dbiblast problem

[Martin Sarachu]

yes, I did that before trying dbiblast

martin

Zheng Jin Tu wrote:
> 
> You may need to run formatdb first then run dbiblast.
> 
> formatdb -i input_seq -p T -o T      (for nucleic acid)
> formatdb -i input_seq -p F -o T      (for protein)
> 
> Thanks,
> 
> Tu
> ============================================================
> 
> On Fri, 7 Jun 2002, Martin Sarachu wrote:
> 
> > Hi,
> >
> > anyone found a solution for the dbiblast problem?
> >
> > I'm trying to index the formatdb'ed humrep.fas (nuc) FASTA database
> >
> > > % dbiblast
> > > Index a BLAST database
> > > Database name: humrep.fsa
> > > Database directory [.]:
> > > Wildcard database filename [humrep.fsa]: humrep.fsa.*
> > > Release number [0.0]:
> > > Index date [00/00/00]:
> > >          N : nucleic
> > >          P : protein
> > >          ? : unknown
> > > Sequence type [unknown]: N
> > >          1 : wublast and setdb/pressdb
> > >          2 : formatdb
> > >          0 : unknown
> > > Blast index version [unknown]: 2
> > >
> > >    EMBOSS An error in dbiblast.c at line 640:
> > >  cannot open ./humrep.fsa.nhr table file ./humrep.fsa.nhr.nin
> >
> >
> > I also get a similar error when trying with nr (prot) database
> >
> > > $ dbiblast
> > > Index a BLAST database
> > > Database name: nr
> > > Database directory [.]:
> > > Wildcard database filename [nr]: nr.*
> > > Release number [0.0]:
> > > Index date [00/00/00]:
> > >          N : nucleic
> > >          P : protein
> > >          ? : unknown
> > > Sequence type [unknown]: P
> > >          1 : wublast and setdb/pressdb
> > >          2 : formatdb
> > >          0 : unknown
> > > Blast index version [unknown]: 2
> > >
> > >    EMBOSS An error in dbiblast.c at line 640:
> > >  cannot open ./nr.phr table file ./nr.phr.pin
> >
> >
> > martin
> >
> > --
> > Martin Sarachu
> > mad at biol.unlp.edu.ar
> > EMBnet Argentina
> > http://www.ar.embnet.org
> >

-- 
Martin Sarachu
mad at biol.unlp.edu.ar
EMBnet Argentina
http://www.ar.embnet.org