[Bioperl-l] Blast doesn't work

[michael watson (IAH-C)]

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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