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,programversion=,sourcename=]
DEBUG: SELECT exon.uniquename as exon_name, exonLoc.fmin,
exonLoc.fmax, exonLoc.strand, af.significance, af.analysis_id,
trans.feature_id as transId, trans.uniquename as transUniquename,
trans.name as transName FROM featureloc exonLoc, feature exon,
analysisfeature af, feature_relationship exon2trans, feature trans,
featureloc transLoc WHERE transLoc.srcfeature_id = 3686 AND
exonLoc.feature_id = exon.feature_id AND exonLoc.srcfeature_id = 3686
AND transLoc.feature_id = af.feature_id AND exon.type_id = 233 AND
exon2trans.subject_id = exon.feature_id AND trans.feature_id =
exon2trans.object_id AND exon2trans.type_id = 37 AND
transLoc.feature_id = trans.feature_id AND transLoc.fmax BETWEEN 0
AND 47300 AND transLoc.fmin BETWEEN 0 AND 47300 AND transLoc.fmin <
27300 AND transLoc.fmax > 6399 ORDER BY af.analysis_id,
trans.feature_id, exonLoc.fmin
ERROR: addGenePredictions could not find CDS feature for transcript 'g2.t1'
DEBUG: setTranscriptNameAndCdsBounds found predicted transcript
AUGUSTUS:26071-12634:26071..12634CDS: 0..0
DEBUG: exon: 26071..25614
DEBUG: exon: 24985..24911
DEBUG: exon: 24820..24680
DEBUG: exon: 24595..24228
DEBUG: exon: 12951..12634
ERROR: addGenePredictions could not find CDS feature for transcript 'gf002.1'
DEBUG: setTranscriptNameAndCdsBounds found predicted transcript
FGenesH:7940-7521:7940..7521CDS: 0..0
DEBUG: exon: 7940..7521
ERROR: addGenePredictions could not find CDS feature for transcript 'gf003.1'
DEBUG: setTranscriptNameAndCdsBounds found predicted transcript
FGenesH:25859-24272:25859..24272CDS: 0..0
DEBUG: exon: 25859..25614
DEBUG: exon: 24985..24911
DEBUG: exon: 24820..24680
DEBUG: exon: 24595..24272
ERROR: addGenePredictions could not find CDS feature for transcript
'mgrape_354-snap.002'
DEBUG: setTranscriptNameAndCdsBounds found predicted transcript
SNAP:25859-24272:25859..24272CDS: 0..0
DEBUG: exon: 25859..25614
DEBUG: exon: 24985..24911
DEBUG: exon: 24820..24680
DEBUG: exon: 24595..24272
DEBUG: Genscan and piecegenie results retrieved
DEBUG: addSearchHits retrieving target seq descriptions
DEBUG: SELECT cvt.cvterm_id FROM cvterm cvt, cv c WHERE c.cv_id =
cvt.cv_id AND c.name='feature_property' AND cvt.name = 'description'
DEBUG:
SELECT leafFeat.uniquename, leafFeatLoc.fmin AS query_fmin,
leafFeatLoc.fmax AS query_fmax, leafFeatLoc.strand AS query_strand,
tgtFeat.feature_id AS target_id, tgtFeat.uniquename AS targetName,
tgtFeat.organism_id AS tgtOrganismId, tgtFeatLoc.fmin AS target_fmin,
tgtFeatLoc.fmax AS target_fmax, tgtFeatLoc.strand AS target_strand,
a.analysis_id, a.program, a.sourcename, a.programversion, af.rawscore,
af.normscore, af.significance, af.identity, leafFeatLoc.residue_info
AS query_residue_info, (SELECT value FROM featureprop WHERE
type_id=1808 and feature_id=tgtFeat.feature_id and rank=0) as
tgtDescription,leafFeat.type_id as featureTypeId,
length(tgtFeat.residues) as tgtSeqLength,tgtFeatLoc.residue_info AS
target_residue_info , leafToParent.object_id AS parent_id
FROM featureloc leafFeatLoc, feature leafFeat, analysisfeature af,
analysis a, featureloc tgtFeatLoc, feature tgtFeat ,
feature_relationship leafToParent, featureloc parentFeatLoc
WHERE leafFeatLoc.srcfeature_id = 3686 AND leafFeatLoc.feature_id =
leafFeat.feature_id AND leafFeatLoc.feature_id = af.feature_id AND
af.analysis_id = a.analysis_id AND leafFeat.feature_id =
tgtFeatLoc.feature_id AND tgtFeatLoc.srcfeature_id != 3686 AND
tgtFeatLoc.srcfeature_id = tgtFeat.feature_id AND (a.program like
'blat') AND parentFeatLoc.fmax BETWEEN 0 AND 47300 AND
parentFeatLoc.fmin BETWEEN 0 AND 47300 AND parentFeatLoc.fmin < 27300
AND parentFeatLoc.fmax > 6399AND leafToParent.subject_id =
leafFeat.feature_id AND leafToParent.object_id =
parentFeatLoc.feature_id AND leafToParent.type_id = 37 AND
parentFeatLoc.srcfeature_id = 3686
ORDER BY a.program, a.programversion, a.sourcename,
tgtFeat.organism_id , tgtFeat.uniquename , leafFeatLoc.strand ,
leafToParent.object_id
DEBUG: Sim4 and blastx retrieved
INFO : read done; writing...
I'm working on getting a sample database for you to try out.
BTW one thing that I found interesting was the output of this query:
guest=# SELECT analysis_id, program, programversion, sourcename FROM analysis ;
analysis_id | program | programversion | sourcename
-------------+--------------+----------------+------------
1 | dabg | dabg |
2 | dchip | dchip |
3 | gcrma | gcrma |
4 | mas5 | mas5 |
5 | mpam | mpam |
6 | plier | plier |
7 | rma | rma |
8 | sea | sea |
9 | vsn | vsn |
11 | RepeatMasker | null |
14 | AUGUSTUS | null |
16 | FGenesH | null |
18 | SNAP | null |
20 | BLASTN | null |
22 | BLASTX | null |
(15 rows)
where it says "null" under programversion, that is actually the text
"null" because the programversion field is not nullable. So I tried
"resulttype=BLASTN.null"
Also, near the end of the output above, there is a query that has this in it:
(a.program like 'blat')
That is almost certainly at the source of the problem. Blat is never
mentioned in my rice.tiers file, so I'm not sure where this is coming
from.
Finally, I'm not sure what release of Apollo this is, but I suspect
that it is the one just before the most recent release.
Thanks,
Scott
On Thu, Jun 11, 2009 at 1:56 PM, Ed Lee<[email protected]> wrote:
Hi Scott,
You can turn on debugging info by changing the following line in
the $APOLLO_ROOT/conf/log4j.properties:
log4j.rootLogger=INFO,stdout
to
log4j.rootLogger=DEBUG,stdout
It should should you all the SQL statements that are being run.
I'm surprised that it's not working with the suggested change, so perhaps
you could provide me with a dump of the data (or access to the database)
along with the style/tiers file you're using I can investigate this
further.
Cheers,
Ed
On Wed, 10 Jun 2009, Scott Cain wrote:
Hi Ed,
I tried that, as well as BLASTN: and BLASTN:na. How do you turn on
logging on the command line so I can try to figure out what is happen?
Also, can you suggest a way to modify the analysis table row to make
it more likely to work?
Thanks,
Scott
On Wed, Jun 10, 2009 at 5:15 PM, Ed Lee<[email protected]> wrote:
Hey Scott,
Try using "BLASTN" as the resulttype instead of "BLASTN:BLASTN".
Cheers,
Ed
On Tue, 9 Jun 2009, Scott Cain wrote:
Hi Ed,
How does the tiers file field "resulttype" map to Chado?
Specifically, I'm trying to use the conf below to extract blast
results from chado where the analysis table row for these results look
like this:
analysis_id | name | program | programversion | sourcename
-------------+--------+---------+----------------+------------
44 | BLASTN | BLASTN | null |
[Tier]
tiername : BLASTN
visible : true
expanded : true
[Type]
tiername : BLASTN
typename : BLASTN:BLASTN
resulttype : BLASTN:BLASTN
color : 204,0,51
usescore : false
minscore : 0
maxscore : 100
glyph : DrawableResultFeatureSet
column : SCORE
column : expect
column : query_frame
column : GENOMIC_RANGE
column : MATCH_RANGE
column : GENOMIC_LENGTH
column : MATCH_LENGTH
sortbycolumn : GENOMIC_RANGE
groupby : HOMOLOGY
weburl :
freshdate: 26-NOV-2007
Thanks,
Scott
--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain
dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain
dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
