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

[Will McLaren]

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> 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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