[ensembl-dev] Failed to instantiate plugin Conservation: Failed to connect to compara database
Guillermo Marco Puche
guillermo.marco at sistemasgenomicos.com
Tue Mar 7 08:25:40 GMT 2017
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.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20170307/b1c111e7/attachment.html>
More information about the Dev
mailing list