Hi Hiram,
We use UCSC genome browser mirror system. We already updated /gbgb/hg18/ and /mysql/hg18/ successfully yesterday, but when Search 'uc001acj.1', see below: UCSC Genome Browser on Human Mar. 2006 Assembly move zoom in zoom out position/search size 310,923 bp. We still encounter error: "Sorry, couldn't locate uc001acj.1 in genome database". Our UCSC genome browser mirror version is CGI_VERSION "198". Please help Thanks & Regards Wuqi -----Original Message----- From: Hiram Clawson [mailto:[email protected]] Sent: Thursday, April 09, 2009 12:37 AM To: OW Jack Ling Cc: WANG Wuqi; [email protected]; Atif SHAHAB; LEE Seow Eng Subject: Re: Search errors in GBrowser OW Jack Ling wrote: > Hi Hiram, > > The /gbdb was last rsync on Aug 08 and we are referring to hg18 > assembly. > > Our queries is that if we use the exact word 'uc001acj.1' in the > position search in the Browser, we got an error mentioned by Wuqi but we > are able to find the 'uc001acj.1' in the knownGene table in Hg18 > database. Also if we go to the browser and search > "chr1:938,741-939,777", we do see the ' uc001acj.1' in the link and > description when clicking on it. Pls see attached for the print screen > of it. > Attached below is the list of 734 hg18 tables that have updated since August 08. You should update your database, your /gbdb/ filesystem, and your genome browser source code. --Hiram affyAllExonProbes.MYI affyExonTissues.MYI affyExonTissuesGs.MYI affyExonTissuesGsExps.MYI affyExonTissuesGsMedian.MYI affyExonTissuesGsMedianDist.MYI affyExonTissuesGsMedianExps.MYI agilentCgh105a.MYI agilentCgh1x1m.MYI agilentCgh244a.MYI agilentCgh2x400k.MYI agilentCgh44k.MYI agilentCgh4x180k.MYI agilentCgh8x60k.MYI agilentCnv2x400k.MYI all_est.MYI all_mrna.MYI author.MYI bioCycMapDesc.MYI bioCycPathway.MYI ccdsGene.MYI ccdsInfo.MYI ccdsKgMap.MYI cds.MYI ceBlastTab.MYI cell.MYI cgapAlias.MYI cgapBiocDesc.MYI cgapBiocPathway.MYI chr*_chainOryLat2.MYI chr*_chainOryLat2Link.MYI chr*_chainTaeGut1.MYI chr*_chainTaeGut1Link.MYI chr*_cox_hap1_chainOryLat2.MYI chr*_cox_hap1_chainOryLat2Link.MYI chr*_cox_hap1_chainTaeGut1.MYI chr*_cox_hap1_chainTaeGut1Link.MYI chr*_cox_hap1_est.MYI chr*_cox_hap1_intronEst.MYI chr*_cox_hap1_mrna.MYI chr*_cox_hap1_rmskRM327.MYI chr*_est.MYI chr*_h2_hap1_chainOryLat2.MYI chr*_h2_hap1_chainOryLat2Link.MYI chr*_h2_hap1_chainTaeGut1.MYI chr*_h2_hap1_chainTaeGut1Link.MYI chr*_h2_hap1_est.MYI chr*_h2_hap1_mrna.MYI chr*_h2_hap1_rmskRM327.MYI chr*_intronEst.MYI chr*_mrna.MYI chr*_qbl_hap2_chainOryLat2.MYI chr*_qbl_hap2_chainOryLat2Link.MYI chr*_qbl_hap2_chainTaeGut1.MYI chr*_qbl_hap2_chainTaeGut1Link.MYI chr*_qbl_hap2_est.MYI chr*_qbl_hap2_intronEst.MYI chr*_qbl_hap2_mrna.MYI chr*_qbl_hap2_rmskRM327.MYI chr*_rmskRM327.MYI description.MYI development.MYI dgv.MYI dmBlastTab.MYI eioJcviNASNeg.MYI eioJcviNASPos.MYI encodeTbaAlignDec07.MYI encodeTbaBinConsDec07.MYI encodeTbaChaiConsDec07.MYI encodeTbaSummaryDec07.MYI ensGene.MYI ensGtp.MYI ensPep.MYI estOrientInfo.MYI extFile.MYI foldUtr3.MYI foldUtr5.MYI fox2ClipSeq.MYI fox2ClipSeqDensityForwardStrand.MYI fox2ClipSeqDensityReverseStrand.MYI gbCdnaInfo.MYI gbExtFile.MYI gbLoaded.MYI gbMiscDiff.MYI gbSeq.MYI gbStatus.MYI gbWarn.MYI geneName.MYI grp.MYI hgFindSpec.MYI hgdpGeo.MYI imageClone.MYI keggPathway.MYI keyword.MYI kg3ToKg4.MYI kgAlias.MYI kgColor.MYI kgProtAlias.MYI kgSpAlias.MYI kgTargetAli.MYI kgXref.MYI kiddEichlerDiscAbc10.MYI kiddEichlerDiscAbc11.MYI kiddEichlerDiscAbc12.MYI kiddEichlerDiscAbc13.MYI kiddEichlerDiscAbc14.MYI kiddEichlerDiscAbc7.MYI kiddEichlerDiscAbc8.MYI kiddEichlerDiscAbc9.MYI kiddEichlerDiscG248.MYI kiddEichlerToNcbi.MYI knownGene.MYI knownGeneOld3.MYI knownGenePep.MYI knownToEnsembl.MYI knownToTreefam.MYI library.MYI lsSnpPdb.MYI mgcFullMrna.MYI mgcGenes.MYI mmBlastTab.MYI mrnaClone.MYI mrnaOrientInfo.MYI multiz44way.MYI multiz44wayFrames.MYI multiz44waySummary.MYI nestedRepeatsRM327.MYI netOryLat2.MYI netTaeGut1.MYI omimGene.MYI omimGeneMap.MYI omimMorbidMap.MYI omimToKnownCanonical.MYI orfeomeGenes.MYI orfeomeMrna.MYI organism.MYI pfamDesc.MYI pgVenter.MYI pgWatson.MYI pgYh1.MYI pgYoruban3.MYI phastCons44way.MYI phastCons44wayPlacental.MYI phastCons44wayPrimates.MYI phastConsElements44way.MYI 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wgEncodeBroadChipSeqPeaksNhekH3k4me2.MYI wgEncodeBroadChipSeqPeaksNhekH3k4me3.MYI wgEncodeBroadChipSeqPeaksNhekH3k9ac.MYI wgEncodeBroadChipSeqPeaksNhekH3k9me1.MYI wgEncodeBroadChipSeqPeaksNhekH4k20me1.MYI wgEncodeBroadChipSeqPeaksNhekPol2b.MYI wgEncodeBroadChipSeqRawSignalRep1Gm12878Control.MYI wgEncodeBroadChipSeqRawSignalRep1Gm12878Ctcf.MYI wgEncodeBroadChipSeqRawSignalRep1Gm12878H3k27ac.MYI wgEncodeBroadChipSeqRawSignalRep1Gm12878H3k27me3.MYI wgEncodeBroadChipSeqRawSignalRep1Gm12878H3k36me3.MYI wgEncodeBroadChipSeqRawSignalRep1Gm12878H3k4me1.MYI wgEncodeBroadChipSeqRawSignalRep1Gm12878H3k4me2.MYI wgEncodeBroadChipSeqRawSignalRep1Gm12878H3k4me3.MYI wgEncodeBroadChipSeqRawSignalRep1Gm12878H3k9ac.MYI wgEncodeBroadChipSeqRawSignalRep1Gm12878H4k20me1.MYI wgEncodeBroadChipSeqRawSignalRep2Gm12878Control.MYI wgEncodeBroadChipSeqRawSignalRep2Gm12878Ctcf.MYI wgEncodeBroadChipSeqRawSignalRep2Gm12878H3k27ac.MYI wgEncodeBroadChipSeqRawSignalRep2Gm12878H3k27me3.MYI wgEncodeBroadChipSeqRawSignalRep2Gm12878H3k36me3.MYI wgEncodeBroadChipSeqRawSignalRep2Gm12878H3k4me1.MYI wgEncodeBroadChipSeqRawSignalRep2Gm12878H3k4me2.MYI wgEncodeBroadChipSeqRawSignalRep2Gm12878H3k4me3.MYI wgEncodeBroadChipSeqRawSignalRep2Gm12878H3k9ac.MYI wgEncodeBroadChipSeqRawSignalRep2Gm12878H4k20me1.MYI wgEncodeBroadChipSeqSignalGm12878Control.MYI wgEncodeBroadChipSeqSignalGm12878Ctcf.MYI wgEncodeBroadChipSeqSignalGm12878H3k27ac.MYI wgEncodeBroadChipSeqSignalGm12878H3k27me3.MYI wgEncodeBroadChipSeqSignalGm12878H3k36me3.MYI wgEncodeBroadChipSeqSignalGm12878H3k4me1.MYI wgEncodeBroadChipSeqSignalGm12878H3k4me2.MYI wgEncodeBroadChipSeqSignalGm12878H3k4me3.MYI wgEncodeBroadChipSeqSignalGm12878H3k9ac.MYI wgEncodeBroadChipSeqSignalGm12878H4k20me1.MYI wgEncodeBroadChipSeqSignalHuvecControl.MYI wgEncodeBroadChipSeqSignalHuvecCtcf.MYI wgEncodeBroadChipSeqSignalHuvecH3k27ac.MYI wgEncodeBroadChipSeqSignalHuvecH3k27me3.MYI wgEncodeBroadChipSeqSignalHuvecH3k36me3.MYI wgEncodeBroadChipSeqSignalHuvecH3k4me1.MYI wgEncodeBroadChipSeqSignalHuvecH3k4me2.MYI wgEncodeBroadChipSeqSignalHuvecH3k4me3.MYI wgEncodeBroadChipSeqSignalHuvecH3k9ac.MYI wgEncodeBroadChipSeqSignalHuvecH3k9me1.MYI wgEncodeBroadChipSeqSignalHuvecH4k20me1.MYI wgEncodeBroadChipSeqSignalHuvecPol2b.MYI wgEncodeBroadChipSeqSignalK562Control.MYI wgEncodeBroadChipSeqSignalK562Ctcf.MYI wgEncodeBroadChipSeqSignalK562H3k27ac.MYI wgEncodeBroadChipSeqSignalK562H3k27me3.MYI wgEncodeBroadChipSeqSignalK562H3k36me3.MYI wgEncodeBroadChipSeqSignalK562H3k4me1.MYI wgEncodeBroadChipSeqSignalK562H3k4me2.MYI wgEncodeBroadChipSeqSignalK562H3k4me3.MYI wgEncodeBroadChipSeqSignalK562H3k9ac.MYI wgEncodeBroadChipSeqSignalK562H3k9me1.MYI wgEncodeBroadChipSeqSignalK562H4k20me1.MYI wgEncodeBroadChipSeqSignalK562Pol2b.MYI wgEncodeBroadChipSeqSignalNhekControl.MYI wgEncodeBroadChipSeqSignalNhekCtcf.MYI wgEncodeBroadChipSeqSignalNhekH3k27ac.MYI wgEncodeBroadChipSeqSignalNhekH3k27me3.MYI 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xenoRefSeqAli.MYI _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
