Hi Arek, Never mind. I'll try other ways.
Thanks, Xiaofeng On Fri, Mar 16, 2012 at 11:19 AM, Arek Kasprzyk <[email protected]> wrote: > 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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