[ensembl-dev] How to specify 2x genebuild databases?
Jan-hinnerk Vogel
jhv at sanger.ac.uk
Thu Nov 4 11:23:19 GMT 2010
Hi,
your Databases.pm file looks OK to me. The warnings are OK to, as
they're only warnings. if something is seriously wrong,
we usually use the throw() subroutine which would interrupt the run /
stop the program execution.
Regards,
Jan
On 2 Nov 2010, at 00:14, 江文恺 wrote:
> 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",
>
>
>
> _______________________________________________
> Dev mailing list
> Dev at ensembl.org
> http://lists.ensembl.org/mailman/listinfo/dev
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