[Bioperl-l] Blast doesn't work

[Anders Stegmann]

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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