ah! Excellent! That is certainly the problem. I'll try I out as soon as I have a real network connection.
Thanks, Scott On Friday, June 12, 2009, Ed Lee <[email protected]> wrote: > Hey Scott, > > Ah, you're having issues with actually loading the BLAST results. > When you mentioned the tiers file, I thought you were having issues > displaying them as you configured (e.g., glyph, color). The tiers > file just defines how to diplay the different types. > > Retrieval from the database is defined in the "chado-adapter.xml" > file in your "$APOLLO_ROOT/conf" directory. In the > "chadoInstance/searchHitPrograms" make sure you have the following: > > <program>BLASTN</program> > > You probably have an element for BLAT which you can probably drop > as you have no BLAST results in the database. > > Cheers, > Ed > > On Fri, 12 Jun 2009, Scott Cain wrote: > > > Hi Ed, > > Here's the section of the output that mentions BLASTN: > > DEBUG: Found rice.tiers in /var/www/.apollo/ > DEBUG: added feature property gene to annotationFeatureProps > DEBUG: added feature property transposable_element to annotationFeatureProps > DEBUG: added feature property tRNA to annotationFeatureProps > DEBUG: added feature property rRNA to annotationFeatureProps > DEBUG: added feature property miRNA to annotationFeatureProps > DEBUG: added feature property pseudogene to annotationFeatureProps > DEBUG: added feature property remark to annotationFeatureProps > DEBUG: added feature property promoter to annotationFeatureProps > DEBUG: added feature property repeat_region to annotationFeatureProps > DEBUG: Tier prop 0 = Annotation > DEBUG: Tier prop 1 = Gene Prediction > DEBUG: Tier prop 2 = BLASTN > DEBUG: Tier prop 3 = BLASTX > DEBUG: Tier prop 4 = Start Codon > DEBUG: Tier prop 5 = Stop Codon > DEBUG: Tier prop 6 = Sequence selection > DEBUG: Tier prop 7 = FgenesH - Gene Prediction > DEBUG: Tier prop 8 = Augustus - Gene Prediction > DEBUG: Tier prop 9 = SNAP - Gene Prediction > DEBUG: Tiers file = /var/www/.apollo/rice.tiers > DEBUG: saved unknown parameter from /usr/local/apollo/conf/rice.style: > Organism=Oryza sativa > DEBUG: createStyle: read style file /usr/local/apollo/conf/rice.style > DEBUG: findFile: orig name is ok: /var/www/.apollo/rice.style > DEBUG: Reading style /var/www/.apollo/rice.style > > But then it never appears to query for the BLASTN results: > > DEBUG: SELECT f.feature_id as feature_id, name, uniquename, type_id, > dbxref_id, fmin, fmax, strand, residues > FROM feature f, featureloc fl > WHERE f.type_id in (253,187,786,743) AND f.feature_id = fl.feature_id > AND is_analysis = false > AND fl.srcfeature_id = 3686 AND fl.fmax BETWEEN 0 AND 47300 AND > fl.fmin BETWEEN 0 AND 47300 AND fl.fmin < 27300 AND fl.fmax > 6399 > DEBUG: SELECT cv.cvterm_id, cv.name FROM cvterm cv, cv c WHERE c.cv_id > = cv.cv_id AND c.name='relationship' > DEBUG: SELECT gene.feature_id as gene_id, trans.feature_id as > transcript_id, exon.feature_id as exon_id, > gene.uniquename as gene_uniquename, gene.name as gene_name, > genetype.name as genetype, trans.uniquename as > transcript_uniquename, trans.name as transcript_name, > trans.type_id as type_id, exon.uniquename as exon_name, > exonloc.rank, exonloc.fmin as fmin, exonloc.fmax as > fmax, exonloc.strand, exonloc.phase, > exonloc.locgroup, trans.timelastmodified as transDate, > gene.dbxref_id as geneDbXRefId FROM featureloc exonloc, feature exon, > feature_relationship exon2trans, feature trans, > feature_relationship trans2gene, feature gene, cvterm genetype WHERE > exonloc.srcfeature_id = 3686 AND exonloc.feature_id = exon.feature_id > AND exon.type_id = 233 AND exon.feature_id = exon2trans.subject_id > AND exon2trans.object_id = trans.feature_id AND exon2trans.type_id = > 37 AND trans.feature_id = trans2gene.subject_id AND > trans2gene.object_id = gene.feature_id AND gene.type_id in > (790,422,339,360,361,741,338,362) AND gene.type_id = > genetype.cvterm_id AND gene.is_analysis = false AND exonloc.fmax > BETWEEN 0 AND 47300 AND exonloc.fmin BETWEEN 0 AND 47300 AND > exonloc.fmin < 27300 AND exonloc.fmax > 6399ORDER BY gene.feature_id, > trans.feature_id, exonloc.fmin > DEBUG: SELECT cds.uniquename AS cds_name, trans.uniquename AS > transcript_uniquename, trans.residues AS transcript_seq, cdsloc.fmin > AS fmin, cdsloc.fmax AS fmax,cdsloc.is_fmin_partial as > is_fmin_partial, cdsloc.is_fmax_partial as is_fmax_partial, > cdsloc.strand, cds.uniquename AS protein_name, cds.residues AS > protein_seq , trans.feature_id as transcript_id FROM featureloc > cdsloc, feature cds, feature_relationship cds2trans, feature trans > WHERE cdsloc.srcfeature_id = 3686 AND cdsloc.feature_id = > cds.feature_id AND cds.type_id IN (190,402) AND cds.feature_id = > cds2trans.subject_id AND cds2trans.object_id = trans.feature_id AND > cds2trans.type_id = 52 AND trans.type_id IN (320, 759) AND > cdsloc.fmax BETWEEN 0 AND 47300 AND cdsloc.fmin BETWEEN 0 AND 47300 > AND cdsloc.fmin < 27300 AND cdsloc.fmax > 6399 > DEBUG: addGenePredictionResults querying for the following programs: > ChadoProgram:[program=FgenesH,programversion=,sourcename=] > DEBUG: SELECT analysis_id, program, programversion, sourcename FROM analysis > WARN : No rows found in the chado analysis table for > ChadoProgram:[program=FgenesH,programvers -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research _______________________________________________ apollo mailing list [email protected] http://mail.fruitfly.org/mailman/listinfo/apollo
