Dear All,
I have been trying to export a query using the biomart database and am having problems. I am trying to export 1000bp upstream of all human genes in the database however the query keeps failing and saying the problem is with my server "Error during query execution: Lost connection to MySQL server during query" (see email below). Is there anything I can do to solve this problem?
Any help on this would be much appreciated. Regards, Harriet -------- Original Message -------- Subject: Your Ensembl BioMart results are ready Date: Mon, 11 Apr 2011 10:27:23 +0100 From: [email protected] <[email protected]> To: Taylor, Harriet B <[email protected]> Your results file FAILED. Here is the reason why: Error during query execution: Lost connection to MySQL server during query Trace begun at /ensemblweb/wwwmart/www_61/biomart-perl/lib/BioMart/Dataset/TableSet.pm line 241 BioMart::Dataset::TableSet::_fillAttributeTableWith('BioMart::Dataset::TableSet=HASH(0xe4f9940)', 'BioMart::Query=HASH(0x1808ed30)', 'BioMart::ResultTable=HASH(0x1807daf0)', 151200, 50000) called at /ensemblweb/wwwmart/www_61/biomart-perl/lib/BioMart/Dataset/TableSet.pm line 124 BioMart::Dataset::TableSet::_getResultTable('BioMart::Dataset::TableSet=HASH(0xe4f9940)', 'query', 'BioMart::Query=HASH(0x1808ed30)', 'batch_start', 151200, 'table', 'BioMart::ResultTable=HASH(0x1807daf0)', 'batch_size', 50000) called at /ensemblweb/wwwmart/www_61/biomart-perl/lib/BioMart/DatasetI.pm line 1170 BioMart::DatasetI::getResultTable('BioMart::Dataset::TableSet=HASH(0xe4f9940)', 'batch_start', 151200, 'query', 'BioMart::Query=HASH(0x1808ed30)', 'table', 'BioMart::ResultTable=HASH(0x1807daf0)', 'batch_size', 50000) called at /ensemblweb/wwwmart/www_61/biomart-perl/lib/BioMart/ResultTable.pm line 195 BioMart::ResultTable::_getBatch('BioMart::ResultTable=HASH(0x1807daf0)') called at /ensemblweb/wwwmart/www_61/biomart-perl/lib/BioMart/ResultTable.pm line 247 BioMart::ResultTable::hasMoreRows('BioMart::ResultTable=HASH(0x1807daf0)') called at /ensemblweb/wwwmart/www_61/biomart-perl/lib/BioMart/Dataset/GenomicSequence.pm line 992 BioMart::Dataset::GenomicSequence::_getResultTable('BioMart::Dataset::GenomicSequence=HASH(0x21240240)', 'query', 'BioMart::Query=HASH(0x18081d30)', 'batch_start', 1999, 'table', 'BioMart::ResultTable=HASH(0x18094cd0)', 'batch_size', 50000) called at /ensemblweb/wwwmart/www_61/biomart-perl/lib/BioMart/DatasetI.pm line 1170 BioMart::DatasetI::getResultTable('BioMart::Dataset::GenomicSequence=HASH(0x21240240)', 'batch_start', 1999, 'query', 'BioMart::Query=HASH(0x18081d30)', 'table', 'BioMart::ResultTable=HASH(0x18094cd0)', 'batch_size', 50000) called at /ensemblweb/wwwmart/www_61/biomart-perl/lib/BioMart/ResultTable.pm line 195 BioMart::ResultTable::_getBatch('BioMart::ResultTable=HASH(0x18094cd0)') called at /ensemblweb/wwwmart/www_61/biomart-perl/lib/BioMart/ResultTable.pm line 247 BioMart::ResultTable::hasMoreRows('BioMart::ResultTable=HASH(0x18094cd0)') called at /ensemblweb/wwwmart/www_61/biomart-perl/lib/BioMart/AttributeTable.pm line 169 BioMart::AttributeTable::nextRow('BioMart::ResultTable=HASH(0x18094cd0)') called at /ensemblweb/wwwmart/www_61/biomart-perl/lib/BioMart/ResultTable.pm line 256 BioMart::ResultTable::nextRow('BioMart::ResultTable=HASH(0x18094cd0)') called at /ensemblweb/wwwmart/www_61/biomart-perl/lib/BioMart/Formatter/FASTA.pm line 70 BioMart::Formatter::FASTA::nextRow('BioMart::Formatter::FASTA=HASH(0x1807e8f0)') called at /ensemblweb/wwwmart/www_61/biomart-perl/lib/BioMart/QueryRunner.pm line 259 BioMart::QueryRunner::printResults('BioMart::QueryRunner=HASH(0x1806f6a0)', 'BioMart::Web::Zlib=GLOB(0x18080b00)', undef) called at /ensemblweb/wwwmart/www_61/biomart-perl/lib/BioMart/Web.pm line 2333 eval {...} at /ensemblweb/wwwmart/www_61/biomart-perl/lib/BioMart/Web.pm line 2320 eval {...} at /ensemblweb/wwwmart/www_61/biomart-perl/lib/BioMart/Web.pm line 2213 BioMart::Web::handle_request('BioMart::Web=HASH(0x7c80f60)', 'CGI=HASH(0x1806f5a0)') called at /ensemblweb/wwwmart/www_61/biomart-perl/cgi-bin/martview line 100 eval {...} at /ensemblweb/wwwmart/www_61/biomart-perl/cgi-bin/martview line 99 ModPerl::ROOT::ModPerl::Registry::ensemblweb_wwwmart_www_61_biomart_2dperl_cgi_2dbin_martview::handler('Apache2::RequestRec=SCALAR(0x180893c0)') called at /localsw/ensembl_web/apache/lib/site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm line 204 eval {...} at /localsw/ensembl_web/apache/lib/site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm line 204 ModPerl::RegistryCooker::run('ModPerl::Registry=HASH(0x18081a90)') called at /localsw/ensembl_web/apache/lib/site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm line 170 ModPerl::RegistryCooker::default_handler('ModPerl::Registry=HASH(0x18081a90)') called at /localsw/ensembl_web/apache/lib/site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/Registry.pm line 31 ModPerl::Registry::handler('ModPerl::Registry', 'Apache2::RequestRec=SCALAR(0x180893c0)') called at -e line 0 eval {...} at -e line 0 Please try your request again, or alternatively contact your service provider including a copy of this email and quoting this reference: martquery_0411091915_309.txt.gz. -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
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