Hi,<br><br>I run the wise on scaffolds, but not sequence slices at 1MB etc.<br>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.<br><br>for example, the problem scaffold is bambus_1325,<br>
-------------------- EXCEPTION --------------------<br>MSG: Problems running BlastMiniGenewise for scaffold:june:bambus_1325:1:47095:1 [<br><br>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.<br>
<br>indeed, i do run the analysis several times, <br>rulemanager has try to rerun the failed jobs for 3 times, but they still fails, so i use job_submission to rerun the analysis.<br><br>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.<br>
<br>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. <br><br>all failed jobs still have overlap problems, but all overlaps are only 1 nucleotide, eg:<br>
> Transcript Exons:<br>
> 5108-5252 (-1)<br>> 4984-4988 (-1)<br>
><br>
> This Exon:<br>
> 4053-4985 (-1)<br><br>I don't understand why could these problems arise.<br><br>
what dose 'dummy transcript' mean?<br><br><br><div class="gmail_quote">2011/6/13 Thibaut Hourlier <span dir="ltr"><<a href="mailto:th3@sanger.ac.uk">th3@sanger.ac.uk</a>></span><br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi Wenkai,<br>
<br>
Have you looked if the two exons come from the same analysis?<br>
If yes, did you have rerun several times this analysis?<br>
Are you fetching these exons from the same database?<br>
<br>
What you can do is create a dummy transcript and you will link the<br>
problematic exon to the dummy transcript.<br>
<br>
You will have to modify in your database:<br>
transcript<br>
exon_transcript<br>
transcript_supporting_feature<br>
exon<br>
<br>
Cheers<br>
Thibaut<br>
<div><div></div><div class="h5"><br>
On Mon, 2011-06-13 at 01:55 +0800, wenkai jiang wrote:<br>
> I have finished PMATCH,BESTPMACH run, then i run targetedgenewise,<br>
> for some jobs (about 50 jobs), i got errors:<br>
><br>
> -------------------- EXCEPTION --------------------<br>
> MSG: Running<br>
> Bio::EnsEMBL::Analysis::Runnable::BlastMiniGenewise=HASH(0x2879ac0)<br>
> failed error:<br>
> -------------------- EXCEPTION --------------------<br>
> MSG: Failed Bio::EnsEMBL::Analysis::Runnable::Genewise=HASH(0x2917c50)<br>
> run<br>
> -------------------- EXCEPTION --------------------<br>
> MSG: Exon overlaps with other exon in same transcript.<br>
> Transcript Exons:<br>
> 5108-5252 (-1)<br>
> 4984-4988 (-1)<br>
><br>
> This Exon:<br>
> 4053-4985 (-1)<br>
><br>
> some settings for targetedgenewise are:<br>
><br>
> EXON_BASED_MASKING => 1,<br>
> GENE_BASED_MASKING => 0,<br>
> PRE_GENEWISE_MASK => 1,<br>
> POST_GENEWISE_MASK => 1,<br>
> REPEATMASKING => [],<br>
> SOFTMASKING => 0,<br>
><br>
> GENEWISE_PARAMETERS => {<br>
> # pass parameters go genewise<br>
> here, i.e. -program =>"/usr/local/ensembl/bin/genewiseXXX"<br>
> # for more options which can be<br>
> passed see Runnable/Genewise.pm<br>
> #-endbias => 1,<br>
> #-matrix => 'BLOSUM80.bla',<br>
> #-gap => 20,<br>
> #-extension => 8,<br>
> #-splice_model => 1<br>
> },<br>
><br>
> any suggestions?<br>
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