hgLoadSqlTab and hgGoldGI error in building a new genome database
张升
My name is zhangsheng,I'm from Chinese Academy of Science.
I'd like to build a new genome database in my local UCSC genome browser,and I fully follow the instruction at
http://genomewiki.ucsc.edu/index.php/Building_a_new_genome_database
However in step 8 and 9,I'm stuck.Here is my commands:
zhangsheng@zhangsheng-Precision-WorkStation-T7500:~$ hgLoadSqlTab Rice chromInfo /home/zhangsheng/kent/src/hg/lib/chromInfo.sql /gbdb/Rice/bed/chromInfo/chromInfo.tab
SQL_CONNECT 112 localhost Rice localhost root
SQL_TIME 112 localhost Rice 0.003s
SQL_QUERY 112 localhost Rice NOSQLINJ SELECT 1 FROM tableList LIMIT 0
SQL_TIME 112 localhost Rice 0.000s
SQL_TABLE_NOT_EXISTS 112 localhost Rice tableList
SQL_FAILOVER_NO_TABLE_CACHE_FOR_DB 112 localhost Rice Rice
SQL_QUERY 112 localhost Rice NOSQLINJ SELECT 1 FROM chromInfo LIMIT 0
SQL_FAILOVER 112 localhost Rice db -> slow-db | SELECT 1 FROM chromInfo LIMIT 0
Couldn't connect to database Rice on genome-mysql.cse.ucsc.edu as genomep.
Unknown database 'Rice'
SQL_TOTAL_TIME 8.280s
SQL_TOTAL_QUERIES 2
SQL_DISCONNECT 112 Rice
hgLoadSqlTab: jksql.c:395: monitorEnter: Assertion `monitorEnterTime == 0' failed.
已放弃 (核心已转储)
zhangsheng@zhangsheng-Precision-WorkStation-T7500:~$ hgGoldGapGl Rice /home/zhangsheng/下载/IRGSP/Rice.agp
SQL_CONNECT 123 localhost Rice localhost root
SQL_TIME 123 localhost Rice 0.003s
SQL_QUERY 123 localhost Rice NOSQLINJ SELECT 1 FROM tableList LIMIT 0
SQL_TIME 123 localhost Rice 0.001s
SQL_TABLE_NOT_EXISTS 123 localhost Rice tableList
SQL_FAILOVER_NO_TABLE_CACHE_FOR_DB 123 localhost Rice Rice
SQL_QUERY 123 localhost Rice NOSQLINJ SELECT 1 FROM gold LIMIT 0
SQL_FAILOVER 123 localhost Rice db -> slow-db | SELECT 1 FROM gold LIMIT 0
Couldn't connect to database Rice on genome-mysql.cse.ucsc.edu as genomep.
Unknown database 'Rice'
SQL_TOTAL_TIME 7.737s
SQL_TOTAL_QUERIES 2
SQL_DISCONNECT 123 Rice
hgGoldGapGl: jksql.c:395: monitorEnter: Assertion `monitorEnterTime == 0' failed.
已放弃 (核心已转储)
I don't konw what's wrong with hgLoadSql and hgGoldGapGI,and I can't find any solution in google or genomewiki.
Could you please help me?
Regards,
Zhangsheng
Jonathan Casper
Hello Zhangsheng,
Thank you for your question about adding a new genome database to your mirror server. From the error output you provided, it looks like the problem is probably due to a line in your ~/.hg.conf file. Open that file and look for a line that looks like "showTableCache=xxxx". Please delete that line. hgLoadSql and hgGoldGapGI should then work correctly. If you copied your ~/.hg.conf file from the files used by the Genome Browser in a Box (GBiB - http://genome.ucsc.edu/goldenPath/help/gbib.html), please be careful. Some of the settings in GBiB files are specifically for GBiB and are not appropriate for other mirror sites.
You may also be interested in creating an assembly hub for your new genome. Assembly hubs are a tool that we created to make it easier to add new genomes to mirror sites, as well as to view your own genomes on our public website athttp://genome.ucsc.edu. More information about how to create an assembly hub is available at http://genomewiki.ucsc.edu/index.php/Assembly_Hubs and http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html. You may also be interested in the answer to this mailing list question: https://groups.google.com/a/soe.ucsc.edu/d/topic/genome/ozSm1vjaxRY/discussion. It gives a bit more information about the requirements for creating an assembly hub.
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.
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Jonathan Casper
UCSC Genome Bioinformatics Group
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