[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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