[Bioperl-l] Blast doesn't work

[Anders Stegmann]

You were right! 
 
Bioperl-1.5.1 is working perfectly with blast. 
 
Thanks very much for all the help everybody, It was very nice of you :-). 
 
Anders.

>>>Jason Stajich <jason.stajich at duke.edu> 12/21/05 4:09 pm >>>
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