[Bioperl-l] Blast doesn't work

[Anders Stegmann]

Okay, 
 
anst at omyil1:~/bioperl-1.4> printenv | grep BLAST 
BLASTDIR=/usr/local/blast/bin 
BLASTMAt=/home/anst/blast 
BLASTDB=/home/anst/blast 
BLASTMAT=/home/anst/blast/ecoli.nt.nin 
 
anders.

>>>michael watson (IAH-C) <michael.watson at bbsrc.ac.uk> 12/21/05 4:05 pm >>>
Can you send me the output from

printenv | grep BLAST

Please?

And in future, include all the commands you use :)

-----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 14:51
To: bioperl-l at bioperl.org
Subject: RE: [Bioperl-l] Blast doesn't work

michael,

Thanks for replying!

I then 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  /home/anst/blast/ecoli.nt.nin/home/anst/blast/ecoli.nt.nin/ecoli.nt
-i  /tmp/6tbl1I7i52  -o  /tmp/NTwbTioMdD

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

The thing is that bioperl is trying to use the ecoli.nt.nin file (in my
blast/data directory) which it shouldn't.

But I found out that my blast/data dir is in the /home/anst/blast/data
path and that my blast/bin dir is in the /usr/local/blast/bin pathway.

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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