help
淚鱼
Brian Lee
Dear Penny,
Thank you for using the UCSC Genome Browser and your question about netClass usage.
The tDb and qDb items, where you have entered maskt and maskq, are meant to represent MySQL databases that should exist in a MySQL server. What you have entered, maskt and maskq, do not exist, explaining the error you are seeing, "Unknown database 'maskt'.
In the example on the wikipage (momentarily unavailable), netClass -noAr noClass.net ci2 cioSav2 cioSav2.net, the "ci2" and "cioSav2" represent two assemblies that netClass accesses on a MySQL server.
To see more about using the public access MySQL database, and adding a .hg.conf file, see this page: http://genome.ucsc.edu/goldenPath/help/mysql.html Example usage: mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -Ne 'show tables' ci2;
It may be helpful to note that the cioSav2 assembly, in the above example, is one that has been added to the development MySQL environment, http://genome-preview.ucsc.edu/cgi-bin/hgTracks?db=cioSav2, but is not available from the Public MySQL server.
We have mailing list archives where people using netClass have asked questions that may have helpful answers for your situation. Please review this answer and search the google group archive for similar questions before mailing the list again:
https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/BYb35wDEwKI/-PKU8C9VI_MJ
Note the information in the above previous answer regarding If you are aligning assemblies that are not hosted by UCSC, that you could set up your own MySQL server and put information for accessing it into a .hg.conf file in your home directory, or skip this netClass step of the alignment process.
Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please first search the google group archive for similar questions before mailing the list at gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
All the best,
Brian Lee
UCSC Genome Bioinformatics Group
--
lpp
excuse me,when I used chainMergeSort (command:chainMergeSort chain/*.chain >all.chain, the chain directory contains chain files),
it shows that Argument list too long,what should I do ?
Hiram Clawson
find ./chain -name "*.chain" | chainMergeSort -inputList=stdin \
| gzip -c > all.chain.gz
On 3/26/15 9:56 PM, lpp wrote:
> dear sir,
> excuse me,when I used chainMergeSort (command:chainMergeSort chain/*.chain >all.chain, the chain directory contains chain files),
> it shows that Argument list too long,what should I do ?
>
>
>
>
>
> 发件人: "Brian Lee"<bria...@soe.ucsc.edu>;
> 发送时间: 2015年2月17日(星期二) 凌晨3:00
> 收件人: "淚鱼"<liang_p...@163.com>;
> 抄送: "genome"<gen...@soe.ucsc.edu>;
> 主题: Re: [genome] help
>
>
>
>
> Dear Penny,
>
> Thank you for using the UCSC Genome Browser and your question about netClass usage.
>
> The tDb and qDb items, where you have entered maskt and maskq, are meant to represent MySQL databases that should exist in a MySQL server. What you have entered, maskt and maskq, do not exist, explaining the error you are seeing, "Unknown database 'maskt'.
>
> In the example on the wikipage (momentarily unavailable), netClass -noAr noClass.net ci2 cioSav2 cioSav2.net, the "ci2" and "cioSav2" represent two assemblies that netClass accesses on a MySQL server.
>
> To see more about using the public access MySQL database, and adding a .hg.conf file, see this page: http://genome.ucsc.edu/goldenPath/help/mysql.html Example usage: mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -Ne 'show tables' ci2;
>
> It may be helpful to note that the cioSav2 assembly, in the above example, is one that has been added to the development MySQL environment, http://genome-preview.ucsc.edu/cgi-bin/hgTracks?db=cioSav2, but is not available from the Public MySQL server.
>
> We have mailing list archives where people using netClass have asked questions that may have helpful answers for your situation. Please review this answer and search the google group archive for similar questions before mailing the list again:
> https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/BYb35wDEwKI/-PKU8C9VI_MJ
>
> Note the information in the above previous answer regarding If you are aligning assemblies that are not hosted by UCSC, that you could set up your own MySQL server and put information for accessing it into a .hg.conf file in your home directory, or skip this netClass step of the alignment process.
>
> Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please first search the google group archive for similar questions before mailing the list at gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
>
> All the best,
>
> Brian Lee
> UCSC Genome Bioinformatics Group
>
> On Sat, Feb 14, 2015 at 10:07 PM, 淚鱼 <liang_p...@163.com> wrote:
> ---penny
>
>
>
>
> --
>