[ensembl-dev] Targetted Genewise
Alex Humberto Di Genova Bravo
digenova at gmail.com
Thu Oct 28 20:43:34 BST 2010
Dear Ensembl Developers:
I am working in a local installataion of the ensembl pipeline. I
complete the raw compute stage of the pipeline without problem and now
I trying to run the Targetted stage of the gene build process, This is
my actual configuration of this analisys:
TargettedGenewise => {
PAF_LOGICNAMES => ['BestPmatch'],
OUTPUT_BIOTYPE => 'targetted',
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
#-program=>'/genoma/gendb/
ensembl/bin/genewise'
#-endbias => 1,
-gene => '/genoma/gendb/ensembl/
lib/cfgwise/human.gf',
-matrix => '/genoma/gendb/
ensembl/lib/cfgwise/BLOSUM80.bla',
-codon => '/genoma/gendb/ensembl/
lib/cfgwise/codon.table',
-gap => 20,
-extension => 8,
-splice_model => 1
},
MINIGENEWISE_PARAMETERS => {
-terminal_padding => 20000,
-exon_padding => 200,
-minimum_intron => 1000,
},
MULTIMINIGENEWISE_PARAMETERS =>{
-minimum_feature_length
=> 50,
},
FILTER_PARAMS => {
-max_exon_length => '20000',
-multi_exon_min_coverage => '25',
-single_exon_min_coverage => '80',
-max_intron_length => '200000',
-min_split_coverage => 95,
-max_low_complexity => 101,
},
SEQFETCHER_PARAMS => {
-db => ['/genoma/gendb/ensembl/
testgenome/protein_danio_rerio_index']
},
BLASTMINIGENEWISE_PARAMETERS => {},
LIMIT_TO_FEATURE_RANGE => 1,
FEATURE_RANGE_PADDING => 20000,
},
Stored in the Config file of BlasMiniGenewise Module, The binaries
(SEQFETCHERT , xdformat, wutblastn and genewise) run in my test
genome without
problems, I confirm that comenting the lines on the
runnables(Blast.pm, genewise.pm and BlastMiniGenewise.pm) that delete
the temporal files.
Currently my databases configuration comprise the REFERENCE_DB and a
separate GENEWISE_DB as is specified in the gene build readme or in
databases readme.
I genereta the input IDs for TargettedGenewise on slice level of 1MB
using the make_input_id script, So When I check the job error there is
a lot of warnings that end whit an error of undefined seq:
-------------------- WARNING ----------------------
MSG: Transcript has no translation, or no start exon - maybe a
pseudogene?
FILE: Tools/GeneBuildUtils/TranscriptUtils.pm LINE: 1921
CALLED BY: Analysis/RunnableDB/BlastMiniGenewise.pm LINE: 648
Ensembl API version = 60
---------------------------------------------------
1
-------------------- WARNING ----------------------
MSG: Transcript has no translation, or no start exon - maybe a
pseudogene?
FILE: Tools/GeneBuildUtils/TranscriptUtils.pm LINE: 1921
CALLED BY: Analysis/RunnableDB/BlastMiniGenewise.pm LINE: 648
Ensembl API version = 60
---------------------------------------------------
Non-coding transcript does not have -1 phases at /genoma/gendb/ensembl/
ensembl-analysis/modules/Bio/EnsEMBL/Analysis/Tools/GeneBuildUtils/
TranscriptUtils.pm line 466.Can't call method "seq" on an undefined
value at /genoma/gendb/ensembl/ensembl-analysis/modules/Bio/EnsEMBL/
Analysis/Tools/GeneBuildUtils/TranslationUtils.pm line 201.
RUNNING: Lost the will to live Error
Job 16910 failed: [
-------------------- EXCEPTION --------------------
MSG: Problems running BlastMiniGenewise for
chromosome:NCBI36:1:25637249:26623296:1 [Can't call method "seq" on an
undefined value at /genoma/gendb/ensembl/ensembl-analysis/modules/Bio/
EnsEMBL/Analysis/Tools/GeneBuildUtils/Tr
anslationUtils.pm line 201.
]
STACK Bio::EnsEMBL::Pipeline::Job::run_module /genoma/gendb/ensembl/
ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/Job.pm:634
STACK (eval) /genoma/gendb/ensembl/ensembl-pipeline/modules/Bio/
EnsEMBL/Pipeline/runner.pl:219
STACK main::run_jobs_with_lsfcopy /genoma/gendb/ensembl/ensembl-
pipeline/modules/Bio/EnsEMBL/Pipeline/runner.pl:218
STACK toplevel /genoma/gendb/ensembl/ensembl-pipeline/modules/Bio/
EnsEMBL/Pipeline/runner.pl:128
Ensembl API version = 60
---------------------------------------------------
]Finished job 16910
and there is no feature stored in GENEWISE_DB, this happend for all
of my jobs, Any suggestion or advice will be very usefull
for me.
Thank in advance
Alex Di Génova.
Ingeniero en Bioinformatica.
Laboratorio de Bioinformatica y Matemática del Genoma.
Centro de Modelamiento Matemático.
Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile.
Avenida Blanco Encalada 2120, Piso 6.
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