[Bio-software] Re: error in run blastpgp

David Lapointe via bio-soft%40net.bio.net (by david.lapointe from gmail.com)
Wed Jan 5 07:37:09 EST 2011


On Jan 4, 6:38 am, hamze rahimi <buksan... from gmail.com> wrote:
> Dear expert
>
> I download blast-2.2.18-ia32-linux.tar.gz and unzipped. when I want run
> under command, I find this error
>
> [buksanbio from localhost bin]$ ./blastpgp -v 5000 -b 0 -j 3 -h 0.002 -d
> /home/buksanbio/nr/ -i 535.fasta -C.Chk  > /dev/null
> [blastpgp] WARNING: Unable to open .pin
>
> or
>
> [buksanbio from localhost bin]$ ./blastpgp -v 5000 -b 0 -j 3 -h 0.002 -d ~/nr/*
> -i 535.fasta -C.Chk  > /dev/null
> [blastpgp] ERROR: Arguments must start with '-' (the offending argument #11
> was: '/home/buksanbio/nrfilt/nr.00.pin')
>
> as recommanded  in doc file I convert database by this command:
> ./formatdb -i ~/.../nr -p T -o T
>
> nr is my database that contain these files:
> nr.00.phr  nr.00.psd  nr.01.pin  nr.01.psi  nr.02.pnd  nr.02.psq  nr.03.pni
> nr.04.phr  nr.04.psd
> nr.00.pin  nr.00.psi  nr.01.pnd  nr.01.psq  nr.02.pni  nr.03.phr  nr.03.psd
> nr.04.pin  nr.04.psi
> nr.00.pnd  nr.00.psq  nr.01.pni  nr.02.phr  nr.02.psd  nr.03.pin  nr.03.psi
> nr.04.pnd  nr.04.psq
> nr.00.pni  nr.01.phr  nr.01.psd  nr.02.pin  nr.02.psi  nr.03.pnd  nr.03.psq
> nr.04.pni  nr.pal
>
> what is problem?
> thanks a lot for any help
>
> --
> Yours sincerely
> Rahimi Hamzeh
> PhD student in Medical Biotechnology
> Pasteur institute
> e mail:
> buksan... from gmail.com

nr is not a directory but the base name of your database. so -d ~/nr/
would not work but ~/nr would. Alternately indicate in .ncbirc where
your formatted databases are located.

D



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