Hi Saba, You are right, the command: rsync -avzP --delete --max-delete=20rsync://hgdownload.cse.ucsc.edu/gbdb/ornAna1 /gbdb/ will not update other directories.
Glad to hear that your problem is solved. In general, the cgi logic, mysql databases and external files must be in sync at all time. In your case, genbank.175.0 is out of sync. Please refer to http://genomewiki.ucsc.edu/index.php/Minimal_Browser_Installation for how to keep genbank files in-sync. We have some scripts to automate building and updating browser. These scripts may provide some additional help on updating your browser. These scripts are in the src/product under the kent source tree. Feel free to contact the mail list again if you require further assistance. - Chin PS: We have a genome mirror mail list ([email protected]) specifically for mirror related issues. To subscribe, please visit https://lists.soe.ucsc.edu/mailman/listinfo/genome-mirror. To see the collection of prior postings to the list, visit the Genome-mirror Archives: http://lists.soe.ucsc.edu/pipermail/genome-mirror To search the archives, visit the contact page: http://genome.ucsc.edu/contacts.html ----- Original Message ----- From: "Saba Sajjadian" <[email protected]> To: [email protected] Sent: Monday, August 23, 2010 2:55:21 PM GMT -08:00 US/Canada Pacific Subject: [Genome] Problem with /gbdb/genbank/ 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
