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

cj5 at sanger.ac.uk cj5 at sanger.ac.uk
Wed Aug 17 12:30:43 BST 2011


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





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