[Bioperl-l] NCBI BLAST results parsing

Chris Fields cjfields at uiuc.edu
Thu Jun 8 14:47:19 EDT 2006


Thomas;

That error isn't related to BioPerl.  This is the standard HTML response
NCBI gives as a web page; the error imbedded in the HTML you received as a
warning has:

ERROR: Cannot accept request, error code: 1Number of unfinished requests
(151) from your IP address reached the HARD limit 150.

So you may have too many requests in the BLAST queue.  

Chris

> -----Original Message-----
> From: Thomas J Keller [mailto:kellert at ohsu.edu]
> Sent: Thursday, June 08, 2006 1:39 PM
> To: Chris Fields
> Cc: John Mifsud; bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] NCBI BLAST results parsing
> 
> I'm having the same problem bp_remote_blast.pl worked yesterday,
> today it's busted. Incidently, I got the following email from NCBI
> this morning:
> The new version of the NCBI SOAP E-Utilities, which includes recent
> changes to the NCBI sequence databases schema, was released today.
> 
> Thank you.
> NCBI E-Utilities Team
> 
> I wouldn't have thought that that would affect
> Bio::Tools::RemoteBlast but something has changed.
> 
> Here's a snippet of the output after $ bp_remote_blast.pl -p blastn -
> d nr -e 1e-3 -i nm_008540.fasta
> 
> -------------------- WARNING ---------------------
> MSG: req was POST http://www.ncbi.nlm.nih.gov/blast/Blast.cgi
> User-Agent: bioperl-Bio_Tools_Run_RemoteBlast/1.4
> Content-Length: 267
> Content-Type: application/x-www-form-urlencoded
> 
> DATABASE=nr&COMPOSITION_BASED_STATISTICS=off&QUERY=%3ENM_008540_2927+%
> 25GC+55.0+Score+5+Mus+musculus+MAD+homolog+4+(Drosophila)+(Smad4)%2C
> +mRNA.%
> 0Acactctgcctgctgcttcactgt&EXPECT=1e-3&SERVICE=plain&FORMAT_OBJECT=Alignm
> ent&CMD=Put&FILTER=L&CDD_SEARCH=off&PROGRAM=blastn
> 
> 
> ---------------------------------------------------
> 
> -------------------- WARNING ---------------------
> MSG: <html><head><title>NCBI Blast</title><meta http-equiv="Content-
> Type" content="text/html; charset=utf-8"/><link rel="stylesheet"
> href="http://www.ncbi.nlm.nih.gov/corehtml/ncbi.css"></head><body
> bgcolor="#FFFFFF" text="#000000" link="#CC6600" vlink="#CC6600"
> onload="StartBlastCgi();"><!--  the header   --> <table border="0"
> width="600" cellspacing="0" cellpadding="0"><tr>     <td width="600"
> colspan=4>    <map name="head_img_map">    <area shape="rect"
> coords="0,0,300,40" href="http://www.ncbi.nlm.nih.gov" alt="NCBI home
> page">       <area shape="rect" coords="301,0,600,40" href="http://
> www.ncbi.nlm.nih.gov/blast" alt="NCBI BLAST home page">    </map>
> <IMG SRC="html/blastheader.gif" USEMAP="#head_img_map" BORDER="0"
> NAME="BlastHeaderGif" ALT="BLAST header image" WIDTH="600"
> HEIGHT="45" BORDER="0" ALIGN="middle">    </td></tr><tr
> align="center">    <td width="150" bgcolor="#003366">        <a
> href="http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?
> CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&PAGE=Nucleotides&NCBI_GI=
> yes&FILTER=L&HITLIST_SIZE=100&SHOW_OVERVIEW=yes&AUTO_FORMAT=yes&SHOW_LIN
> KOUT=yes"        class="HELPBAR"><FONT COLOR="#FFFFFF">Nucleotide</
> FONT></a></td>    <td width="150" bgcolor="#003366">        <a
> href="http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?
> CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&PAGE=Proteins&NCBI_GI=yes
> &HITLIST_SIZE=100&COMPOSITION_BASED_STATISTICS=yes&SHOW_OVERVIEW=yes&AUT
> O_FORMAT=yes&CDD_SEARCH=yes&FILTER=L&SHOW_LINKOUT=yes"
> class="HELPBAR"><FONT COLOR="#FFFFFF">Protein</FONT></a></td>    <td
> width="150" bgcolor="#003366">        <a href="http://
> www.ncbi.nlm.nih.gov/blast/Blast.cgi?
> CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&PAGE=Translations&NCBI_GI
> =yes&FILTER=L&HITLIST_SIZE=100&SHOW_OVERVIEW=yes&AUTO_FORMAT=yes&SHOW_LI
> NKOUT=yes"        class="HELPBAR"><FONT COLOR="#FFFFFF">Translations</
> FONT></a></td>    <td width="150" bgcolor="#003366">        <a
> href="http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?
> CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&PAGE=Formating&NCBI_GI=ye
> s&SHOW_OVERVIEW=yes&AUTO_FORMAT=yes&SHOW_LINKOUT=yes"
> class="HELPBAR"><FONT COLOR="#FFFFFF">Retrieve results for an RID</
> FONT></a></td></tr></table><br><!--  the contents   --> <form
> action="Blast.cgi" enctype="application/x-www-form-urlencoded"
> method="POST"><script src="blastcgi.js"></script><SCRIPT
> LANGUAGE="JavaScript"> <!--document.images['BlastHeaderGif'].src =
> 'html/head_formating.gif';// --></SCRIPT><br><hr><font
> color="red">ERROR: Cannot accept request, error code: 1Number of
> unfinished requests (151)  from your IP address reached the HARD
> limit 150.</font><hr></form>   </body></html>
> ---------------------------------------------------
> 
> On Jun 8, 2006, at 6:12 AM, Chris Fields wrote:
> 
> > I would say, based on previous responses, update to the latest CVS
> > (bioperl-live).  You could also try updating
> > Bio::Tools::Run::RemoteBlast.pm and Bio::SearchIO::blast.pm if you
> > don't want to update the entire toolkit.  Running these with BLAST
> > 2.2.14 output seems to work fine.
> >
> > Though this is the likely fix, if you have additional problems next
> > time please make sure to include more information.  We have no idea
> > what OS, bioperl version, perl version you are running.  And a code
> > snippet and bug description would be nice (i.e. "it doesn't work" -
> > not a good description; "the script freezes" is a little more
> > informative).
> >
> > Chris
> >
> > On Jun 8, 2006, at 6:38 AM, John Mifsud wrote:
> >
> >> Dear all,
> >>
> >> Firstly I hope this is the right email list to write to!
> >>
> >> Secondly, I have a little program that parses the BLAST results i
> >> have got
> >> running remotely to the NCBI server and takes out all the hit
> >> sequences and
> >> converts them to FASTA format.
> >>
> >> Now when using BROAD BLAST and getting results this works fine
> >> (tblastn ver
> >> 2.2.9). However, NCBI have just updated their BLAST server (to
> >> 2.2.14) and
> >> the output is different and the parsing no longer works. I was
> >> wondering if
> >> anyone knew of a new SearchIO module / script that is designed to
> >> blast the
> >> updated NCBI BLAST output?
> >>
> >> Thanks for your time,
> >>
> >>
> >> John
> >>
> >> _______________________________________________
> >> 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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