Hi Xiaofeng, this is the problem that we need to address properly and I do apologize for your inconvenience. Until this is properly resolved would you mind trying one chromosome at a time and tell me if this works for you?
a On Fri, Mar 16, 2012 at 11:16 AM, Xiaofeng Xin <[email protected]> wrote: > 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 > > > > > -- Arek Kasprzyk, MD, MSc, PhD BioMart Project Lead
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