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

Chris Fields cjfields at uiuc.edu
Sun Apr 15 23:51:05 EDT 2007


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
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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