Hi Arek, Thanks for the reply. I want to get all sequences of the known 5'UTR of mouse mRNAs. As to the header, I will need Ensembl Gene ID, Ensembl Transcript ID, Entrez Gene ID, Gene Name, chr, 5'URT start (coordinate on chromosome), 5'UTR end (coordinate on chromosome), strand.
If not convenient for you to get the data for me, I can try smaller query. Thanks, Xiaofeng On Fri, Mar 16, 2012 at 11:08 AM, Arek Kasprzyk <[email protected]> wrote: > Hi Xiaofeng, > How big is the dataset that you are trying to download? Could you give us > more details about your query? > > We have been having problems with UTR sequences recently. Perhaps you could > try a smaller dataset until this problem gets addressed? > > > > a > > > > On Mon, Mar 12, 2012 at 11:49 AM, Xiaofeng Xin <[email protected]> wrote: >> >> Hi, >> >> I am retrieving 5'UTR sequences for Mus musculus, but I keep getting >> FAILED results, like this one forwarded. Please help me with the >> request. >> >> Thanks, >> Xiaofeng >> >> ---------- Forwarded message ---------- >> From: <[email protected]> >> Date: Mon, Mar 12, 2012 at 11:43 AM >> Subject: Your BioMart results are ready >> To: [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 >> /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Dataset/TableSet.pm >> line 241 >> >> BioMart::Dataset::TableSet::_fillAttributeTableWith('BioMart::Dataset::TableSet=HASH(0x169b44f0)', >> 'BioMart::Query=HASH(0x328c9168)', >> 'BioMart::ResultTable=HASH(0x328ca1a0)', 6400, 6400) called at >> >> /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Dataset/TableSet.pm >> line 124 >> >> BioMart::Dataset::TableSet::_getResultTable('BioMart::Dataset::TableSet=HASH(0x169b44f0)', >> 'query', 'BioMart::Query=HASH(0x328c9168)', 'batch_start', 6400, >> 'table', 'BioMart::ResultTable=HASH(0x328ca1a0)', 'batch_size', 6400) >> called at >> /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/DatasetI.pm >> line 1170 >> >> BioMart::DatasetI::getResultTable('BioMart::Dataset::TableSet=HASH(0x169b44f0)', >> 'batch_start', 6400, 'query', 'BioMart::Query=HASH(0x328c9168)', >> 'table', 'BioMart::ResultTable=HASH(0x328ca1a0)', 'batch_size', 6400) >> called at >> /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/ResultTable.pm >> line 195 >> BioMart::ResultTable::_getBatch('BioMart::ResultTable=HASH(0x328ca1a0)') >> called at >> /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/ResultTable.pm >> line 247 >> BioMart::ResultTable::hasMoreRows('BioMart::ResultTable=HASH(0x328ca1a0)') >> called at >> /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Dataset/GenomicSequence.pm >> line 992 >> >> BioMart::Dataset::GenomicSequence::_getResultTable('BioMart::Dataset::GenomicSequence=HASH(0xfe39b58)', >> 'query', 'BioMart::Query=HASH(0x328cb3a0)', 'batch_start', 573, >> 'table', 'BioMart::ResultTable=HASH(0x3287f0f8)', 'batch_size', 6400) >> called at >> /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/DatasetI.pm >> line 1170 >> >> BioMart::DatasetI::getResultTable('BioMart::Dataset::GenomicSequence=HASH(0xfe39b58)', >> 'batch_start', 573, 'query', 'BioMart::Query=HASH(0x328cb3a0)', >> 'table', 'BioMart::ResultTable=HASH(0x3287f0f8)', 'batch_size', 6400) >> called at >> /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/ResultTable.pm >> line 195 >> BioMart::ResultTable::_getBatch('BioMart::ResultTable=HASH(0x3287f0f8)') >> called at >> /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/ResultTable.pm >> line 247 >> BioMart::ResultTable::hasMoreRows('BioMart::ResultTable=HASH(0x3287f0f8)') >> called at >> /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/AttributeTable.pm >> line 169 >> BioMart::AttributeTable::nextRow('BioMart::ResultTable=HASH(0x3287f0f8)') >> called at >> /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/ResultTable.pm >> line 256 >> BioMart::ResultTable::nextRow('BioMart::ResultTable=HASH(0x3287f0f8)') >> called at >> /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Formatter/FASTA.pm >> line 70 >> >> BioMart::Formatter::FASTA::nextRow('BioMart::Formatter::FASTA=HASH(0x328c8f10)') >> called at >> /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/QueryRunner.pm >> line 248 >> >> BioMart::QueryRunner::printResults('BioMart::QueryRunner=HASH(0x328c68d0)', >> 'BioMart::Web::Zlib=GLOB(0x328c9150)', undef) called at >> /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Web.pm line >> 2308 >> eval {...} at >> /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Web.pm >> line 2295 >> eval {...} at >> /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Web.pm >> line 2201 >> BioMart::Web::handle_request('BioMart::Web=HASH(0x3285ff40)', >> 'CGI=HASH(0x32899a20)') called at >> /srv/biomart_server/biomart.org/biomart-perl/cgi-bin/martview line 96 >> eval {...} at >> /srv/biomart_server/biomart.org/biomart-perl/cgi-bin/martview >> line 95 >> >> ModPerl::ROOT::ModPerl::Registry::srv_biomart_server_biomart_2eorg_biomart_2dperl_cgi_2dbin_martview::handler('Apache2::RequestRec=SCALAR(0x32872cf0)') >> called at /usr/lib/perl5/ModPerl/RegistryCooker.pm line 204 >> eval {...} at /usr/lib/perl5/ModPerl/RegistryCooker.pm line 204 >> ModPerl::RegistryCooker::run('ModPerl::Registry=HASH(0x32864f98)') >> called at /usr/lib/perl5/ModPerl/RegistryCooker.pm line 170 >> >> ModPerl::RegistryCooker::default_handler('ModPerl::Registry=HASH(0x32864f98)') >> called at /usr/lib/perl5/ModPerl/Registry.pm line 31 >> ModPerl::Registry::handler('ModPerl::Registry', >> 'Apache2::RequestRec=SCALAR(0x32872cf0)') 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_0312114200_445.txt.gz. >> _______________________________________________ >> Users mailing list >> [email protected] >> https://lists.biomart.org/mailman/listinfo/users > > > > > -- > > Arek Kasprzyk, MD, MSc, PhD > BioMart Project Lead > > _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
