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Dear Ensembl devs,<br>
<br>
I'm still having troubles with the Ensembl Perl API for this
command (for human data on GRCh37):<br>
<br>
variant_effect_predictor.pl --vcf -o STDOUT --cache --dir_cache
/home/cbrcmod/scratch/modules/out/modulebin/VEP/84/.vep --fork 15
--force_overwrite --species homo_sapiens --assembly GRCh37 --port
3337 ...<br>
<br>
DBD::mysql::db selectall_arrayref failed: Can't read dir of '.'
(errno: 5) at
/home/cbrcmod/scratch/modules/out/modulebin/VEP/84/perl/Bio/EnsEMBL/Registry.pm
line 1766.<br>
<br>
-------------------- WARNING ----------------------<br>
MSG: homo_sapiens is not a valid species name (check DB and API
version)<br>
FILE: Bio/EnsEMBL/Registry.pm LINE: 1327<br>
CALLED BY: Bio/EnsEMBL/Registry.pm LINE: 1102<br>
Date (localtime) = Wed Aug 31 10:01:43 2016<br>
Ensembl API version = 84<br>
---------------------------------------------------<br>
<br>
-------------------- EXCEPTION --------------------<br>
MSG: Can not find internal name for species 'homo_sapiens'<br>
STACK Bio::EnsEMBL::Registry::get_adaptor
/home/cbrcmod/scratch/modules/out/modulebin/VEP/84/perl/Bio/EnsEMBL/Registry.pm:1104<br>
STACK main::connect_to_dbs
/home/cbrcmod/scratch/modules/out/modulebin/VEP/84/bin/variant_effect_predictor.pl:1264<br>
STACK main::configure
/home/cbrcmod/scratch/modules/out/modulebin/VEP/84/bin/variant_effect_predictor.pl:811<br>
STACK toplevel
/home/cbrcmod/scratch/modules/out/modulebin/VEP/84/bin/variant_effect_predictor.pl:145<br>
Date (localtime) = Wed Aug 31 10:01:43 2016<br>
Ensembl API version = 84<br>
---------------------------------------------------<br>
<br>
Best wishes,<br>
Chris<br>
<br>
On 31/08/16 09:59, Thomas Maurel wrote:<br>
</div>
<blockquote
cite="mid:BD6B1F4B-82ED-44F2-9A44-BC54390298FF@ebi.ac.uk"
type="cite">
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Dear Julien,
<div class=""><br class="">
</div>
<div class="">Our ensembl gene mart via the R package seems to be
working fine for me this morning:</div>
<div class=""><br class="">
</div>
<div class="">> mart <-
useMart("ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl",host="<a
moz-do-not-send="true" href="http://www.ensembl.org" class="">www.ensembl.org</a>")</div>
<div class="">
<div class="">>
getBM(attributes=c('ensembl_gene_id','ensembl_transcript_id','description'),filters
= 'ensembl_gene_id', values = 'ENSG00000252303', mart = mart)</div>
<div class=""> ensembl_gene_id ensembl_transcript_id
description</div>
<div class="">1 ENSG00000252303 ENST00000516494 RNA, U6
small nuclear 280, pseudogene [Source:HGNC
Symbol;Acc:HGNC:47243]</div>
</div>
<div class=""><br class="">
</div>
<div class="">Could you please let me know:</div>
<blockquote style="margin: 0 0 0 40px; border: none; padding:
0px;" class="">
<div class="">1) The mart that you are using</div>
<div class="">2) The ensembl website that you are pointing to</div>
<div class="">3) The error that you are getting</div>
</blockquote>
<div class=""><br class="">
</div>
<div class="">Thanks a lot,</div>
<div class="">Regards,</div>
<div class="">Thomas</div>
<div class="">
<div>
<blockquote type="cite" class="">
<div class="">On 31 Aug 2016, at 07:51, Julien Roux <<a
moz-do-not-send="true" href="mailto:julien.roux@unil.ch"
class="">julien.roux@unil.ch</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="">Dear Ensembl team,<br class="">
<br class="">
Thanks for bringing the website up, it was missed a lot!
;)<br class="">
<br class="">
This morning I have trouble to connect to the database
via the R package BiomaRt (the web version of biomart
works just fine). Is this related to the downtime?<br
class="">
<br class="">
Best,<br class="">
<br class="">
Julien<br class="">
<br class="">
-- <br class="">
Julien Roux<br class="">
Department of Ecology and Evolution, University of
Lausanne, Switzerland<br class="">
<a moz-do-not-send="true"
href="http://www.unil.ch/dee/home/menuinst/people/post-docs--associates/dr-julien-roux.html"
class="">http://www.unil.ch/dee/home/menuinst/people/post-docs--associates/dr-julien-roux.html</a><br
class="">
Tel: +41 78 700 2931<br class="">
Twitter: @_julien_roux<br class="">
<br class="">
<br class="">
_______________________________________________<br
class="">
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br class="">
Posting guidelines and subscribe/unsubscribe info:
<a class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br
class="">
Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a><br class="">
</div>
</div>
</blockquote>
</div>
<br class="">
<div class="">
<div class="">
<div class="" style="orphans: 2; widows: 2;">--</div>
<div class="" style="orphans: 2; widows: 2;">Thomas Maurel<br
class="">
Bioinformatician - Ensembl Production Team<br class="">
European Bioinformatics Institute (EMBL-EBI)<br class="">
European Molecular Biology Laboratory<br class="">
Wellcome Trust Genome Campus<br class="">
Hinxton<br class="">
Cambridge CB10 1SD<br class="">
United Kingdom</div>
</div>
</div>
<br class="">
</div>
<br>
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<pre wrap="">_______________________________________________
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</pre>
</blockquote>
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