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
