[Bio-software] Need help in running blastall through CGI

ambarish biswas via bio-soft%40net.bio.net (by ambarishbiswas from gmail.com)
Sat Jul 21 10:32:22 EST 2007


Hi,
    I'm trying to call "blastall" through a CGI script, but the database
option "-d nt" is not being available through CGI Scripts.I have formated
the nt.gz file properly and  I successfully executed the blastall program
from command line too but not from the CGI Script. The .ncbirc file is also
in place. Following is the error message of the command "blastall -p blastn
-d nt -i /tmp/CP000670.fna -o output.txt"

[blastall] WARNING: Unable to open nr.nin
[blastall] WARNING: gi|145212960|gb|CP000670.1|: Unable to open nr.nin


clearly its not finding the "blast/data" folder. To solve that problem i
have specified the "-d /home/user/blast/data/nt"
 But then the error message appeared as below:

[blastall] WARNING: Unable to open nt.00.nin
[blastall] WARNING: Unable to open nt.01.nin
[blastall] WARNING: Unable to open nt.02.nin
[blastall] WARNING: Unable to open nt.03.nin
...............................
[blastall] WARNING: gi|145212960|gb|CP000670.1|: Unable to open nt.00.nin
[blastall] WARNING: gi|145212960|gb|CP000670.1|: Unable to open nt.01.nin
[blastall] WARNING: gi|145212960|gb|CP000670.1|: Unable to open nt.02.nin
[blastall] WARNING: gi|145212960|gb|CP000670.1|: Unable to open nt.03.nin
......................


I have tried all possible way, given the path in $PATH, also used $env etc.
But still couldn't fix the problem. So, need your help, i have kept the
blastall program in the /root/bin folder so its available everywhere, only
the problem is with the "/data" folder. can you please suggest a way. I'm
working with this problem so long and now its being really hard on me.

Thanks in advance.


-- 
With Best Regards,
---------
Ambarish Biswas,
DBS, NUS,
Singapore,
Email: ambarish from nus.edu.sg
Mobile: +65-91025692


More information about the Bio-soft mailing list