Formating DB's for BLAST on NT

Wayne Parrott wayne at workingobjects.com
Sat Dec 12 12:31:46 EST 1998


Richard:

I recently setup an experimental blast server on my NT system.
Procedure:
1) install blast executables
2) create an ncbi.ini file which the blast programs use to locate
supporting files. See example below
3) place the ncbi.ini file in you winnt directory
4) format your db(s). DBs should be in the same directory as the blast
executables
5) run blastall

;;;
;;; minimal ini file for blast support
;;;
[NCBI]
;;edit the following line to point to the data directory. 
DATA=D:\biosoftware\blast\data

--------------------------------------------------------
Following is the ncbi.ini from my system
--------------------------------------------------------
[NCBI]
DATA=D:\biosoftware\blast\data
MEDIA=ENTREZ_NET
[NET_SERV]
DISP_USERNAME=wayne
DIRECT_SVC_CON=TRUE
DISP_RECONN_ACTION=ASK
DISPATCHER=130.14.25.211
DISP_ALT_1=dispatch1.nlm.nih.gov
DISP_ALT_2=130.14.25.2
DISP_ALT_3=dispatch2.nlm.nih.gov
DISP_ALT_4=dispatch3.nlm.nih.gov
DISP_ALT_5=130.14.25.1
DISPSERIALNO=7
[REFERENCE_FROM_NET]
MEDIA=ENTREZ_NET
[SEQUENCE_FROM_NET]
MEDIA=ENTREZ_NET
[LINKS_FROM_NET]
MEDIA=ENTREZ_NET
ENTR_SEQ__ENTR_SEQ=1
ENTR_REF__ENTR_SEQ=1
ENTR_SEQ__ENTR_REF=1
ENTR_REF__ENTR_REF=1
[ENTR_LINK]
CHANNELS=LINKS_FROM_NET
[ENTR_REF]
CHANNELS=REFERENCE_FROM_NET
[ENTR_SEQ]
CHANNELS=SEQUENCE_FROM_NET
[ENTREZ_NET]
TYPE=NET
SERVICE_NAME=Entrez
RESOURCE_NAME=Entrez
RESOURCE_TYPE=Entrez
SERV_VERS_MIN=1
SERV_VERS_MAX=0
RES_VERS_MIN=1
RES_VERS_MAX=0

-----------------------------------------------------------------------
 Wayne Parrott                   email: wayne at workingobjects.com      |
 WorkingObjects.com              voice: (972)491-3704                 |
 "Distributed Object Technology    fax: (972)491-7284                 |
   for Life Sciences"              web: http://www.workingobjects.com |
----------------------------------------------------------------------- 
 "The main thing, is to keep the main thing, the main thing" 
   lyrics by Scott Krippayne


rjacob-nospam at itsa.ucsf.edu wrote:
> 
> I'm trying to set up an in lab BLAST server on an NT box using NCBI
> BLAST version 2.0. I've unpacked the programs and downloaded a few
> databases. For BLAST to use the database it needs to be formated with
> the "formatdb" program. Unfortunately I always obtain an error:
> 
> ================[ Dec 11, 1998 11:45 AM ]========================
> Version 2.0.6 [Sept-16-1998]
> Started database file "D:\Blast\ecoli_aa"
> FATAL ERROR: [067:001] FindPath failed
> FATAL ERROR: [067:000] Failure to read sequence. FastaToSeqEntry()
> failed.
> 
> Formated 0 sequences
> 
> Does anyone have any clues to what I might be doing wrong or not
> doing?
> The databases used are amino acid databases in FASTA format from the
> NCBI. I've tried variations of all the options in "formatdb" to no
> improvement. The documentation I have read did not mention this
> problem or any other special procedures that i must do before using
> the database.
> 
> Thanks in advance for you help.
> 
> Richard




More information about the Bio-soft mailing list