[Bioperl-l] Problems using Bio::Tools::Blast

gert thijs gert.thijs@esat.kuleuven.ac.be
Fri, 11 Aug 2000 17:37:54 +0200

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gert thijs wrote:
> This script returns the following exception:
> -------------------- EXCEPTION --------------------
> MSG: Blast file gi_609339_gb_U18675.blastn2.nr.temp.html is incomplete: can't
> find program name.
> Possibly an unrecognized report format.
> SCRIPT: ./ParseBlastReport2.pl
> Bio::Tools::Blast::Run::Webblast::_blast(1175)
> Bio::Tools::Blast::Run::Webblast::blast_remote(580)
> Bio::Tools::Blast::_run_remote(1244)
> Bio::Tools::Blast::run(1178)
> Bio::Tools::SeqAnal::_initialize(279)
> Bio::Root::Object::new(462)
> main::./ParseBlastReport2.pl(33)
> ---------------------------------------------------

I have been looking at the all the intermediate file, referred to in the
message, and it seems to me that the error is not produced while processing
the results but while reading the page returned by the ncbi queueing system. 
Scrolling through the code of Bio::Tools::Blast::Run::webbblast.pm I saw that
the error message is produced while searching for the text 'BLAST[NPX]\s'. But
this line isn't in the intermediate queueing files.
I have attached this intermediate files to this mail.

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<BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099">
<A HREF="http://www.ncbi.nlm.nih.gov/BLAST/images/blast_form.map"> 
<IMG SRC="/BLAST/images/blast_form_1.gif" BORDER=0 ISMAP>
<FORM ACTION="/blast/blast.cgi" METHOD=POST NAME="QFormat" >
<BR><B>Your request has been successfully submitted and put into the Blast Queue.<BR></B>
<PRE><b>Query=</b> gi|609339|gb|U18675.1|ATU18675 Arabidopsis thaliana
4-coumarate--coenzyme A ligase (At4CL1) mRNA, complete cds
         (1260 letters)

</PRE>You are using a new system that allows users to retrieve results at their convenience and format their results multiple <BR>times with different formatting options. This system also allows the NCBI to more efficiently use <BR>computational resources, better serving the community.  A <a href="/BLAST/qblast.html">description</A> of the queueing system is available.<BR><BR><B>The request ID is </B>
<INPUT TYPE="text" SIZE=25 NAME="RID" VALUE="965997627-10235-11372"> <INPUT TYPE="submit" VALUE="Format results"><BR>The results are estimated to be ready in <B> 1 </B> min <B> 18 </B> sec but may be done sooner.<BR>
Please press "Format results" when you wish to check your results.<BR>You may change the formatting parameters for your result via the form below and press "Format results" again.<BR>
You may also request results of a different search by entering any other valid request ID to see other recent jobs.<HR>
&nbsp;&nbsp;&nbsp;&nbsp;<INPUT TYPE="checkbox" NAME="NCBI_GI"  CHECKED >
 &nbsp;&nbsp;<a href="/BLAST/newoptions.html#ncbi-gi"> NCBI-gi</a>
&nbsp;&nbsp;&nbsp;&nbsp;<INPUT TYPE="checkbox" NAME="OVERVIEW"  CHECKED > &nbsp;&nbsp;<a href="/BLAST/newoptions.html#graphical-overview">Graphical Overview</a>
&nbsp;&nbsp;<a href="/BLAST/options.html#alignmentviews">Alignment view</a>
<select name = "ALIGNMENT_VIEW">
<option value=0 selected> Pairwise
<option value=1> query-anchored with identities
<option value=2> query-anchored without identities
<option value=3> flat query-anchored with identities
<option value=4> flat query-anchored without identities
<option value=11> Get ASN.1 for SeqAnnot
<option value=13> Get ASN.1 for the Blast Object
<a href="/BLAST/newoptions.html#descriptions">Descriptions</a>
<select name = "DESCRIPTIONS">
 <option> 0 
 <option> 10 
 <option> 50 
 <option selected> 100 
 <option> 250 
 <option> 500 
&nbsp;&nbsp;<a href="/BLAST/newoptions.html#alignments">Alignments</a>
<select name = "ALIGNMENTS">
 <option> 0 
 <option> 10 
 <option> 50 
 <option selected> 100 
 <option> 250 
 <option> 500 

<SCRIPT LANGUAGE="JavaScript"> document.QFormat.RID.focus(); </SCRIPT><ADDRESS>
Comments and suggestions to:&lt; <a href="mailto:blast-help@ncbi.nlm.nih.gov">blast-help@ncbi.nlm.nih.gov</a> &gt</ADDRESS>