[Bioperl-l] Finding all human paralogues

[Torsten Seemann]

> Many thanks for your good help. I have followed your advice, and updated the 
> path to the fasta file, both in BLASTDB, BLASTDATADIR and in the code. But 
> even now it doesn't work. The directory of my fasta file 
> is: /home/Yuval/FastaDBs and the one of the Blast binaries 
> is: /home/Yuval/Applications/blast/bin
> 
> And I keep getting the same error message:
> 
> [blastall] WARNING: test: Unable to open Homo_sapiens.NCBI354.feb.pep.fa.pin
> 
> ------------- EXCEPTION  -------------
> MSG: blastall call crashed: 256 /home/Yuval/Applications/blast/bin/blastall 
> -pblastp  -d  /home/Yuval/FastaDBs/Homo_sapiens.NCBI354.feb.pep.fa

(I assume there was a space between -p and blastp)

> -i  /tmp/98fwqIYOMi  -o  /tmp/vlRcHscPcH

This doesn't look like a BioPerl problem anymore. It says it can't find the 
blast index files for Homo_sapiens.NCBI354.feb.pep.fa. But the "-d xxxx" line 
is trying to load them from the right place. I assume you have run
formatdb to create the indices, and they are in /home/Yuval/FastaDBs/, and that 
there were no errors ?

% cd /home/Yuval/FastaDBs/
% formatdb -i Homo_sapiens.NCBI354.feb.pep.fa -p T -o T
% cat formatdb.log
% ls -lsa Homo_sapiens.NCBI354.feb.pep.fa.*

and that this last "ls" lists about seven index files called 
Homo_sapiens.NCBI354.feb.pep.fa.pin, .psq, .p?? etc
And they are READABLE by the user who is running Blast (hopefully "Yuval")?

If so, can you run blast on the command line?

% blastall -i SOME_PROTEIN.FA -d 
/home/Yuval/FastaDBs/Homo_sapiens.NCBI354.feb.pep -p blastp

BioPerl will probably never run your blast if you can't get that working.

-- 
Torsten Seemann
Victorian Bioinformatics Consortium, Monash University, Australia
http://www.vicbioinformatics.com/
Phone: +61 3 9905 9010