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
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> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>
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