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

[Will McLaren]

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> 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 -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@
> 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 -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.
>>
>> _______________________________________________
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>>
>>
>
>
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