<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt;"><span>Hi </span><span style="font-size: 12pt;">Rhoda, </span></div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: transparent; font-style: normal;"><span style="font-size: 12pt;"><br></span></div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: transparent; font-style: normal;"><span style="font-size: 12pt;">Thank for your help . </span></div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: transparent; font-style: normal;"><span style="font-size: 12pt;">Now the following code is
working.</span></div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: transparent; font-style: normal;"><span style="font-size: 12pt;"><br></span></div><div style="background-color: transparent;"><span><div style="background-color: transparent;">ensembl = useMart("ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl",host="www.ensembl.org/biomart/martservice/")</div><div style="background-color: transparent;">getBM(attributes=c("peptide","entrezgene"),filters="entrezgene",values=c("5728","100"),mart=ensembl)</div></span></div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt;"></div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt;"> </div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt;"><span style="font-family: 'times new roman'; font-weight:
bold;"><i>/.......Tanvir Ahamed</i></span><br><br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; margin-top: 5px; padding-left: 5px;"> <div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt;"> <div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt;"> <div dir="ltr"> <hr size="1"> <font size="2" face="Arial"> <b><span style="font-weight:bold;">From:</span></b> Rhoda Kinsella <rhoda@ebi.ac.uk><br> <b><span style="font-weight: bold;">To:</span></b> Mohammad Tanvir Ahamed <mashranga@yahoo.com> <br><b><span style="font-weight: bold;">Cc:</span></b> Ensembl developers list <dev@ensembl.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Wednesday, 8 May 2013, 14:58<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [ensembl-dev] Problem with biomaRt::getSequence<br> </font> </div> <div class="y_msg_container"><br><div
id="yiv6221284387"><div>Hi Tanvir Ahamed,<div>If you add a forward slash (/) at the end of <span style="background-color:rgb(255, 255, 255);">host="<a rel="nofollow" target="_blank" href="http://www.ensembl.org/biomart/martview">www.ensembl.org/biomart/martview</a>" it will work. </span></div><div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(4, 51, 255);"><span style="color:#942193;"><br></span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(4, 51, 255);"><span style="color:#942193;"><br></span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(4, 51, 255);"><span style="color:#942193;">> </span>listMarts(host="<a rel="nofollow" target="_blank" href="http://www.ensembl.org/biomart/martservice/">www.ensembl.org/biomart/martservice/</a>")</div><div style="margin: 0px; font-size: 11px; font-family: Monaco;">
biomart version</div><div style="margin: 0px; font-size: 11px; font-family: Monaco;">1 ENSEMBL_MART_ENSEMBL Ensembl Genes 71</div><div style="margin: 0px; font-size: 11px; font-family: Monaco;">2 ENSEMBL_MART_SNP Ensembl Variation 71</div><div style="margin: 0px; font-size: 11px; font-family: Monaco;">3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 71</div><div style="margin: 0px; font-size: 11px; font-family: Monaco;">4 ENSEMBL_MART_VEGA Vega 51</div><div style="margin: 0px; font-size: 11px; font-family: Monaco;">5 REACTOME REACTOME (CSHL US)</div><div style="margin: 0px; font-size: 11px; font-family: Monaco;">6 pride PRIDE (EBI
UK)</div></div><div><br></div><div><br></div><div>Hope that helps</div><div>Regards</div><div>Rhoda</div><div><font face="times new roman, new york, times, serif"><span style="font-size:16px;"><br></span></font></div><div><font face="times new roman, new york, times, serif"><span style="font-size:16px;"><br></span></font><div><div><div>On 8 May 2013, at 13:49, Mohammad Tanvir Ahamed <<a rel="nofollow" ymailto="mailto:mashranga@yahoo.com" target="_blank" href="mailto:mashranga@yahoo.com">mashranga@yahoo.com</a>> wrote:</div><br class="yiv6221284387Apple-interchange-newline"><blockquote type="cite"><div style="background-color: rgb(255, 255, 255); font-family: 'times new roman', 'new york', times, serif; font-size: 12pt;"><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt;"><span>Hi Rhoda, </span></div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 16px; background-color:
transparent; font-style: normal;"><span>Thank for your reply. </span></div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 16px; background-color: transparent; font-style: normal;"><span>I have also mail this problem to BioMart mail list and waiting for reply . </span></div><div style="background-color:transparent;"><span>According to your suggestion , When i run the commend i get the following error </span></div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 16px; background-color: transparent; font-style: normal;"><span><br></span></div><div style="background-color:transparent;"><span><div style="background-color:transparent;">> ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl",host="<a rel="nofollow" target="_blank" href="http://www.ensembl.org/biomart/martview">www.ensembl.org/biomart/martview</a>")</div><div
style="background-color:transparent;"><br></div><div style="background-color:transparent;">Entity 'nbsp' not defined</div><div style="background-color:transparent;">Entity 'hellip' not defined</div><div style="background-color:transparent;">Entity 'hellip' not defined</div><div style="background-color:transparent;">Entity 'hellip' not defined</div><div style="background-color:transparent;">Entity 'hellip' not defined</div><div style="background-color:transparent;">Entity 'hellip' not defined</div><div style="background-color:transparent;">Entity 'hellip' not defined</div><div style="background-color:transparent;">Entity 'hellip' not defined</div><div style="background-color:transparent;">Entity 'nbsp' not defined</div><div style="background-color:transparent;">Entity 'nbsp' not defined</div><div style="background-color:transparent;">Entity 'copy' not defined</div><div style="background-color:transparent;">Entity 'nbsp' not defined</div><div
style="background-color:transparent;">Entity 'nbsp' not defined</div><div style="background-color:transparent;">Entity 'nbsp' not defined</div><div style="background-color:transparent;">Error: 1: Entity 'nbsp' not defined</div><div style="background-color:transparent;">2: Entity 'hellip' not defined</div><div style="background-color:transparent;">3: Entity 'hellip' not defined</div><div style="background-color:transparent;">4: Entity 'hellip' not defined</div><div style="background-color:transparent;">5: Entity 'hellip' not defined</div><div style="background-color:transparent;">6: Entity 'hellip' not defined</div><div style="
background-color:transparent;">7: Entity 'hellip' not defined</div><div style="background-color:transparent;">8: Entity 'hellip' not defined</div><div style="background-color:transparent;">9: Entity 'nbsp' not defined</div><div style="background-color:transparent;">10: Entity 'nbsp' not defined</div><div style="background-color:transparent;">11: Entity 'copy' not defined</div><div style="background-color:transparent;">12: Entity 'nbsp' not defined</div><div style="background-color:transparent;">13: Entity 'nbsp' not defined</div><div style="background-color:transparent;">14: Entity 'nbsp' not defined</div></span></div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt;"></div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt;"> </div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt;"><span style="font-family: 'times new roman'; font-weight:
bold;"><i>/.......Tanvir Ahamed</i></span><br><br><blockquote style="border-left-width:2px;border-left-style:solid;border-left-color:rgb(16, 16, 255);margin-left:5px;margin-top:5px;padding-left:5px;"> <div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt;"> <div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt;"> <div dir="ltr"> <hr size="1"> <font size="2" face="Arial"> <b><span style="font-weight:bold;">From:</span></b> Rhoda Kinsella <<a rel="nofollow" ymailto="mailto:rhoda@ebi.ac.uk" target="_blank" href="mailto:rhoda@ebi.ac.uk">rhoda@ebi.ac.uk</a>><br> <b><span style="font-weight:bold;">To:</span></b> Mohammad Tanvir Ahamed <<a rel="nofollow" ymailto="mailto:mashranga@yahoo.com" target="_blank" href="mailto:mashranga@yahoo.com">mashranga@yahoo.com</a>>; Ensembl developers list <<a rel="nofollow" ymailto="mailto:dev@ensembl.org" target="_blank"
href="mailto:dev@ensembl.org">dev@ensembl.org</a>> <br> <b><span style="font-weight:bold;">Sent:</span></b> Wednesday, 8 May 2013, 14:05<br> <b><span style="font-weight:bold;">Subject:</span></b> Re: [ensembl-dev] Problem with biomaRt::getSequence<br> </font> </div> <div class="yiv6221284387y_msg_container"><br><div id="yiv6221284387">Hi Tanvir Ahamed,<div>I suspect that
you are running your biomaRt query against the BioMart central portal at <a rel="nofollow" target="_blank" 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 rel="nofollow" target="_blank" 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 rel="nofollow" target="_blank" href="http://www.biomart.org/">www.biomart.org</a> issues you should email their mailing list (<a rel="nofollow" ymailto="mailto:users@biomart.org" target="_blank" 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 rel="nofollow" ymailto="mailto:mashranga@yahoo.com" target="_blank" href="mailto:mashranga@yahoo.com">mashranga@yahoo.com</a>> wrote:</div><br
class="yiv6221284387Apple-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;"><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 rel="nofollow" ymailto="mailto:Dev@ensembl.org" target="_blank" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>Posting guidelines and subscribe/unsubscribe info: <a rel="nofollow" target="_blank" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog: <a rel="nofollow" target="_blank" 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="yiv6221284387Apple-interchange-newline">
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<br></div></div><br><br></div> </div> </div> </blockquote></div> </div></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="yiv6221284387Apple-interchange-newline">
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