[ensembl-dev] Failed to instantiate plugin Conservation: Failed to connect to compara database

[Guillermo Marco Puche]

Thank you Will! Indeed I had a problem with ensembl-compara API local 
install.

Regards,
Guillermo


On 03/08/2017 04:48 PM, Will McLaren wrote:
> OK, next thing to check is that your ensembl-compara API checkout is 
> up to date (it should be on release/87).
>
> Will
>
> On 8 March 2017 at 15:25, Guillermo Marco Puche 
> <guillermo.marco at sistemasgenomicos.com 
> <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>
>     Hi Will,
>
>     My bad that '-host' was a typo when posting command to dev mail
>     list. I've actually tested it with both local database and remote
>     database and I'm getting the same error. However this is the
>     corrected command I'm testing right now:
>
>     variant_effect_predictor.pl <http://variant_effect_predictor.pl>  -i test.vcf -o test_out.vcf -config /home/ensembl_test/87.conf -dir_plugins /home/ensembl_test -dir_cache /share/references/vep -host*ensembldb.ensembl.org <http://ensembldb.ensembl.org>*  -fork 4
>
>     Regards,
>     Guillermo.
>
>
>     On 03/08/2017 04:13 PM, Will McLaren wrote:
>>     Hi Guillermo,
>>
>>     You have nothing following your "-host" entry in your command
>>     line; odd that this doesn't cause any other errors, but probably
>>     the root of your issue.
>>
>>     Regards
>>
>>     Will McLaren
>>     Ensembl Variation
>>
>>     On 7 March 2017 at 08:25, Guillermo Marco Puche
>>     <guillermo.marco at sistemasgenomicos.com
>>     <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>>
>>         Dear devs,
>>
>>         I'm having trouble running Conservation plugin on latest
>>         Ensembl 87 version. Here's the log:
>>
>>         variant_effect_predictor.pl <http://variant_effect_predictor.pl>  -i test.vcf -o test_out.vcf -config /home/ensembl_test/87.conf -dir_plugins /home/ensembl_test -dir_cache /share/references/vep -host -fork 4
>>
>>         2017-03-07 09:15:31 - Read configuration from /home/ensembl_test/87.conf
>>         2017-03-07 09:15:44 - Read existing cache info
>>         2017-03-07 09:15:44 - Auto-detected FASTA file in cache directory***2017-03-07 09:18:27 - Failed to instantiate plugin
>>         Conservation: Failed to connect to compara database*
>>         2017-03-07 09:18:34 - Starting...
>>         2017-03-07 09:18:34 - Detected format of input file as vcf
>>         2017-03-07 09:18:34 - Read 51 variants into buffer
>>         2017-03-07 09:18:34 - Calculating consequences
>>         2017-03-07 09:18:36 - Writing output
>>         2017-03-07 09:18:36 - Processed 51 total variants (26 vars/sec, 26 vars/sec total)
>>         2017-03-07 09:18:36 - Finished!
>>
>>
>>         I've cloned it from VEP plugin repo just to be sure I've
>>         latest version. I've tested it against both local Ensembl DB
>>         installation and remote host both failing.
>>
>>         This is my config file:
>>
>>         cache    1
>>         plugin Conservation
>>         force_overwrite    1
>>         no_escape    1
>>         no_progress     0
>>         no_stats    1
>>         hgvs    1
>>         canonical    1
>>         symbol    1
>>         ccds    1
>>         check_existing    1
>>         allele_number    1
>>         check_alleles    1
>>         domains    1
>>         gmaf    1
>>         maf_1kg    1
>>         maf_esp    1
>>         numbers    1
>>         uniprot    1
>>         biotype    1
>>         tsl    1
>>         pubmed    1
>>         polyphen    b
>>         regulatory    1
>>         sift    b
>>         xref_refseq    1
>>         vcf    1
>>
>>         Regards,
>>         Guillermo.
>>
>>         _______________________________________________
>>         Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
>>         Posting guidelines and subscribe/unsubscribe info:
>>         http://lists.ensembl.org/mailman/listinfo/dev
>>         <http://lists.ensembl.org/mailman/listinfo/dev>
>>         Ensembl Blog: http://www.ensembl.info/
>>
>>
>>
>>
>>     _______________________________________________
>>     Dev mailing listDev at ensembl.org <mailto:Dev at ensembl.org>
>>     Posting guidelines and subscribe/unsubscribe info:http://lists.ensembl.org/mailman/listinfo/dev
>>     <http://lists.ensembl.org/mailman/listinfo/dev>
>>     Ensembl Blog:http://www.ensembl.info/
>     _______________________________________________ Dev mailing list
>     Dev at ensembl.org <mailto:Dev at ensembl.org> Posting guidelines and
>     subscribe/unsubscribe info:
>     http://lists.ensembl.org/mailman/listinfo/dev
>     <http://lists.ensembl.org/mailman/listinfo/dev> Ensembl Blog:
>     http://www.ensembl.info/ 
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20170309/16827355/attachment.html>