[ensembl-dev] How to specify 2x genebuild databases?
江文恺
jiangwenkai at mail.kib.ac.cn
Tue Nov 2 00:14:34 GMT 2010
Hi,
I try to build gene models for one 2x genome with a reference genome,
The alignment and genomes slices are successfully generated, but i got several warning messages by test_RunnableDB
Does this warning means that the setting for my database.pm is wrong?
There are not examples for database.pm setting with low coverage genome annotation pipeline, can someone supply me an example.
Thanks~
Wenkai
the error message is:
jiangwenkai at node69:~/oryza> perl ~/ensembl/ensembl-pipeline/scripts/test_RunnableDB -dbuser jwk -dbpass jwk -dbhost node69
/ -dbport 3307 -dbname oryza_glaberrima_core_6_59_1 -input_id chromosome::9:9831700:9834758: -write -logic_name
/ WGA2Genes -runnabledb_path Bio/EnsEMBL/Analysis/RunnableDB
Fetching WGA2Genes from oryza_glaberrima_core_6_59_1
Fetching WGA2Genes from oryza_glaberrima_core_6_59_1
Attaching DNA_DB REFERENCE_DB to TARGET_CORE_DB...
Not attaching DNA_DB to REFERENCE_DB ...
Attaching DNA_DB oryza_glaberrima_core_6_59_1 to oryza_glaberrima_core_6_59_1
-------------------- WARNING ----------------------
MSG: You haven't defined a DNA_DBNAME in Config/Databases.pm
FILE: Analysis/RunnableDB/BaseGeneBuild.pm LINE: 211
CALLED BY: Analysis/RunnableDB/WGA2Genes.pm LINE: 97
---------------------------------------------------
-------------------- WARNING ----------------------
MSG: You haven't defined a DNA_DBNAME in Config/Databases.pm
FILE: Analysis/RunnableDB/BaseGeneBuild.pm LINE: 211
CALLED BY: Analysis/RunnableDB/WGA2Genes.pm LINE: 99
---------------------------------------------------
-------------------- WARNING ----------------------
MSG: Should not be an deletion and insertion on the same alignment region. cigar_line=117M696I3D
FILE: Bio/EnsEMBL/BaseAlignFeature.pm LINE: 793
CALLED BY: Bio/EnsEMBL/BaseAlignFeature.pm LINE: 141
---------------------------------------------------
-------------------- WARNING ----------------------
MSG: Cannot get attributes without an adaptor.
FILE: Bio/EnsEMBL/Slice.pm LINE: 1159
CALLED BY: Bio/EnsEMBL/Transcript.pm LINE: 1575
---------------------------------------------------
-------------------- WARNING ----------------------
MSG: Cannot get attributes without an adaptor.
FILE: Bio/EnsEMBL/Slice.pm LINE: 1159
CALLED BY: Bio/EnsEMBL/Transcript.pm LINE: 1580
---------------------------------------------------
-------------------- WARNING ----------------------
MSG: Cannot get attributes without an adaptor.
FILE: Bio/EnsEMBL/Slice.pm LINE: 1159
CALLED BY: Bio/EnsEMBL/Transcript.pm LINE: 1585
---------------------------------------------------
-------------------- WARNING ----------------------
MSG: Cannot get attributes without an adaptor.
FILE: Bio/EnsEMBL/Slice.pm LINE: 1159
CALLED BY: Bio/EnsEMBL/Transcript.pm LINE: 1575
---------------------------------------------------
-------------------- WARNING ----------------------
MSG: Cannot get attributes without an adaptor.
FILE: Bio/EnsEMBL/Slice.pm LINE: 1159
CALLED BY: Bio/EnsEMBL/Transcript.pm LINE: 1580
---------------------------------------------------
-------------------- WARNING ----------------------
MSG: Cannot get attributes without an adaptor.
FILE: Bio/EnsEMBL/Slice.pm LINE: 1159
CALLED BY: Bio/EnsEMBL/Transcript.pm LINE: 1585
---------------------------------------------------
Use of uninitialized value in printf Bio/EnsEMBL/Analysis/RunnableDB/WGA2Genes.pm line 1178.
Use of uninitialized value in printf Bio/EnsEMBL/Analysis/RunnableDB/WGA2Genes.pm line 1178.
Use of uninitialized value in printf Bio/EnsEMBL/Analysis/RunnableDB/WGA2Genes.pm line 1178.
-------------------- WARNING ----------------------
MSG: Cannot get attributes without an adaptor.
FILE: Bio/EnsEMBL/Slice.pm LINE: 1159
CALLED BY: Bio/EnsEMBL/Transcript.pm LINE: 1575
---------------------------------------------------
-------------------- WARNING ----------------------
MSG: Cannot get attributes without an adaptor.
FILE: Bio/EnsEMBL/Slice.pm LINE: 1159
CALLED BY: Bio/EnsEMBL/Transcript.pm LINE: 1580
---------------------------------------------------
-------------------- WARNING ----------------------
MSG: Cannot get attributes without an adaptor.
FILE: Bio/EnsEMBL/Slice.pm LINE: 1159
CALLED BY: Bio/EnsEMBL/Transcript.pm LINE: 1585
---------------------------------------------------
There is 1 features output
But the process did produce results for one agp file, which contain:
#
# WGA2Genes output for chromosome::9:9831700:9834758:
# Genes are: LOC_Os09g16120
#
##-AGP #
##-AGP ## AGP for LOC_Os09g16120-0 source-region=9/9831700-9834758 (iid=chromosome::9:9831700:9834758:)
##-AGP #
##-AGP LOC_Os09g16120-0 1 494 1 W scaffold1369 5865 6358 -
##-AGP LOC_Os09g16120-0 495 594 2 N 100
##-AGP LOC_Os09g16120-0 595 3132 3 W scaffold1369 3212 5749 -
##-GENES # Gene report for LOC_Os09g16120-0
##-GENES ##-ATTRIBUTE transcript=LOC_Os09g16120-0.LOC_Os09g16120_LOC_Os09g16120.1 code=HitSimilarity value=96.3
##-GENES ##-ATTRIBUTE transcript=LOC_Os09g16120-0.LOC_Os09g16120_LOC_Os09g16120.1 code=HitCoverage value=100.0
##-GENES ##-ATTRIBUTE transcript=LOC_Os09g16120-0.LOC_Os09g16120_LOC_Os09g16120.1 code=PropNonGap value=100.0
##-GENES ##-ATTRIBUTE transcript=LOC_Os09g16120-0.LOC_Os09g16120_LOC_Os09g16120.1 code=NonGapHCov value=100.0
##-GENES ##-ATTRIBUTE transcript=LOC_Os09g16120-0.LOC_Os09g16120_LOC_Os09g16120.1 code=NumStops value=0
##-GENES ##-ATTRIBUTE transcript=LOC_Os09g16120-0.LOC_Os09g16120_LOC_Os09g16120.1 code=GapExons value=0
##-GENES ##-ATTRIBUTE transcript=LOC_Os09g16120-0.LOC_Os09g16120_LOC_Os09g16120.1 code=SourceTran value=LOC_Os09g16120.1
##-GENES LOC_Os09g16120-0 WGA2Genes Exon 1793 1911 1 0 2 exon=LOC_Os09g16120-0.LOC_Os09g16120_L
OC_Os09g16120.1_0; transcript=LOC_Os09g16120-0.LOC_Os09g16120_LOC_Os09g16120.1; gene=LOC_Os09g16120-0.LOC_Os09g16120
##-GENES LOC_Os09g16120-0 WGA2Genes Supporting 1793 1909 1 exon=LOC_Os09g16120-0.LOC_Os09g16120_LOC_Os09g
16120.1_0; hname=LOC_Os09g16120.1; hstart=1; hend=39; external_db_id=; hcoverage=100
##-GENES LOC_Os09g16120-0 WGA2Genes Exon 2605 2674 1 2 0 exon=LOC_Os09g16120-0.LOC_Os09g16120_L
OC_Os09g16120.1_1; transcript=LOC_Os09g16120-0.LOC_Os09g16120_LOC_Os09g16120.1; gene=LOC_Os09g16120-0.LOC_Os09g16120
##-GENES LOC_Os09g16120-0 WGA2Genes Supporting 2606 2674 1 exon=LOC_Os09g16120-0.LOC_Os09g16120_LOC_Os09g
16120.1_1; hname=LOC_Os09g16120.1; hstart=41; hend=63; external_db_id=; hcoverage=100
##-GENES LOC_Os09g16120-0 WGA2Genes Exon 3012 3068 1 0 0 exon=LOC_Os09g16120-0.LOC_Os09g16120_L
OC_Os09g16120.1_2; transcript=LOC_Os09g16120-0.LOC_Os09g16120_LOC_Os09g16120.1; gene=LOC_Os09g16120-0.LOC_Os09g16120
##-GENES LOC_Os09g16120-0 WGA2Genes Supporting 3012 3068 1 exon=LOC_Os09g16120-0.LOC_Os09g16120_LOC_Os09g
16120.1_2; hname=LOC_Os09g16120.1; hstart=64; hend=82; external_db_id=; hcoverage=100
The following is the database specification in my pipeline: Are there any errors?
My database.pm is set as:
TARGET_CORE_DB => {
-dbname => 'oryza_glaberrima_core_6_59_1',
-host => 'node69',
-port => '3307',
-user => 'jwk',
-pass => 'jwk',
-species => 'Oryza glaberrima',
},
QUERY_CORE_DB => {
-dbname => 'oryza_sativa_core_6_59_6',
-host => 'node69',
-port => '3307',
-user => 'jwk',
-pass => 'jwk',
-species => 'Oryza sativa',
},
COMPARA_DB => {
-dbname => 'Coryza',
-host => 'node69',
-port => '3307',
-user => 'jwk',
-pass => 'jwk',
-species => 'Oryza glaberrima',
-species => 'Oryza sativa',
},
REFERENCE_DB => {
-dbname => 'oryza_glaberrima_core_6_59_1',
-host => 'node69',
-port => '3307',
-user => 'jwk',
-pass => 'jwk',
},
DNA_DBNAME => "REFERENCE_DB",
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20101102/40f6024c/attachment.html>
More information about the Dev
mailing list