[Bioperl-l] Command line error in BLAST+

Peter Cock p.j.a.cock at googlemail.com
Fri Sep 16 04:15:46 EDT 2011

On Fri, Sep 16, 2011 at 6:12 AM, Manju Rawat <manju.rawat2 at gmail.com> wrote:
> Hi,
> I have installed the latest version of blast and download the database
> correctly Using this tutorial
> http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/unix_setup.html
> But when i running blastn-help command in terminal it showing me error that
> blastn: error while loading shared libraries: libbz2.so.1: cannot open
> shared object file: No such file or directory.
> and when i am running the blastall command then it showing that
> *legacy_blast.pl blastall -p blastn -i amino.fa -d nr -o blast.out*
> Can't exec "/usr/bin/blastn": No such file or directory at /usr/bin/
> legacy_blast.pl line 85.
> Program failed, try executing the command manually.
> While i have set the path of environment variable
> PATH=$PATH:/home/abc/ncbi-blast-2.2.25+/bin
> I have checked everything but not able tp fine the error..
> Pl help me.
> Thanks
> Manju

You're using the BioPerl wrapper for legacy blast (blastall),
which is not installed. Instead you have the new blast+
suite which includes a wrapper using the perl script
legacy_blast.pl to imitate the old blastall tool (in this
case it calls the new tool blastn).

Fix 1: Edit legacy_blast.pl to use the path to blastn etc
under your home directory

Fix 2: Install BLAST+ at system level

Fix 3: Use the BioPerl wrapper for BLAST+ instead.

I'd go with option 3.


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