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

Chris Fields cjfields at uiuc.edu
Mon Apr 16 15:37:58 EDT 2007


The 'verbose' setting doesn't change the way the BLAST query is sent,  
it just sends the raw output from the repeated attempts to retrieve  
the report (using the RID) to STDERR.  The error you saw won't be  
fixed by doing so.

What I was interested in was the raw HTML output dumped to the  
screen.  If it is querying the NCBI server it should dump stuff that  
includes something like this:

...
<HTML>
<p></p>
<!--
QBlastInfoBegin
         Status=WAITING
QBlastInfoEnd
--><p></p>
<SCRIPT LANGUAGE="JavaScript"><!--
...

which indicates you have a request in the BLAST queue.  If you aren't  
seeing anything then the problem is likely network-related on your  
end, so getting the latest RemoteBlast won't help.  Do any other  
BioPerl modules requiring network access work (Bio::DB::GenBank, for  
instance)?  If not it could be a proxy issue...

Just in case, here's the browsable CVS location for RemoteBlast:

http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/Bio/ 
Tools/Run/RemoteBlast.pm?cvsroot=bioperl

Click on the download link and save over your local version.

chris

On Apr 16, 2007, at 2:10 PM, DeeGee wrote:

>
> 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!!!




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