[ensembl-dev] Plants mirror question -- Oryza_sativa broken?
Michael Rogoff
miker at htblis.com
Thu Aug 12 16:10:24 BST 2010
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On Aug 11, 2010, at 1:08 PM, ek at ebi.ac.uk wrote:
>
> can you post the content of your eg-plugins/plants/conf/SiteDefs.pm and
> the output of
>
> # rm conf/packed/*
> # ctrl_scripts/restart_server -r
Absolutely. I've attached plants/conf/SiteDefs.pm and conf/Plugins.pm, and the requested output follows below. There is some extra debugging info that I've put in to help determine what is happening. I added "warn $species;" on line 58 of plants/modules/EnsEMBL/Web/ConfigPacker.pm but I do not see that in the output which makes me wonder if that module isn't being properly plugged in. I do have it in Plugins.pm as you can see.
I also added a similar line to the ensembl ConfigPacker which you can see in the output:
Oryza_sativa Indica Group at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1188.
I'm assuming that the "Indica Group" is what is causing the problem?
Thanks so much for your help!!! Hopefully we are getting close? Output follows.
--------------------------------------------------------------
Starting up Ensembl server on host: host
Executing perl startup file
------------------------------------------------------------------------------
- INFO : 0.000 : 0.000 : Parser >> Starting to parse tree
------------------------------------------------------------------------------
- INFO : 0.000 : 0.000 : Parser >> Child objects attached
- INFO : 1.488 : 1.488 : Filesystem >> Trawled web tree
------------------------------------------------------------------------------
- INFO : 1.489 : 0.000 : Parser >> Parsing ini files and munging dbs
------------------------------------------------------------------------------
- INFO : 1.688 : 0.200 : Parsing >> DEFAULTS ini file
- INFO : 1.705 : 0.017 : Parsing >> Arabidopsis_lyrata ini file
- INFO : 1.778 : 0.073 : ** DB ** >> Arabidopsis_lyrata database
Skipping DAS source Phenotypes - unable to find 'url' property (tried looking in registry and INI) at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1083.
Skipping DAS source Superfam - unable to find 'url' property (tried looking in registry and INI) at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1083.
Skipping DAS source DS_549 - unable to find 'url' property (tried looking in registry and INI) at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1083.
Skipping DAS source UniProt - unable to find 'url' property (tried looking in registry and INI) at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1083.
- INFO : 40.568 : 38.790 : ** DAS ** >> Arabidopsis_lyrata DAS sources
- INFO : 40.585 : 0.016 : Parsing >> Arabidopsis_thaliana ini file
- INFO : 40.690 : 0.106 : ** DB ** >> Arabidopsis_thaliana database
Skipping DAS source Phenotypes - unable to find 'url' property (tried looking in registry and INI) at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1083.
Skipping DAS source Superfam - unable to find 'url' property (tried looking in registry and INI) at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1083.
Skipping DAS source DS_549 - unable to find 'url' property (tried looking in registry and INI) at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1083.
Skipping DAS source UniProt - unable to find 'url' property (tried looking in registry and INI) at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1083.
- INFO : 40.732 : 0.041 : ** DAS ** >> Arabidopsis_thaliana DAS sources
- INFO : 40.760 : 0.028 : Parsing >> Oryza_indica ini file
- INFO : 40.930 : 0.170 : ** DB ** >> Oryza_indica database
Skipping DAS source Phenotypes - unable to find 'url' property (tried looking in registry and INI) at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1083.
Skipping DAS source Superfam - unable to find 'url' property (tried looking in registry and INI) at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1083.
Skipping DAS source DS_549 - unable to find 'url' property (tried looking in registry and INI) at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1083.
Skipping DAS source UniProt - unable to find 'url' property (tried looking in registry and INI) at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1083.
- INFO : 40.970 : 0.040 : ** DAS ** >> Oryza_indica DAS sources
- INFO : 40.987 : 0.017 : Parsing >> Oryza_sativa ini file
Missing analysis entry unmapped_object - 38
- INFO : 41.392 : 0.405 : ** DB ** >> Oryza_sativa database
Skipping DAS source Phenotypes - unable to find 'url' property (tried looking in registry and INI) at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1083.
Skipping DAS source Superfam - unable to find 'url' property (tried looking in registry and INI) at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1083.
Skipping DAS source DS_549 - unable to find 'url' property (tried looking in registry and INI) at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1083.
Skipping DAS source UniProt - unable to find 'url' property (tried looking in registry and INI) at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1083.
- INFO : 41.433 : 0.041 : ** DAS ** >> Oryza_sativa DAS sources
- INFO : 41.451 : 0.018 : Parsing >> Populus_trichocarpa ini file
- INFO : 41.616 : 0.165 : ** DB ** >> Populus_trichocarpa database
Skipping DAS source Phenotypes - unable to find 'url' property (tried looking in registry and INI) at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1083.
Skipping DAS source Superfam - unable to find 'url' property (tried looking in registry and INI) at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1083.
Skipping DAS source DS_549 - unable to find 'url' property (tried looking in registry and INI) at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1083.
Skipping DAS source UniProt - unable to find 'url' property (tried looking in registry and INI) at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1083.
- INFO : 41.656 : 0.040 : ** DAS ** >> Populus_trichocarpa DAS sources
- INFO : 41.673 : 0.017 : Parsing >> Sorghum_bicolor ini file
- INFO : 41.726 : 0.053 : ** DB ** >> Sorghum_bicolor database
Skipping DAS source Phenotypes - unable to find 'url' property (tried looking in registry and INI) at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1083.
Skipping DAS source Superfam - unable to find 'url' property (tried looking in registry and INI) at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1083.
Skipping DAS source DS_549 - unable to find 'url' property (tried looking in registry and INI) at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1083.
Skipping DAS source UniProt - unable to find 'url' property (tried looking in registry and INI) at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1083.
- INFO : 41.765 : 0.039 : ** DAS ** >> Sorghum_bicolor DAS sources
- INFO : 41.782 : 0.017 : Parsing >> Brachypodium_distachyon ini file
- INFO : 41.834 : 0.052 : ** DB ** >> Brachypodium_distachyon database
Skipping DAS source Phenotypes - unable to find 'url' property (tried looking in registry and INI) at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1083.
Skipping DAS source Superfam - unable to find 'url' property (tried looking in registry and INI) at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1083.
Skipping DAS source DS_549 - unable to find 'url' property (tried looking in registry and INI) at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1083.
Skipping DAS source UniProt - unable to find 'url' property (tried looking in registry and INI) at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1083.
- INFO : 41.874 : 0.040 : ** DAS ** >> Brachypodium_distachyon DAS sources
- INFO : 41.893 : 0.019 : Parsing >> Vitis_vinifera ini file
- INFO : 42.007 : 0.114 : ** DB ** >> Vitis_vinifera database
Skipping DAS source Phenotypes - unable to find 'url' property (tried looking in registry and INI) at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1083.
Skipping DAS source Superfam - unable to find 'url' property (tried looking in registry and INI) at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1083.
Skipping DAS source DS_549 - unable to find 'url' property (tried looking in registry and INI) at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1083.
Skipping DAS source UniProt - unable to find 'url' property (tried looking in registry and INI) at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1083.
- INFO : 42.047 : 0.040 : ** DAS ** >> Vitis_vinifera DAS sources
- INFO : 42.122 : 0.075 : Parsing >> MULTI ini file
[WARN] Can't connect to DATABASE_COMPARA_PAN_ENSEMBL
[WARN] DBI connect('database=ensembl_compara_pan_homology_5_58;host=apu;port=3306','ensembl',...) failed: Unknown database 'ensembl_compara_pan_homology_5_58' at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker_base.pm line 91
- INFO : 42.568 : 0.447 : ** DB ** >> MULTI database
- INFO : 42.641 : 0.073 : Creating >> merged species config
------------------------------------------------------------------------------
- INFO : 42.641 : 0.000 : Parser >> Post processing ini files
------------------------------------------------------------------------------
Arabidopsis_lyrata at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1188.
- INFO : 42.643 : 0.002 : munging >> Arabidopsis_lyrata config
Arabidopsis_thaliana at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1188.
- INFO : 42.648 : 0.005 : munging >> Arabidopsis_thaliana config
Oryza_sativa Indica Group at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1188.
- INFO : 42.653 : 0.005 : munging >> Oryza_indica config
Oryza_sativa Japonica Group at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1188.
- INFO : 42.658 : 0.005 : munging >> Oryza_sativa config
Populus_trichocarpa at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1188.
- INFO : 42.659 : 0.002 : munging >> Populus_trichocarpa config
Sorghum_bicolor at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1188.
- INFO : 42.661 : 0.001 : munging >> Sorghum_bicolor config
Brachypodium_distachyon at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1188.
- INFO : 42.662 : 0.001 : munging >> Brachypodium_distachyon config
Vitis_vinifera at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ConfigPacker.pm line 1188.
- INFO : 42.667 : 0.005 : munging >> Vitis_vinifera config
- INFO : 42.667 : 0.000 : munging >> MULTI config
------------------------------------------------------------------------------
Placing .cvsignore and robots.txt into /usr/local/ensembl58plant/public-plugins/mirror/htdocs
------------------------------------------------------------------------------
"my" variable $width masks earlier declaration in same scope at /usr/local/ensembl58plant/eg-plugins/common/modules/Bio/EnsEMBL/GlyphSet/genetree.pm line 165.
Subroutine _init redefined at /usr/local/ensembl58plant/eg-plugins/common/modules/Bio/EnsEMBL/GlyphSet/genetree.pm line 15.
Subroutine ambiguity_code redefined at /usr/local/ensembl58plant/eg-plugins/common/modules/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 60.
Subroutine unambiguity_code redefined at /usr/local/ensembl58plant/eg-plugins/common/modules/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 86.
Subroutine variation_class redefined at /usr/local/ensembl58plant/eg-plugins/common/modules/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 110.
Subroutine sequence_with_ambiguity redefined at /usr/local/ensembl58plant/eg-plugins/common/modules/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 181.
Subroutine hgvs_variant_notation redefined at /usr/local/ensembl58plant/eg-plugins/common/modules/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 240.
Subroutine get_url redefined at /usr/local/ensembl58plant/modules/EnsEMBL/Web/ExtURL.pm line 29.
Subroutine get_url redefined at /usr/local/ensembl58plant/eg-plugins/common/modules/EnsEMBL/Web/ExtURL.pm line 12.
Subroutine ambiguity_code redefined at /usr/local/ensembl58plant/eg-plugins/common/modules/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 60.
Subroutine unambiguity_code redefined at /usr/local/ensembl58plant/eg-plugins/common/modules/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 86.
Subroutine variation_class redefined at /usr/local/ensembl58plant/eg-plugins/common/modules/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 110.
Subroutine sequence_with_ambiguity redefined at /usr/local/ensembl58plant/eg-plugins/common/modules/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 181.
Subroutine hgvs_variant_notation redefined at /usr/local/ensembl58plant/eg-plugins/common/modules/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 240.
Subroutine content redefined at /usr/local/ensembl58plant/eg-plugins/common/modules/EnsEMBL/Web/Component/Gene/ComparaParalogs.pm line 9.
Subroutine render redefined at /usr/local/ensembl58plant/eg-plugins/common/modules/EnsEMBL/Web/Document/HTML/FTPtable.pm line 10.
Subroutine _render_species_dropdown redefined at /usr/local/ensembl58plant/eg-plugins/common/modules/EnsEMBL/Web/Document/HTML/SpeciesList.pm line 11.
Subroutine render redefined at /usr/local/ensembl58plant/eg-plugins/common/modules/EnsEMBL/Web/Document/HTML/SpeciesPage.pm line 13.
Subroutine render redefined at /usr/local/ensembl58plant/eg-plugins/common/modules/EnsEMBL/Web/Document/HTML/WhatsNew.pm line 19.
==============================================================================
Server information:
==============================================================================
Ensembl version: 58
External address: http://host:88/
Real address: http://host:88
Cache namespace: http://host:88
Server root: /usr/local/ensembl58plant
PID file: /usr/local/ensembl58plant/logs/host.httpd.pid
Access logs: /usr/local/ensembl58plant/logs/host.access_log ensembl_extended
Error logs: /usr/local/ensembl58plant/logs/host.error_log
CSS file: http://host:88/minified/047c251f5a5b785250efef56e58bc6c3.css
JavaScript file: http://host:88/minified/b2ab869384ca0cf110543596cae66475.js
Plugins installed: EnsEMBL::Mirror
EnsEMBL::EnsemblPlants
EnsEMBL::EnsemblGenomes
EnsEMBL::Ensembl
==============================================================================
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