[ensembl-dev] Blastminwise run error

[wenkai jiang]

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?
 <dev at ensembl.org>
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