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

Rafael Hernández rafahd87 at gmail.com
Mon Mar 4 18:03:41 GMT 2013

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
*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

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.
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