[ensembl-dev] VEP Conservation Plugin error

Thu Oct 10 09:19:38 BST 2013

Hello Will,

I've reinstalled the whole API and I'm still getting the same errors.
I'm testing it with remote ensembl installation to discard there's a 
problem with my own DB. In fact I still get the same error. I'm using 
example.vcf file provided with vep as input.

I attach a log in this e-mail with the vep command (same I posted in my 
previous e-mail) and the whole output.

Thank you !

Best regards,
Guillermo.

On 10/07/2013 05:02 PM, Guillermo Marco Puche wrote:
> Hello Will,
>
> I'm testing it with example.vcf included in vep73 package.
>
> This is the command i'm using:
>
> *./variant_effect_predictor.pl -i example.vcf -o example.vep 
> -dir_plugins /home/likewise-open/SGNET/gmarco/vep_config/Plugins 
> -plugin Conservation --database --force_overwrite*
>
>
> I've installed bioperl, ensembl core, compara, variation, 
> functgenomics & ontology api (downloaded this morning).
>
> It's strange because indeed output file has conservation score in 
> output. I don't know what all those errors come from.
>
>
> Best regards,
> Guillermo.
>
> On 10/07/2013 04:29 PM, Will McLaren wrote:
>> Hello,
>>
>> I don't see any similar issues testing with a small input file.
>>
>> The Conservation plugin depends on the ensembl-compara API module - 
>> check that you have updated it to the latest version (73). Note that 
>> this is not done by the VEP installer since the ensembl-compara 
>> module is not required by the core VEP.
>>
>> If you're using CVS, just do:
>>
>> cd /home/likewise-open/SGNET/gmarco/src/ensembl-compara/
>> cvs up -dPr branch-ensembl-73
>>
>> If you still see the issue, can you please provide a sample of input 
>> and the command line flags you were using that recreates the error.
>>
>> Thanks
>>
>> Will McLaren
>> Ensembl Variation
>>
>>
>>
>> On 7 October 2013 11:54, Guillermo Marco Puche 
>> <guillermo.marco at sistemasgenomicos.com 
>> <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>>
>>     Hello,
>>
>>     I recently updated to ensembl73 database. I've found the
>>     following problem with Conservation plugin:
>>
>>     Cannot find the core database of 'takifugu_rubripes' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
>>
>>     Cannot find the core database of 'ciona_savignyi' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
>>
>>     Cannot find the core database of 'macaca_mulatta' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
>>
>>     Cannot find the core database of 'echinops_telfairi' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
>>
>>     Cannot find the core database of 'gasterosteus_aculeatus' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
>>
>>     (...)
>>
>>     -------------------- WARNING ----------------------
>>
>>     MSG: Unable to find method_link_species_set with method_link_type of Conservation_score and species_set_tag value of mammals
>>
>>     FILE: Compara/DBSQL/MethodLinkSpeciesSetAdaptor.pm LINE: 567
>>
>>     CALLED BY: vep_config/Plugins/Conservation.pm  LINE: 82
>>
>>     Date (localtime)    = Mon Oct  7 12:36:33 2013
>>
>>     Ensembl API version = 73
>>
>>     ---------------------------------------------------
>>
>>     2013-10-07 12:36:33 - Failed to instantiate plugin Conservation: Failed to fetch MLSS for Conservation_score and mammals
>>
>>
>>     Thank you.
>>
>>     Best regards,
>>     Guillermo.
>>
>>     _______________________________________________
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>>
>>
>>
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>
>
> _______________________________________________
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./variant_effect_predictor.pl -i example.vcf -o example.vep -dir_plugins /home/likewise-open/SGNET/gmarco/repos/scripts/genomics/global/annotation/ensembl_73/vep_config/Plugins/ -plugin Conservation --database --force_overwrite
Cannot find the core database of 'takifugu_rubripes' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'ciona_savignyi' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'macaca_mulatta' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'echinops_telfairi' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'gasterosteus_aculeatus' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'oryzias_latipes' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'ornithorhynchus_anatinus' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'monodelphis_domestica' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'tupaia_belangeri' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'erinaceus_europaeus' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'sorex_araneus' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'microcebus_murinus' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'pongo_abelii' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'equus_caballus' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'tetraodon_nigroviridis' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'ochotona_princeps' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'cavia_porcellus' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'choloepus_hoffmanni' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'procavia_capensis' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'tursiops_truncatus' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'tarsius_syrichta' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'dipodomys_ordii' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'vicugna_pacos' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'pteropus_vampyrus' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'dasypus_novemcinctus' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'taeniopygia_guttata' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'macropus_eugenii' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'loxodonta_africana' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'drosophila_melanogaster' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'oryctolagus_cuniculus' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'ailuropoda_melanoleuca' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'danio_rerio' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'anolis_carolinensis' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'meleagris_gallopavo' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'nomascus_leucogenys' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'xenopus_tropicalis' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'callithrix_jacchus' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'myotis_lucifugus' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'petromyzon_marinus' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'sarcophilus_harrisii' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'bos_taurus' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'gorilla_gorilla' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'otolemur_garnettii' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'pan_troglodytes' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'gadus_morhua' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'saccharomyces_cerevisiae' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'ciona_intestinalis' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'latimeria_chalumnae' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'oreochromis_niloticus' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'ictidomys_tridecemlineatus' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'sus_scrofa' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'mus_musculus' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'canis_familiaris' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'pelodiscus_sinensis' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'xiphophorus_maculatus' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'mustela_putorius_furo' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'felis_catus' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'rattus_norvegicus' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'gallus_gallus' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'caenorhabditis_elegans' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'anas_platyrhynchos' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
Cannot find the core database of 'ficedula_albicollis' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
2013-10-10 10:10:35 - Loaded plugin: Conservation
2013-10-10 10:10:35 - Fetching regulatory features for plugin: Conservation
2013-10-10 10:10:36 - Starting...
2013-10-10 10:10:36 - Detected format of input file as vcf
2013-10-10 10:10:36 - Read 173 variants into buffer
2013-10-10 10:10:36 - Reading transcript data from cache and/or database
[================================================================================================================================================]  [ 100% ]
2013-10-10 10:11:19 - Retrieved 387 transcripts (0 mem, 0 cached, 559 DB, 172 duplicates)
2013-10-10 10:11:19 - Reading regulatory data from cache and/or database
[================================================================================================================================================]  [ 100% ]
2013-10-10 10:12:41 - Retrieved 535 regulatory features (0 mem, 0 cached, 541 DB, 6 duplicates)
2013-10-10 10:12:41 - Analyzing chromosome 21
2013-10-10 10:12:41 - Analyzing variants
[================================================================================================================================================]  [ 100% ]
2013-10-10 10:13:10 - Analyzing RegulatoryFeatures
[================================================================================================================================================]  [ 100% ]
2013-10-10 10:13:10 - Analyzing MotifFeatures
[================================================================================================================================================]  [ 100% ]
2013-10-10 10:13:10 - Calculating consequences
[================================================================================================================================================]  [ 100% ]
2013-10-10 10:13:59 - Analyzing chromosome 22
2013-10-10 10:13:59 - Analyzing variants
[================================================================================================================================================]  [ 100% ]
2013-10-10 10:15:29 - Analyzing RegulatoryFeatures
[================================================================================================================================================]  [ 100% ]
2013-10-10 10:15:29 - Analyzing MotifFeatures
[================================================================================================================================================]  [ 100% ]
2013-10-10 10:15:29 - Calculating consequences
[================================================================================================================================================]  [ 100% ]
2013-10-10 10:18:24 - Processed 173 total variants (0 vars/sec, 0 vars/sec total)
2013-10-10 10:18:24 - Wrote stats summary to example.vep_summary.html
2013-10-10 10:18:24 - Finished!