Hello Tiandao, This is a MySQL option problem about "load local"
http://dev.mysql.com/doc/refman/5.1/en/load-data-local.html The MySQL server needs to be started with the option to allow this type of statement. When you encounter mySQL errors, the resource http://dev.mysql.com may be a good place to start, especially for well documented browser tasks, as it is unlikely to be a problem with the browser source. We hope this helps! Tanks, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 5/7/10 7:03 PM, Tiandao Li wrote: > Hi, > > I followed all the steps from online help without any error mesg except the > next one: > > [l...@research hiv]$ /opt/kent/hgLoadSqlTab HIV5LTR chromInfo > /home/litd/bin/kent/src/hg/lib/chromInfo.sql bed/chromInfo/chromInfo.tab > Scanning through 1 files > Can't start query: > LOAD DATA INFILE '/home/litd/hiv/bed/chromInfo/chromInfo.tab' INTO TABLE > chromInfo > > mySQL error 13: Can't get stat of > '/home/litd/hiv/bed/chromInfo/chromInfo.tab' (Errcode: 13) > > This may be related to the chromInfo needed, but for my virus no chrom info. > > In step 11, online example > > INSERT INTO dbDb > (name, description, nibPath, organism, > defaultPos, active, orderKey, genome, scientificName, > htmlPath, hgNearOk, hgPbOk, sourceName) > VALUES > ("abcDef1", "July 2008", "/gbdb/abcDef1", "A. organism", > "chr1:10459784-10469783", 1, 123, "A. organism", "Genus species", > "/gbdb/abcDef1/html/description.html", 0, 0, "new genome version 1.0"); > > I left defaultPos blank. After building genome database, I can find new > created database, however, when I click 'submit', it showed error > > Error(s): > Please go back and enter a coordinate rangeor a search term in the > "position" field. > For example: chr22:20100000-20200000. > > I don't know how to put chr info in database, or just put a fake one, such > as chr1:1-10000? > > Any help? > > Thanks!!! > > > On Fri, May 7, 2010 at 5:08 PM, Hiram Clawson<[email protected]> wrote: > >> >> Please examine step 5 of the instructions at: >> >> http://genomewiki.ucsc.edu/index.php/Building_a_new_genome_database >> >> Should be something like this: >> >> $ twoBitInfo yourGenome.2bit stdout | sort -k2nr> chrom.sizes >> $ awk '{printf "%s\t%s\t/path/to/yourGenome.2bit\n", $1,$2}' chrom.sizes> >> chromInfo.tab >> $ hgLoadSqlTab yourGenome chromInfo /path/to/kent/src/hg/lib/chromInfo.sql >> chromInfo.tab >> >> --Hiram >> >> Tiandao Li wrote: >> >>> Hi, >>> >>> We have a custom genome of virus about 10K, I followed the online doc >>> http://genomewiki.ucsc.edu/index.php/Building_a_new_genome_database to >>> build >>> a database. The question is no chromInfo available for this virus, how >>> could >>> I load the chromInfo table >>> >>> >>> [l...@research hiv]$ /opt/kent/hgLoadSqlTab HIV5LTR chromInfo >>> /home/litd/bin/kent/src/hg/lib/chromInfo.sql bed/chromInfo/chromInfo.tab >>> Scanning through 1 files >>> Can't start query: >>> LOAD DATA INFILE '/home/litd/hiv/bed/chromInfo/chromInfo.tab' INTO >>> TABLE >>> chromInfo >>> >>> mySQL error 13: Can't get stat of >>> '/home/litd/hiv/bed/chromInfo/chromInfo.tab' (Errcode: 13) >>> >>> >>> What should I do? And how to handle defaultPos in dbDbInsert.sql file? >>> >>> Thanks, >>> >>> >>> Tiandao >>> _______________________________________________ >>> Genome maillist - [email protected] >>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >>> >>> >> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
