[ensembl-dev] Enseml API consequence predictions, Lost connection

[Will McLaren]

Hi Chris,

This is a recurring issue we are seeing many users experiencing; a fix
from the core team is forthcoming in Ensembl release 64 that should
address this issue.

Will

On 17 August 2011 12:30,  <cj5 at sanger.ac.uk> wrote:
> Hi,
>
> Whilst running scripts to retrieve large numbers of consequence
> predictions, I keep getting the following error at seemingly random
> intervals after an hour or so of run time:
> DBD::mysql::st execute failed: Lost connection to MySQL server during
> query at
> /software/vertres/lib/all/ensembl/62/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/TranscriptVariationAdaptor.pm
> line 384, <$__ANONIO__> line 4541.
>
> The line in TranscriptVariationAdaptor.pm tarces back to the select
> stament in sub _get_nsSNP_prediction
>
> The script is pretty much as described in the tutorial and example scripts:
>
>    my $vf =  Bio::EnsEMBL::Variation::VariationFeature->new(....
>
>            foreach my
> $tva(@{$tv->get_all_alternate_TranscriptVariationAlleles}) {
>
>                foreach my $tool (qw(SIFT PolyPhen Condel)) {
>                    my $lc_tool = lc($tool);
>                    my $pred_meth   = $lc_tool.'_prediction';
>                    my $score_meth  = $lc_tool.'_score';
>
>                    my $pred = $tva->$pred_meth;
>
>                    if($pred) {
>                        my $score = $tva->$score_meth;
> etc
>
> I should also say that I'm running against an archive db :
>
>    $registry->load_registry_from_db ( -host => 'ensdb-archive'...
>
> Other than building a local database as suggested in a previous thread,
> are there any suggestions as to how I might reduce the frequencies of
> these lost connections, or recover from them ?
>
> Many thanks
> Chris
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>