transposonpsi-users

[Transposonpsi-users] transposon PSI

[Ives V. <iv...@ps...>]

Hello, 

I am using transposon PSI for looking if there are transposons in a fasta seq with this command: 

transposonPSI.pl sctg_285.fa nuc 

It is not working, I have this error 

Error, formatdb -i transposonPSI.7461.vampire.psblocal.tmp/sctg_285/sctg_285.seq -p F (ret -1) at /software/shared/apps/x86_64/TransposonPSI/08222010//transposonPSI.pl line 115, <$filehandle> line 1. 

Do you have any comments on this? 

Thanks in advance, 

Ives 

-- 

==================================================================
Ives Vanstechelman 

Tel:+32 (0)9 331 38 63                        fax:+32 (0)9 3313809
VIB Department of Plant Systems Biology,          Ghent University
Technologiepark 927, 9052 Gent, BELGIUM iv...@ps... http://www.psb.vib-ugent.be ================================================================== 

Re: [Transposonpsi-users] transposon PSI

[Brian H. <bh...@br...>]

Hi Ives,

The software requires that you have the old NCBI blastall software
installed, including the formatdb utility.  I think you can get it
here:

ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST

best,

-brian




On Wed, Oct 3, 2012 at 5:58 AM, Ives Vanstechelman
<iv...@ps...> wrote:
> Hello,
>
> I am using transposon PSI for looking if there are transposons in a fasta
> seq with this command:
>
> transposonPSI.pl sctg_285.fa nuc
>
> It is not working, I have this error
>
> Error, formatdb -i
> transposonPSI.7461.vampire.psblocal.tmp/sctg_285/sctg_285.seq -p F (ret -1)
> at /software/shared/apps/x86_64/TransposonPSI/08222010//transposonPSI.pl
> line 115, <$filehandle> line 1.
>
> Do you have any comments on this?
>
> Thanks in advance,
>
> Ives
>
> --
>
> ==================================================================
> Ives Vanstechelman
>
> Tel:+32 (0)9 331 38 63                        fax:+32 (0)9 3313809
> VIB Department of Plant Systems Biology,          Ghent University
> Technologiepark 927, 9052 Gent, BELGIUM
> iv...@ps...                 http://www.psb.vib-ugent.be
> ==================================================================
>
>
>
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-- 
--
Brian J. Haas
Manager, Genome Annotation and Analysis, Research and Development
The Broad Institute
http://broad.mit.edu/~bhaas