<html><head><base href="x-msg://994/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Gavin<div><br></div><div>Have you checked the unmapped objects? These should give you a clue.<div><br></div><div>Also, you might want to check the pipeline output i.e. 'monitor' and the ProbeAlign reports. This should show you see exactly what features you are trying to xref.</div><div><br></div><div><div style="font-size: 12px; ">Nathan Johnson</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 12px; ">Scientific Programmer</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 12px; ">European Bioinformatics Institute</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 12px; ">Wellcome Trust Genome Campus</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 12px; ">Hinxton</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 12px; ">Cambridge CB10 1SD</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 12px; ">Email: <a href="mailto:njohnson@ebi.ac.uk">njohnson@ebi.ac.uk</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 12px; ">TelNo: (+44)1223 492629</div><div style="font-size: 12px; "><br class="khtml-block-placeholder"></div><div style="font-size: 12px; "><br class="khtml-block-placeholder"></div></div><div><br><div><div>On 2 Mar 2011, at 12:31, Oliver, Gavin wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div lang="EN-US" link="blue" vlink="purple"><div class="Section1" style="page: Section1; "><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; line-height: 24px; "><font size="2" face="Arial"><span style="font-size: 10pt; line-height: 19px; font-family: Arial; ">Hi,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; line-height: 24px; "><font size="2" face="Arial"><span style="font-size: 10pt; line-height: 19px; font-family: Arial; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; line-height: 24px; "><font size="2" face="Arial"><span style="font-size: 10pt; line-height: 19px; font-family: Arial; ">I have rerun my array annotations with v61. Everything seemed fine until I looked at the log and saw that perhaps 2 probesets per array have actually mapped to a transcript.<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; line-height: 24px; "><font size="2" face="Arial"><span style="font-size: 10pt; line-height: 19px; font-family: Arial; ">Can you think of something obvious that might have gone wrong here? The log output is below.<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; line-height: 24px; "><font size="2" face="Arial"><span style="font-size: 10pt; line-height: 19px; font-family: Arial; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; line-height: 24px; "><font size="2" face="Arial"><span style="font-size: 10pt; line-height: 19px; font-family: Arial; ">Best,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; line-height: 24px; "><font size="2" face="Arial"><span style="font-size: 10pt; line-height: 19px; font-family: Arial; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; line-height: 24px; "><font size="2" face="Arial"><span style="font-size: 10pt; line-height: 19px; font-family: Arial; ">Gavin<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; line-height: 24px; "><font size="2" face="Arial"><span style="font-size: 10pt; line-height: 19px; font-family: Arial; ">(Nathan I’m posting here incase you didn’t receive my mail)</span></font><font size="2" face="Arial"><span style="font-size: 10pt; line-height: 19px; font-family: Arial; "><o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">:: :: Running on<span class="Apple-converted-space"> </span><a href="http://probe2transcript.pl" style="color: blue; text-decoration: underline; ">probe2transcript.pl</a><span class="Apple-converted-space"> </span>on:<span class="Apple-converted-space"> </span><a href="http://ni-cr-svc-slv.phar-services.com" style="color: blue; text-decoration: underline; ">ni-cr-svc-slv.phar-services.com</a> :: :: - Mon Feb 21 09:01:02 2011<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">:: Params are: --species homo_sapiens --transcript_dbname homo_sapiens_core_61_37f --transcript_host ni-cr-svc-bs3 --transcript_port 3306 --transcript_user root --transcript_pass pass --xref_host ni-cr-svc-bs3 --xref_dbname homo_sapiens_funcgen_61_37f --xref_user root --xref_pass pass --unannotated_5_utr 0 --unannotated_3_utr 0 -annotated_5_prime_extend 0 -annotated_3_prime_extend 0 --threshold 0.000005 --mismatches 2 -vendor AFFY -format AFFY_UTR -arrays ADXOCv1a520630 ADXBRCv2a520413 ADXECv1a520743 ADXLCv1a520538 ADXCRCG2a520319 HG-U133_Plus_2 ADXPCv1a520642 -import_edb<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">:: No probe DB params specified, defaulting to xref params<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">:: :: Checking existing Xrefs :: ::<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">:: You have specified -utr_multiplier and a -3|5_prime_extend, -3|5_prime_extend will override where appropriate<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">:: Setting 3 unannotated UTR length to 0<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">:: Setting 5 unannotated UTR length to 0<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">:: Identified 167074 transcripts for probe mapping<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">:: Allowed mismatches = 2<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">:: Caching arrays per ProbeSet - Mon Feb 21 09:01:21 2011<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">:: Performing overlap analysis. % Complete:<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">:: 0 :: 1 :: 2 :: 3 :: 4 :: 5 :: 6 :: 7 :: 8 :: 9 :: 10 :: 11 :: 12 :: 13 :: 14 :: 15 :: 16 :: 17 :: 18 :: 19 :: 20 :: 21 :: 22 :: 23 :: 24 :: 25 :: 26 :: 27 :: 28 :: 29 :: 30 :: 31 :: 32 :: 33 :: 34 :: 35 :: 36 :: 37 :: 38 :: 39 :: 40 :: 41 :: 42 :: 43 :: 44 :: 45 :: 46 :: 47 :: 48 :: 49 :: 50 :: 51 :: 52 :: 53 :: 54 :: 55 :: 56 :: 57 :: 58 :: 59 :: 60 :: 61 :: 62 :: 63 :: 64 :: 65 :: 66 :: 67 :: 68 :: 69 :: 70 :: 71 :: 72 :: 73 :: 74 :: 75 :: 76 :: 77 :: 78 :: 79 :: 80 :: 81 :: 82 :: 83 :: 84 :: 85 :: 86 :: 87 :: 88 :: 89 :: 90 :: 91 :: 92 :: 93 :: 94 :: 95 :: 96 :: 97 :: 98 :: 99 ::<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">:: Failed to extend 1 transcripts<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">:: Seen 0 5 prime UTRs with and average length of 0<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">:: Seen 0 3 prime UTRs with and average length of 0<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">:: :: Writing ADXOCv1a520630 ADXBRCv2a520413 ADXECv1a520743 ADXLCv1a520538 ADXCRCG2a520319 HG-U133_Plus_2 ADXPCv1a520642 Xrefs :: :: - Mon Feb 21 18:26:37 2011<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">:: Logging probesets that don't map to any transcripts - Mon Feb 21 18:26:37 2011<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">:: Updating 0 promiscuous probesets - Mon Feb 21 18:40:28 2011<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">:: UnmappedObjects loaded: 598994<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">:: ADXBRCv2a520413 distinct ProbeSet xrefs mapped(total xrefs): 1/60856(1)<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">:: ADXOCv1a520630 distinct ProbeSet xrefs mapped(total xrefs): 4/120373(7)<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">:: ADXECv1a520743 distinct ProbeSet xrefs mapped(total xrefs): 4/111012(7)<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">:: ADXLCv1a520538 distinct ProbeSet xrefs mapped(total xrefs): 4/60416(10)<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">:: ADXCRCG2a520319 distinct ProbeSet xrefs mapped(total xrefs): 2/61528(2)<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">:: HG-U133_Plus_2 distinct ProbeSet xrefs mapped(total xrefs): 1/54675(4)<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">:: ADXPCv1a520642 distinct ProbeSet xrefs mapped(total xrefs): 2/121563(2)<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">:: Mapped 9/167074 transcripts - Mon Feb 21 18:40:39 2011<o:p></o:p></span></font></div></div>_______________________________________________<br>Dev mailing list<br><a href="mailto:Dev@ensembl.org" style="color: blue; text-decoration: underline; ">Dev@ensembl.org</a><br><a href="http://lists.ensembl.org/mailman/listinfo/dev" style="color: blue; text-decoration: underline; ">http://lists.ensembl.org/mailman/listinfo/dev</a><br></div></span></blockquote></div><br><div>
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