[Bioperl-l] Blast doesn't work
andreas.boehm at virchow.uni-wuerzburg.de
Wed Dec 21 09:26:59 EST 2005
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/
More information about the Bioperl-l