Hi Saba, Thank you for your interest in the UCSC Genome Browser. We are currently working on answering your question and hope to have a reply to you soon.
Thank you, Mary --------------------- Mary Goldman UCSC Bioinformatics Group On 8/23/10 2:55 PM, Saba Sajjadian wrote: > Hi, > > We are using mirror browser which is not up to date. It is still v211. > Also the underlying database is pretty old, mysql v. 4.0.27-log which > caused problem during the updates. > We are thinking about setting up a new mysql version, transferring all > the current data to new database and then syncing the browser and > updating it , however; we would like to be able to still have our > browser up and running using the old version until the new version is > completely set up. > > Right now we have couple of problems and I would like to know if it is > possible to solve them on our current version (v211). > > We have recently downloaded new database, ornAna1. I changed the > definition of couple of tables not defined in mysql 4.0, eg. I removed > |CURRENT_TIMESTAMP tags. > I also updated /| gbdb/ornAna1. > > The browser works fine in general, however; when we look for some > specific locations on chromosomes, eg. chrX5, this error appears: > > External file /gbdb/genbank/./data/processed/genbank.175.0/full/mrna.fa > cannot be opened or has wrong size. Old size 2808956882, new size -1, > error No such file or directory > > I would like to know what is causing this problem and how I can solve > it. Just to mention again, that with our current status (current version > of mysql), we can not just update or sync the browser with yours. I need > to download files or make updates one by one, inorder to make sur that > evrything is acceptable in mysql v4.0.27. > > Also when using the following command, are folders other than ornAna1 in > gbdb updated or not? > > rsync -avzP --delete > --max-delete=20rsync://hgdownload.cse.ucsc.edu/gbdb/ornAna1 /gbdb/ > > > It would be great if you could help me with this problem, I know that > the problem is mainly caused by our old version. But any suggestions > would be appreciated. > > Thanks > Saba Sajjadian > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
