max ideograms exceeded

[Daniel Jackson]

Hi all,

Am learning how to use Circos and would like to challenge it by plotting my entire dataset, 1,488 ideograms - I realise it will probably look like a spaghetti salad but I'm stubborn ;-).

When I do this I get a sensible warning that says "You have asked to draw [1488] ideograms, but the maximum is currently set at [0]. To increase this number change max_ideograms in etc/housekeeping.conf."

That's the first thing I do, but I keep getting the same error. I guess I'm missing something here.....?

Thanks in advance for any Circos wisdom!

[Daniel Jackson]

Hi all,

I cracked this one myself. I should have explained the situation more thoroughly - I'm actually using Circoletto (a script that employs circos to visualise BLAST results - see http://www.ncbi.nlm.nih.gov/pubmed/20736339). A local installation of circoletto comes with its own configuration files which need to be modified if you want to visualise more than the default number of ideograms. Simply modify the  /circoletto/conf4offline/housekeeping.conf file within the circoletto distribution.

Cheers,

Dan

[Yongqing Jiang]

Hi Dan,

I got the same error message when I used circoletto. However when I check the housekeeping.conf file in its distribution, I cannot find the corresponding commends. So I tried insert a statement in this file, "max_ideogram = 200". But, it still gave me the same error message. Can you please tell me how you modified this housekeeping file?

regards,

yongqing 

在 2013年10月24日星期四UTC+11下午9时28分21秒，Daniel Jackson写道：

[Martin Krzywinski]

Yes, there is a maximum number of ideograms that is set in etc/housekeeping.conf. Comment this out, or increase the value of the parameter.

Yongqing -- are you sure that you're importing the housekeeping file from circos.conf, like this

<<include etc/housekeeping.conf>>

Add -cdump to the circos command and grep for max_ideogram

circos ... -cdump | grep max_ideogram

This will dump all configuration parameter values and return the line that max_ideogram appears on.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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