reply. i set the RemoteBlast factory to a verbosity of 1,
and i get the same error message. i'm new to all these. so, could you plz
tell me how can i do the RemoteBlast in CVS that you've suggested.

cheers!!!
 

Chris Fields wrote:
> 
> This sounds like a similar issue that popped up a few weeks ago  
> related to URLAPI changes for remote BLAST access.  That was fixed on  
> NCBI's end but I also added a fix to RemoteBlast in CVS that works as  
> well.
> 
> Saying that, my guess is the same as Dave's, that there are  
> connectivity issues.  What happens when you set the RemoteBlast  
> factory to a verbosity of 1?  This will spill out debugging output  
> from the repeated queries to the NCBI server (so if there are  
> problems they'll show up there).
> 
> ...
> my $factory = Bio::Tools::Run::RemoteBlast->new(
>                                  '-prog'  => 'blastp',
>                                  '-data' => 'swissprot',
>                                   _READMETHOD => "Blast",
>                                   -verbose => 1    # debugging output
>                           );
> ...
> 
> If you see the BLAST report but get the same error try using the  
> RemoteBlast in CVS to see if it fixes the problem.
> 
> chris
> 
> 
> On Apr 15, 2007, at 9:43 PM, David Messina wrote:
> 
>> You're right, it's not the input sequence. I just tried it with your
>> script and it worked.
>>
>>
>>> is it possible that the script is not being about to read the
>>> RemoteBlast.pm?
>>
>> I think the program wouldn't compile if that were the case, and your
>> error message would be about not finding RemoteBlast.pm rather than
>> the one you got.
>>
>>
>>> but the thing is, i can run the standalone blast on the
>>> command line, although i've never been able the run the same with
>>> cgi module
>>> (by gettting the input from an html textarea). i don't understand.
>>
>> This result really suggests that perl and Bioperl are not the issue.
>> I'm not saying the following to give you the brushoff, but given the
>> numerous ways in which web-based apps can fail and in which
>> webservers can be installed, it might be best for you to find someone
>> at your institution who can sit down with you and work through it.
>>
>> Dave
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

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