Hi Wuqi, The 'genbank.168.0' file no longer exists here. To correct the error, update the tables from:
ftp://hgdownload.cse.ucsc.edu/goldenPath/mm8/database/ Specifically, you need new versions of the following tables: all_est all_mrna author ccdsGene ccdsInfo ccdsKgMap cds cell chr10_est chr10_intronEst chr10_mrna chr10_random_est chr10_random_intronEst chr10_random_mrna chr11_est chr11_intronEst chr11_mrna chr12_est chr12_intronEst chr12_mrna chr13_est chr13_intronEst chr13_mrna chr13_random_est chr13_random_intronEst chr13_random_mrna chr14_est chr14_intronEst chr14_mrna chr15_est chr15_intronEst chr15_mrna chr15_random_est chr15_random_intronEst chr15_random_mrna chr16_est chr16_intronEst chr16_mrna chr17_est chr17_intronEst chr17_mrna chr17_random_est chr17_random_intronEst chr17_random_mrna chr18_est chr18_intronEst chr18_mrna chr19_est chr19_intronEst chr19_mrna chr1_est chr1_intronEst chr1_mrna chr1_random_est chr1_random_intronEst chr1_random_mrna chr2_est chr2_intronEst chr2_mrna chr3_est chr3_intronEst chr3_mrna chr4_est chr4_intronEst chr4_mrna chr5_est chr5_intronEst chr5_mrna chr5_random_est chr5_random_intronEst chr5_random_mrna chr6_est chr6_intronEst chr6_mrna chr7_est chr7_intronEst chr7_mrna chr7_random_est chr7_random_intronEst chr7_random_mrna chr8_est chr8_intronEst chr8_mrna chr8_random_est chr8_random_intronEst chr8_random_mrna chr9_est chr9_intronEst chr9_mrna chr9_random_est chr9_random_intronEst chr9_random_mrna chrM_est chrM_intronEst chrM_mrna chrUn_random_est chrUn_random_intronEst chrUn_random_mrna chrX_est chrX_intronEst chrX_mrna chrX_random_est chrX_random_intronEst chrX_random_mrna chrY_est chrY_intronEst chrY_mrna chrY_random_est chrY_random_intronEst chrY_random_mrna description development estOrientInfo gbCdnaInfo gbExtFile gbLoaded gbMiscDiff gbSeq gbStatus gbWarn geneName imageClone keyword library mgcFullMrna mgcGenes mrnaClone mrnaOrientInfo organism productName refFlat refGene refLink refSeqAli refSeqStatus refSeqSummary sex source tissue xenoMrna xenoRefFlat xenoRefGene xenoRefSeqAli -- Brooke Rhead UCSC Genome Bioinformatics Group WANG Wuqi wrote on 1/28/10 10:25 PM: > Hi Brooke Rhead, > > When our users browse the tracks of mm8 to encounter problems, > I find that the directory 'genbank.168.0' is empty. > This may be rsync unsuccessful at that time. > > We have from 'genbank.162.0' to 'genbank.174.0', only missing 'genbank.168.0', > If we can download this data, this will solve users' problems. > > Thanks & Regards > > Wuqi > > > -----Original Message----- > From: Brooke Rhead [mailto:[email protected]] > Sent: Friday, January 29, 2010 11:46 AM > To: WANG Wuqi > Cc: [email protected] > Subject: Re: [Genome] How to dwonload genbank data 'genbank.168.0' ? > > > Hi Wuqi, > > You are correct: we only keep the most current genbank files. GenBank > data files and many tables (such as gbLoaded, gbStatus, refGene, etc.) > are updated frequently. Both the files AND the tables need to be > up-to-date in order for the Genome Browser to work properly. It sounds > like you need to update your tables so that they work with the latest > (genbank.175.0) data files. > > Is there some reason you specifically need the 'genbank.168.0' version > of the data files? > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > On 01/28/10 19:00, WANG Wuqi wrote: >> Hi Brooke Rhead, >> >> Thanks for your email. >> >> In fact, there is NOT 'genbank.168.0' in ftp server >> ftp://hgdownload.cse.ucsc.edu/. >> >> Currently, only FTP directory has the following data, >> >> FTP directory /gbdb/genbank/data/processed/ at hgdownload.cse.ucsc.edu >> To view this FTP site in Windows Explorer, click Page, and then click >> Open FTP Site in Windows Explorer. >> -------------------------------------------------------------------------------- >> Up to higher level directory >> >> 01/12/2010 06:33PM Directory . >> 07/20/2008 12:00AM Directory .. >> 01/24/2010 09:20AM Directory genbank.175.0 >> 01/24/2010 09:20AM Directory refseq.38 >> ---------------------------------------------------------------------- >> ---------- >> >> Here, does not have 'genbank.168.0' we wanted, so we can not rsync. >> >> Could you put this data temporarily to ftp server for our download. >> >> >> Thanks & Regards >> >> Wuqi >> >> >> >> >> -----Original Message----- >> From: Brooke Rhead [mailto:[email protected]] >> Sent: Friday, January 29, 2010 2:35 AM >> To: WANG Wuqi >> Cc: 'Hiram Clawson'; [email protected] >> Subject: Re: [Genome] How to dwonload genbank data 'genbank.168.0' ? >> >> >> Hello Wuqi, >> >> The genbank data and the genbank tables need to be kept in sync. You >> may need to update either the files or the tables. Here is a >> previously-answered question on the topic: >> >> https://lists.soe.ucsc.edu/pipermail/genome-mirror/2009-February/00116 >> 2.html >> >> -- >> Brooke Rhead >> UCSC Genome Bioinformatics Group >> >> >> >> WANG Wuqi wrote on 1/27/10 10:15 PM: >>> Hi Hiram, >>> >>> Our ucsc genome mirror side genbank data 'genbank.168.0' is missing, >>> but in ftp://hgdownload.cse.ucsc.edu/, there is not such available >>> data for download. >>> >>> Please give advice >>> >>> >>> Thanks & regards >>> >>> Wuqi >>> >>> _______________________________________________ >>> Genome maillist - [email protected] >>> https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
