[BiO BB] NCBI: rpsblast segmentation fault
Magda Mansour
magda_mansour at yahoo.fr
Fri May 27 10:51:28 EDT 2005
Hello,
When I run rpsblast with the CDD (conserved domain
database) downloaded from the NCBI, I have no
problems.
When I run it on a custom database made from 2
profiles using formatrpsdb, I get a segmentation fault
amd
NOTE: [000.000] RDBTaxInfoInit: Unable to open
in the rpsblast.log file
Here are the commands I use to make my small DB:
toolbox-C/ncbi/build/blastpgp
-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.
toolbox-C/ncbi/build/formatrpsdb
-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).
toolbox-C/ncbi/build/rpsblast
-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,
Yours,
Magda.
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