[Bioperl-l] Blast doesn't work

Anders Stegmann anst at kvl.dk
Wed Dec 21 10:33:56 EST 2005

Yes, I did create a file named .ncbirc and it is placed in my blast working dir (/home/anst/blast/). It say's: 


>>>Andreas Boehm <andreas.boehm at virchow.uni-wuerzburg.de> 12/21/05 3:26 pm >>>

did you create a file named .ncbirc in your working directory?
If yes, then please post a snipped of an strace. We then can have a look
on what your program is trying to to.


Anders Stegmann wrote:
>SUSE 10.0 is the brand new version the linux SUSE OS.
>writing: export PATH=/usr/local/blast/bin:$PATH./bptutorial 23
>gives me:
>bash: export PATH=/usr/local/blast/bin:/home/anst/bin:/usr/local/bin:/usr/bin:/usr/X11R6/bin:/bin:/home/anst/blast/bin:/usr/games:/opt/gnome/bin:/opt/kde3/bin:/usr/lib/mit/bin:/usr/lib/mit/sbin./bptutorial 23: No such file or directory
>Yes! there is definitely a file called blastall in the /usr/local/blast/bin directory and it works if I use it independently of bioperl.
>The thing is that I have never before needed/used to download the ncbi blast program independently.
>Shouldn't it be enough to install the Bundle?
>Also, when writing
>perl -w bptutorial.pl 23
>I get:
>Beginning run_standaloneblast example...
>[blastall] WARNING: Test1: Unable to open ecoli.nt.nin
>------------- EXCEPTION  -------------
>MSG: blastall call crashed: 256 /usr/local/blast/bin/blastall -p  blastn  -d  /usr/local/blast/bin/data/ecoli.nt  -i  /tmp/zM1t9HD2jq  -o  /tmp/FCGPZQlclD
>STACK Bio::Tools::Run::StandAloneBlast::_runblast Bio/Tools/Run/StandAloneBlast.pm:732
>STACK Bio::Tools::Run::StandAloneBlast::_generic_local_blast Bio/Tools/Run/StandAloneBlast.pm:680
>STACK Bio::Tools::Run::StandAloneBlast::blastall Bio/Tools/Run/StandAloneBlast.pm:536
>STACK main::__ANON__ bptutorial.pl:3279
>STACK main::run_examples bptutorial.pl:4156
>STACK toplevel bptutorial.pl:4245
>Notice in line 2: Unable to open ecoli.nt.nin. This is a remnant from an E.coli. database formatation I did much earlier and independently of bioperl.
>Thus, the ncbi standaloneblast program works, but not with bioperl!
>Why does bioperl fetch an unrelated file in the /usr/local/blast/data directory?
>Is like it is trying to run something it shouldn't.
> >>>Torsten Seemann <torsten.seemann at infotech.monash.edu.au> 12/21/05 12:50 pm >>> >I have tried  >export BLASTDIR=/usr/local/blast/bin  (where my blastall binary is) >I get the same?  (I assume you are on Unix, not Windows)  Does it work when you do this?  export PATH=/usr/local/blast/bin:$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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