<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Tanvir Ahamed,<div>I suspect that you are running your biomaRt query against the BioMart central portal at <a href="http://www.biomart.org">www.biomart.org</a> which the Ensembl project is not responsible for maintaining. Can you try setting your host to <a href="http://www.ensembl.org/biomart/martview/">http://www.ensembl.org/biomart/martview/</a> and let me know if you have the same issue? For any <a href="http://www.biomart.org">www.biomart.org</a> issues you should email their mailing list (<a href="mailto:users@biomart.org">users@biomart.org</a>).</div><div>Regards</div><div>Rhoda</div><div><br><div><div>On 8 May 2013, at 12:16, Mohammad Tanvir Ahamed <<a href="mailto:mashranga@yahoo.com">mashranga@yahoo.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div><div style="background-color: rgb(255, 255, 255); font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; position: static; z-index: auto; "><div><span><div style="font-family: arial, helvetica, sans-serif; font-size: 10pt;">Hi,</div><div style="font-family: arial, helvetica, sans-serif; font-size: 10pt;">I can run the code some days ago . But cant run now. </div><div style="font-family: arial, helvetica, sans-serif; font-size: 10pt;"><br></div><div style="background-color: transparent; font-family: arial, helvetica, sans-serif; font-size: 13px;"><span style="font-weight: bold; text-decoration: underline;">Problem 1:</span> Output is ok</div><div style="background-color: transparent; font-family: arial, helvetica, sans-serif; font-size: 13px;">ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl)</div><div style="font-size: 12pt; background-color: transparent;"><font size="2">utr5 = getSequence(chromosome=3, start=185514033,
end=185535839, </font><span style="background-color: transparent;"><font size="2">type="entrezgene",seqType="5utr", mart=ensembl)</font></span><font size="2" style="background-color: transparent;"> </font></div><div style="background-color: transparent; font-family: arial, helvetica, sans-serif; font-size: 13px;"><font size="2" style="background-color: transparent;"><span style="text-decoration: underline;">Output :</span> </font></div><div style="font-size: 12pt; background-color: transparent;"><font size="2" style="background-color: transparent;"><div style="text-align: right; background-color: transparent;"> 5utr
entrezgene</div><div style="text-align: right; background-color: transparent;"> Sequence unavailable 10644</div><div style="text-align: right; background-color: transparent;"> GGAGCGCCGGGTACCGGGCCGGGGGAGCCGCGGGCTCTCGGGGAAGAGACGG 10644</div><div style="text-align: right; background-color: transparent;">3 GGGGGGCGGAGGAGGAGGAGAGACGAGGGCAGCGGAGGAGGCGAGGAGCGCCGGGTACCGGGCCGGGGGAGCCGCGGGCTCTCGGGGAAGAGACGG 10644</div><div style="text-align: right; background-color:
transparent;"> CGGAGGAGGCGAGGAGCGCCGGGTACCGGGCCGGGGGAGCCGCGGGCTCTCGGGGAAGAGACGG 10644</div><div style="text-align: right; background-color: transparent;"> No UTR is annotated for this transcript 10644</div></font></div><div style="font-family: arial, helvetica, sans-serif; font-size: 10pt;"></div><div style="font-family: arial, helvetica, sans-serif; font-size: 10pt;"> </div><div style="font-family: arial, helvetica, sans-serif; font-size: 10pt;"><span style="font-weight: bold; text-decoration: underline;">Problem 2:Problem is here</span><br></div><div style="background-color:
transparent;"><span><div style="font-size: 13px; background-color: transparent;">protein = getSequence(id=c(100, 5728),type="entrezgene",<span style="background-color: transparent;">seqType="peptide", mart=ensembl)</span></div><div style="font-size: 13px; background-color: transparent; font-family: arial, helvetica, sans-serif;"><span style="background-color: transparent;"><br></span></div><div style="background-color: transparent;"><span style="background-color: transparent; font-size: 13px;"><div style="background-color: transparent;">Error in getBM(c(seqType, type), filters = type, values = id, mart = mart, : </div><div style="background-color: transparent;"> Query ERROR: caught BioMart::Exception::Database: Error during query execution: Can't create/write to file '/mnt/ephemeral0/mysqltmp/#sql_40a_0.MYI' (Errcode: 2)</div><div style="background-color: transparent;"><br></div><div style="background-color: transparent; font-family:
arial, helvetica, sans-serif;">I need help please.</div></span></div></span></div></span></div><div></div><div> </div><div><span style="font-family: 'times new roman'; font-weight: bold;"><i>/.......Tanvir Ahamed</i></span><br></div></div></div>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a><br></blockquote></div><br><div>
<div>Rhoda Kinsella Ph.D.</div><div>Ensembl Production Project Leader,</div><div>European Bioinformatics Institute (EMBL-EBI),</div><div>Wellcome Trust Genome Campus,</div><div>Hinxton,</div><div>Cambridge,</div><div>CB10 1SD</div><div><br></div><br class="Apple-interchange-newline">
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