Hi Shin, the best place to report such problems is [email protected] where i am forwarding your email. Someone there will be able to help you
a On Wed, Jul 27, 2011 at 9:48 AM, Shinichiro Wachi <[email protected]> wrote: > Dear Arek, > > > > > > I would like to let you know that server is having a difficult time > responding to the following query: > > > > http://www.biomart.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.sequences.ensembl_gene_id|hsapiens_gene_ensembl.default.sequences.ensembl_transcript_id|hsapiens_gene_ensembl.default.sequences.5utr|hsapiens_gene_ensembl.default.sequences.5_utr_start|hsapiens_gene_ensembl.default.sequences.5_utr_end|hsapiens_gene_ensembl.default.sequences.external_gene_id|hsapiens_gene_ensembl.default.sequences.chromosome_name|hsapiens_gene_ensembl.default.sequences.start_position|hsapiens_gene_ensembl.default.sequences.end_position&FILTERS=&VISIBLEPANEL=resultspanel > > > > The symptoms are: > > > > 1) preview of the data will not show up (the circular pattern will keep > cycling) , > > 2) the text nor download of the result will not show up > > 3) Fasta output option will not appear (TSV is the only option in the > drop-down menu), and > > 4) email reply seems to indicate MySQL server failure (the response from > server is attached below) > > > > Other mirrors (West and East US coast Emsembl, as well as European site) > seems to have similar problems. Please let me know if this is a problem that > can be fixed, and if you know of a good solution. > > > > Thank you very much! > > > > > > Shin Wachi > > > > > > > > > > Response from server for email notification: > > > > 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_63/biomart-perl/lib/BioMart/Dataset/TableSet.pm line > 241 > BioMart::Dataset::TableSet::_fillAttributeTableWith('BioMart::Dataset::TableSet=HASH(0xce79ad0)', > 'BioMart::Query=HASH(0x16f571f0)', 'BioMart::ResultTable=HASH(0x16fa1780)', > 901200, 50000) called at > /ensemblweb/wwwmart/www_63/biomart-perl/lib/BioMart/Dataset/TableSet.pm line > 124 > BioMart::Dataset::TableSet::_getResultTable('BioMart::Dataset::TableSet=HASH(0xce79ad0)', > 'query', 'BioMart::Query=HASH(0x16f571f0)', 'batch_start', 901200, 'table', > 'BioMart::ResultTable=HASH(0x16fa1780)', 'batch_size', 50000) called at > /ensemblweb/wwwmart/www_63/biomart-perl/lib/BioMart/DatasetI.pm line 1170 > BioMart::DatasetI::getResultTable('BioMart::Dataset::TableSet=HASH(0xce79ad0)', > 'batch_start', 901200, 'query', 'BioMart::Query=HASH(0x16f571f0)', 'table', > 'BioMart::ResultTable=HASH(0x16fa1780)', 'batch_size', 50000) called at > /ensemblweb/wwwmart/www_63/biomart-perl/lib/BioMart/ResultTable.pm line 195 > > BioMart::ResultTable::_getBatch('BioMart::ResultTable=HASH(0x16fa1780)') > called at /ensemblweb/wwwmart/www_63/biomart-perl/lib/BioMart/ResultTable.pm > line 247 > > BioMart::ResultTable::hasMoreRows('BioMart::ResultTable=HASH(0x16fa1780)') > called at > /ensemblweb/wwwmart/www_63/biomart-perl/lib/BioMart/Dataset/GenomicSequence.pm > line 992 > BioMart::Dataset::GenomicSequence::_getResultTable('BioMart::Dataset::GenomicSequence=HASH(0x204bbcf0)', > 'query', 'BioMart::Query=HASH(0x16f1e030)', 'batch_start', 131283, 'table', > 'BioMart::ResultTable=HASH(0x16f57d90)', 'batch_size', 50000) called at > /ensemblweb/wwwmart/www_63/biomart-perl/lib/BioMart/DatasetI.pm line 1170 > BioMart::DatasetI::getResultTable('BioMart::Dataset::GenomicSequence=HASH(0x204bbcf0)', > 'batch_start', 131283, 'query', 'BioMart::Query=HASH(0x16f1e030)', 'table', > 'BioMart::ResultTable=HASH(0x16f57d90)', 'batch_size', 50000) called at > /ensemblweb/wwwmart/www_63/biomart-perl/lib/BioMart/ResultTable.pm line 195 > > BioMart::ResultTable::_getBatch('BioMart::ResultTable=HASH(0x16f57d90)') > called at /ensemblweb/wwwmart/www_63/biomart-perl/lib/BioMart/ResultTable.pm > line 247 > > BioMart::ResultTable::hasMoreRows('BioMart::ResultTable=HASH(0x16f57d90)') > called at > /ensemblweb/wwwmart/www_63/biomart-perl/lib/BioMart/AttributeTable.pm line > 169 > > BioMart::AttributeTable::nextRow('BioMart::ResultTable=HASH(0x16f57d90)') > called at /ensemblweb/wwwmart/www_63/biomart-perl/lib/BioMart/ResultTable.pm > line 256 > > BioMart::ResultTable::nextRow('BioMart::ResultTable=HASH(0x16f57d90)') > called at > /ensemblweb/wwwmart/www_63/biomart-perl/lib/BioMart/Formatter/FASTA.pm line > 70 > > BioMart::Formatter::FASTA::nextRow('BioMart::Formatter::FASTA=HASH(0x16f29f20)') > called at /ensemblweb/wwwmart/www_63/biomart-perl/lib/BioMart/QueryRunner.pm > line 259 > BioMart::QueryRunner::printResults('BioMart::QueryRunner=HASH(0x16fb5570)', > 'BioMart::Web::Zlib=GLOB(0x16fca240)', undef) called at > /ensemblweb/wwwmart/www_63/biomart-perl/lib/BioMart/Web.pm line 2336 eval > {...} at /ensemblweb/wwwmart/www_63/biomart-perl/lib/BioMart/Web.pm line > 2323 eval {...} at > /ensemblweb/wwwmart/www_63/biomart-perl/lib/BioMart/Web.pm line 2216 > BioMart::Web::handle_request('BioMart::Web=HASH(0x16fc4450)', > 'CGI=HASH(0x16f7aed0)') called at > /ensemblweb/wwwmart/www_63/biomart-perl/cgi-bin/martview line 100 eval {...} > at /ensemblweb/wwwmart/www_63/biomart-perl/cgi-bin/martview line 99 > > ModPerl::ROOT::ModPerl::Registry::ensemblweb_wwwmart_www_63_biomart_2dperl_cgi_2dbin_martview::handler('Apache2::RequestRec=SCALAR(0x16f735c0)') > 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(0x16f68670)') 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(0x16f68670)') > 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(0x16f735c0)') 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_0726205904_821.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. > > > > > > > > ________________________________ > This email may contain material that is confidential and/or proprietary to > Proteostasis Therapeutics, Inc for the sole use of the intended recipient. > Any review, reliance or distribution by others or forwarding without express > permission is strictly prohibited. If you are not the intended recipient, > please contact the sender and delete all copies. > _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
