Dear Harriet,
I was trying to reproduce the problem at our side, but could not get what you
experienced. We have been experiencing a lot of traffic recently, which could
be the reason for the failed queries. If you continue receiving this error
message, I recommend reducing the query size by, for example, setting
chromosome filters.
Regards,
Elena
Details of the query that I tried based on your description:
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query virtualSchemaName = "default" formatter = "FASTA" header = "0"
uniqueRows = "0" count = "" datasetConfigVersion = "0.6" >
<Dataset name = "hsapiens_gene_ensembl" interface = "default" >
<Filter name = "upstream_flank" value = "1000"/>
<Attribute name = "ensembl_gene_id" />
<Attribute name = "ensembl_transcript_id" />
<Attribute name = "coding_gene_flank" />
</Dataset>
</Query>
From: Harriet Taylor <[email protected]<mailto:[email protected]>>
Date: Mon, 11 Apr 2011 07:11:52 -0400
To: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: [BioMart Users] Results file FAILED - "Error during query execution:
Lost connection to MySQL server during query" - Help?
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]<mailto:[email protected]>
<[email protected]><mailto:[email protected]>
To: Taylor, Harriet B
<[email protected]><mailto:[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
195BioMart::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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