[ensembl-dev] Ensembl Genomes BLAST: Parsing failed ERROR

[ek]

Indeed the plugin is only intended to be used with EBI blast web 
service

if you want to run a local BLAST you would need to modify the files in 
the plugin accordingly ..

Eugene
On 2013-03-04 18:03, Rafael Hernández wrote:
> Hi again Ensembl devs,
>
> I solved the problem of the empty comboboxes adding the EG BLAST
> module to the Plugins.pm and after that the dna and peptides 
> databases
> are showed (LATESTGP, ...).
> However, the parsing step still failing, but another problem appeared
> before this one.
>
> When I run the blast, Ensemble generates the following command:
>
> [...] export BLASTFILTER=/local/bin/wu_blast/filter; export
> BLASTDB=/usr/local/blastdb/ensembl_protists;  cat
> /usr/local/ensembl_protists/blastqueue/BLA_dl/8iCXWDa/N0kXvsKh.fasta 
> |
> blastall -d Plasmodium_falciparum.ASM276v1.17.dna.toplevel.fa -p
> blastn  -S NORMAL -b 250 -e 10  >  [...]
>
> In this command the -S NORMAL flag is used to set the sensitivity,
> however for _blastall _the -S doesn't configure the sensitivity, it's
> used to set the STRAND
> The trouble is located in
> _eg-plugins/blast/modules/EnsEMBL/Web/BlastView/MetaDataBlast.pm, _in
> the following line (943):
>
>   my $sensitivity = uc( $blastview::CGI->param('sensitivity') );
>
>   # set sensitivity parmeter for EBI BLAST
>   eval{ $factory->option('-S', $sensitivity )};
>   if( $@ =~ /MSG:s(.+)/ ){ warn($@) && return $1 }
>   if( $@ ){ warn($@) && return $@ }
>
> So, I think I've a problem in the BLAST configuration and Ensembl
> tries to work with EBI BLAST instead of NCBI BLAST and when trying to
> parse the BLAST results it crashes... Any idea?
>  In the previous email I attached the content of my MULTI.ini file, 
> Is
> it correct?
>
> Thank you and regards,
>
> Rafa Hernández de Diego
>
> SLU-Global Bioinformatics Center
> Swedish University for Agricultural Sciences (SLU)
>  Gerda Nilssons väg 2,  
>  Box 7023, 750 07 Uppsala, Sweden.