[ensembl-dev] Blastminwise run error

[wenkai jiang]

Hi,

I run the wise on scaffolds, but not sequence slices at 1MB etc.
I have checked the seq_region_id in exon table, but no exon info related to
the problem scaffold can be found in this table.

for example, the problem scaffold is bambus_1325,
-------------------- EXCEPTION --------------------
MSG: Problems running BlastMiniGenewise for
scaffold:june:bambus_1325:1:47095:1 [

then i trace the exon table for 'bambus_1325', no exon can be found, also no
transcript can be found to related to bambus_1325 in transcript table.

indeed, i do run the analysis several times,
rulemanager has try to rerun the failed jobs for 3 times, but they still
fails, so i use job_submission to rerun the analysis.

But as the case mentioned here, no exon was found to be related to the
problematic region, so it won't be caused by database operations.

fortunately, i almost resolved these problem jobs by changing the wise
parameters, eg, the default gap extention penalty is 2, when i increase this
to 8, only 3 jobs remained as problematic.

all failed jobs still have overlap problems, but all overlaps are only 1
nucleotide, eg:
> Transcript Exons:
>   5108-5252 (-1)
>   4984-4988 (-1)
>
> This Exon:
>   4053-4985 (-1)

I don't understand why could these problems arise.

what dose 'dummy transcript' mean?


2011/6/13 Thibaut Hourlier <th3 at sanger.ac.uk>

> Hi Wenkai,
>
> Have you looked if the two exons come from the same analysis?
> If yes, did you have rerun several times this analysis?
> Are you fetching these exons from the same database?
>
> What you can do is create a dummy transcript and you will link the
> problematic exon to the dummy transcript.
>
> You will have to modify in your database:
> transcript
> exon_transcript
> transcript_supporting_feature
> exon
>
> Cheers
> Thibaut
>
> On Mon, 2011-06-13 at 01:55 +0800, wenkai jiang wrote:
> > I have finished PMATCH,BESTPMACH run, then i run targetedgenewise,
> > for some jobs (about 50 jobs), i got errors:
> >
> > -------------------- EXCEPTION --------------------
> > MSG: Running
> > Bio::EnsEMBL::Analysis::Runnable::BlastMiniGenewise=HASH(0x2879ac0)
> > failed error:
> > -------------------- EXCEPTION --------------------
> > MSG: Failed Bio::EnsEMBL::Analysis::Runnable::Genewise=HASH(0x2917c50)
> > run
> > -------------------- EXCEPTION --------------------
> > MSG: Exon overlaps with other exon in same transcript.
> > Transcript Exons:
> >   5108-5252 (-1)
> >   4984-4988 (-1)
> >
> > This Exon:
> >   4053-4985 (-1)
> >
> > some settings for targetedgenewise are:
> >
> >              EXON_BASED_MASKING => 1,
> >              GENE_BASED_MASKING => 0,
> >              PRE_GENEWISE_MASK => 1,
> >              POST_GENEWISE_MASK => 1,
> >              REPEATMASKING => [],
> >              SOFTMASKING => 0,
> >
> >              GENEWISE_PARAMETERS => {
> >                                      # pass parameters go genewise
> > here, i.e. -program =>"/usr/local/ensembl/bin/genewiseXXX"
> >                                      # for more options which can be
> > passed see Runnable/Genewise.pm
> >                                      #-endbias => 1,
> >                                      #-matrix => 'BLOSUM80.bla',
> >                                      #-gap => 20,
> >                                      #-extension => 8,
> >                                      #-splice_model => 1
> >                                     },
> >
> > any suggestions?
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>
>
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