<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div>Hi</div><div><br></div><div>Since you're in the EBI you will probably have more luck using the internal mirrors of ensembl databases. The kind of error you are seeing happens when you're either a long distance away from the server or the server you're querying is under excessive load. If you search confluence you should find the connection details </div><div><br></div><div>Andy</div><div><br>Sent from my mobile.</div><div><br>On 31 Oct 2014, at 09:57, Nathalie Conte <<a href="mailto:nconte@ebi.ac.uk">nconte@ebi.ac.uk</a>> wrote:<br><br></div><blockquote type="cite"><div><meta http-equiv="Content-Type" content="text/html charset=us-ascii">Hi, Could I have some help with this please?<div>Thanks</div><div>N<br><div><div>On 21 Oct 2014, at 09:55, Nathalie Conte <<a href="mailto:nconte@ebi.ac.uk">nconte@ebi.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html charset=us-ascii"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">HI<div>I am using variation API to fetch all SNPs from ensembl with a phenotype associated to them - </div><div>I am writing the info to a file, and each time I run the script, it will stop after a while and trow this error</div><div><b>error file:</b></div><div><div>DBD::mysql::st execute failed: MySQL server has gone away at /net/isilon5/ma/home/nconte/src/ensembl/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm line 831.</div><div>DBD::mysql::st execute failed: MySQL server has gone away at /net/isilon5/ma/home/nconte/src/ensembl/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm line 831.</div></div><div><br></div><div><b>this is the out file:</b></div><div><div>Exited with exit code 110.</div><div>Resource usage summary:</div><div><br></div><div> CPU time : 9269.09 sec.</div><div> Max Memory : 62 MB</div><div> Average Memory : 59.93 MB</div><div> Total Requested Memory : -</div><div> Delta Memory : -</div><div> (Delta: the difference between total requested memory and actual max usage.)</div><div> Max Swap : 377 MB</div><div><br></div><div> Max Processes : 3</div><div> Max Threads : 4</div><div><br></div><div>The output (if any) is above this job summary.</div></div><div><br></div><div>Any tips welcome</div><div>thanks</div><div>Nathalie</div><div><br></div><div><b>script:</b></div><div><blockquote cite="mid:20141014162952.F3D3513349D_43D4F80B@hx-mx2.ebi.ac.uk" type="cite"><div>#!/usr/local/bin/perl</div><div>use strict;</div><div>use warnings;</div><div>use DBI;</div><div>use Bio::EnsEMBL::Registry;</div><div><br></div><div><br></div><div>Bio::EnsEMBL::Registry->load_registry_from_db(</div><div> -host=>"<a moz-do-not-send="true" href="http://ensembldb.ensembl.org/">ensembldb.ensembl.org</a>", -user=>"anonymous",</div><div> -port=>'5306', 'db_version' => 75,);</div><div>open (OUTFILE2, ">/outtest6.txt") or die "problem open OUTfile";</div><div><br></div><div>my $vs_adaptor = Bio::EnsEMBL::Registry->get_adaptor('human','variation','variationset');</div><div>my $vs = $vs_adaptor->fetch_by_name('All phenotype-associated variants');</div><div>my $iterator = $vs->get_Variation_Iterator();</div><div>while ($iterator->has_next()) {</div><div>my $var = $iterator->next();</div><div>my $variant=$var->name();</div><div>my @vfs = @{$var->get_all_VariationFeatures()};</div><div>my $cons=$var->display_consequence ();</div><div>my $source=$var->source;</div><div>my $p_value;</div><div>foreach my $vf (@vfs) {</div><div> my @pfs = @{$var->get_all_PhenotypeFeatures()};</div><div> foreach my $pf(@pfs) {</div><div> $p_value=$pf->p_value;</div><div>print OUTFILE2 $variant, "\t",$cons, "\t",$source, "\t", $p_value, "\n";</div><div>}</div><div>}</div><div>}</div></blockquote></div></div></blockquote></div><br></div></div></blockquote><blockquote type="cite"><div><span>_______________________________________________</span><br><span>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a></span><br><span>Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a></span><br><span>Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a></span><br></div></blockquote></body></html>