[Bioperl-l] Blast doesn't work

[Jason Stajich]

Make sure you are using the latest version of bioperl - NCBI changed  
the interface and we now have Bio::SearchIO as the default parser.   
It works fine for me on bioperl 1.5.1

#23 shouldn't have to work as root, but I haven't been following the  
thread so I don't know what you are changing.

On Dec 21, 2005, at 10:02 AM, Anders Stegmann wrote:

> Michael,
>
> It worked as root!!!
>
> the blaststandalone bptutorial 23 is working!
>
> great job.
>
> BUT bptutorial 22 is still not working. still getting
>
> Beginning run_remoteblast example...
> submitted Blast job
> retrieving results...
>
> -------------------- WARNING ---------------------
> MSG: Possible error (1) while parsing BLAST report!
> ---------------------------------------------------
> Use of uninitialized value in substitution (s///) at Bio/Tools/ 
> BPlite.pm line 337, <GEN3> line 29.
> Use of uninitialized value in substitution (s///) at Bio/Tools/ 
> BPlite.pm line 338, <GEN3> line 29.
> Use of uninitialized value in substitution (s///) at Bio/Tools/ 
> BPlite.pm line 339, <GEN3> line 29.
> Use of uninitialized value in patt
>
> any suggestions?
>
> Anders.
>
>
>
>>>> michael watson (IAH-C) <michael.watson at bbsrc.ac.uk> 12/21/05  
>>>> 3:01 pm >>>
> Dude
>
> Try
>
> find / -name ecoli.nt.nin
>
> This will give you the location of your blast data directory.  For an
> example, mine is in /usr/local/blast/data/ecoli.nt.nin
>
> Now
>
> export PATH=$PATH:/usr/local/blast/bin
> export BLASTDB=/usr/local/blast/data/ # get this from the find command
> above
> export BLASTMAT=/usr/local/blast/data/ # get this from the find
> command above
>
> perl -w bptutorial.pl 23
>
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org
> [mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Anders
> Stegmann
> Sent: 21 December 2005 13:41
> To: bioperl-l at bioperl.org
> Subject: [Bioperl-l] Blast doesn't work
>
> Torsten,
>
> SUSE 10.0 is the brand new version the linux SUSE OS.
>
> writing: export PATH=/usr/local/blast/bin:$PATH./bptutorial 23
>
> gives me:
>
> bash: export
> PATH=/usr/local/blast/bin:/home/anst/bin:/usr/local/bin:/usr/bin:/ 
> usr/X1
> 1R6/bin:/bin:/home/anst/blast/bin:/usr/games:/opt/gnome/bin:/opt/ 
> kde3/bi
> n:/usr/lib/mit/bin:/usr/lib/mit/sbin./bptutorial 23: No such file or
> directory
>
> Yes! there is definitely a file called blastall in the
> /usr/local/blast/bin directory and it works if I use it  
> independently of
> bioperl.
>
> The thing is that I have never before needed/used to download the ncbi
> blast program independently.
> Shouldn't it be enough to install the Bundle?
>
> Also, when writing
>
> perl -w bptutorial.pl 23
>
> I get:
>
> Beginning run_standaloneblast example...
> [blastall] WARNING: Test1: Unable to open ecoli.nt.nin
>
> ------------- EXCEPTION  -------------
> MSG: blastall call crashed: 256 /usr/local/blast/bin/blastall -p   
> blastn
> -d  /usr/local/blast/bin/data/ecoli.nt  -i  /tmp/zM1t9HD2jq  -o
> /tmp/FCGPZQlclD
>
> STACK Bio::Tools::Run::StandAloneBlast::_runblast
> Bio/Tools/Run/StandAloneBlast.pm:732
> STACK Bio::Tools::Run::StandAloneBlast::_generic_local_blast
> Bio/Tools/Run/StandAloneBlast.pm:680
> STACK Bio::Tools::Run::StandAloneBlast::blastall
> Bio/Tools/Run/StandAloneBlast.pm:536
> STACK main::__ANON__ bptutorial.pl:3279 STACK main::run_examples
> bptutorial.pl:4156 STACK toplevel bptutorial.pl:4245
>
> Notice in line 2: Unable to open ecoli.nt.nin. This is a remnant  
> from an
> E.coli. database formatation I did much earlier and independently of
> bioperl.
> Thus, the ncbi standaloneblast program works, but not with bioperl!
>
> Why does bioperl fetch an unrelated file in the /usr/local/blast/data
> directory?
> Is like it is trying to run something it shouldn't.
>
> Anders.
>>>> Torsten Seemann <torsten.seemann at infotech.monash.edu.au> 12/21/05
> 12:50 pm >>> >I have tried  >export BLASTDIR=/usr/local/blast/bin
> (where my blastall binary is) >I get the same?  (I assume you are on
> Unix, not Windows)  Does it work when you do this?  export
> PATH=/usr/local/blast/bin:$PATH ./bptutorial 23  Is there definitely a
> file called 'blastall' in /usr/local/blast/bin which is EXECUTABLE and
> READABLE by the user running the tutorial?  -- Torsten Seemann  
> Victorian
> Bioinformatics Consortium, Monash University, Australia
> http://www.vicbioinformatics.com/
>
>
>
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--
Jason Stajich
Duke University
http://www.duke.edu/~jes12