[BiO BB] NCBI: rpsblast segmentation fault

Magda Mansour magda_mansour at yahoo.fr
Fri May 27 10:51:28 EDT 2005


When I run rpsblast with the CDD (conserved domain
database) downloaded from the NCBI, I have no
When I run it on a custom database made from 2
profiles using formatrpsdb, I get a segmentation fault
NOTE: [000.000] RDBTaxInfoInit: Unable to open 
in the rpsblast.log file

Here are the commands I use to make my small DB:

	-d DB/pdb90 
	-i trial_db_3/CAA64315.fasta 
	-o trial_db_3/CAA64315.out 
	-C trial_db_3/matric_C.chk	
	-Q trial_db_3/matrix_Q 	
	-u1 -J T -j 4 
for 2 different sequences.

	-i trial_db_3/DB_formatrps.pn 
	-o trial_db_3/index 
	-t trial_db_3/DB_formatrps 
	-n trial_db_3/DB_formatrps
	-l trial_db_3/formatrpsdb.log
The output files seem very similar to those of the
NCBI  DB. (but I can't access all of them).

	-i trial_db_3/P00179.fasta 
	-d trial_db_3/DB_formatrps 
	-o trial_db_3/P00179_rps.out 
	-l trial_db_3/rpsblast.log 
	=>	Segmentation fault!!!
	NOTE: [000.000] RDBTaxInfoInit: Unable to open 

Did I forget any important parameter in any step?
Isn't it possible to make a database from 2 profiles
only? Is there anything wrong with the extensions?

Another question, is it possible to create a profile
from the output of rpsblast??

Thank you,


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