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

[Guillermo Marco Puche]

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*  -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.
>
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