Request for Session 5 Code

[ch Govardhan]

Hello ,

I have located the code for every session except Session 5. Could you please provide the code for Session 5 or tell me where I can find it?

[Martin Krzywinski]

Hi, 

Session 5 of the course

https://circos.ca/documentation/course/

asks you to replicate this image

This image and config is bundled with the Circos distribution as a way to test that your installation is working.

You'll find all the data and conf files in example/

m

Martin Krzywinski

science + art

https://mk.bcgsc.ca

On Wed, Dec 3, 2025 at 12:33 PM ch Govardhan <govardhanc...@gmail.com> wrote:

Hello ,

I have located the code for every session except Session 5. Could you please provide the code for Session 5 or tell me where I can find it?

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[ramy qabel]

  *** CIRCOS ERROR ***

      cwd: /home/phagegenome/circos-0.69-9/Escherichia

      command: /home/phagegenome/miniconda3/bin/circos -conf
      Escherichia_NODE_11_length_130605_cov_14.558217_pilon_individual.circos.conf

  CONFIGURATION FILE ERROR

  Configuration parameter [svg_font_scale] in parent block [_root] has been
  defined more than once in the block shown above, and has been interpreted as a
  list. This is not allowed. Did you forget to comment out an old value of the
  parameter?

  If you are having trouble debugging this error, first read the best practices
  tutorial for helpful tips that address many common problems

      http://www.circos.ca/documentation/tutorials/reference/best_practices

  The debugging facility is helpful to figure out what's happening under the
  hood

      http://www.circos.ca/documentation/tutorials/configuration/debugging

  If you're still stumped, get support in the Circos Google Group.

      http://groups.google.com/group/circos-data-visualization

  Please include this error, all your configuration, data files and the version
  of Circos you're running (circos -v). Do not email me directly -- please use
  the group.

  Stack trace:
 at /home/phagegenome/miniconda3/bin/../lib/Circos/Error.pm line 425.
        Circos::Error::fatal_error("configuration", "multivalue", "svg_font_scale", "_root") called at /home/phagegenome/miniconda3/bin/../lib/Circos/Configuration.pm line 441
        Circos::Configuration::check_multivalues(HASH(0xeb7a350), undef) called at /home/phagegenome/miniconda3/bin/../lib/Circos/Configuration.pm line 294
        Circos::Configuration::populateconfiguration("configfile", "Escherichia_NODE_11_length_130605_cov_14.558217_pilon_individ"..., "_cwd", "/home/phagegenome/circos-0.69-9/Escherichia", "debug_group", "output,summary", "_argv", "-conf Escherichia_NODE_11_length_130605_cov_14.558217_pilon_i"...) called at /home/phagegenome/miniconda3/bin/../lib/Circos.pm line 153
        Circos::run("Circos", "configfile", "Escherichia_NODE_11_length_130605_cov_14.558217_pilon_individ"..., "_argv", "-conf Escherichia_NODE_11_length_130605_cov_14.558217_pilon_i"..., "_cwd", "/home/phagegenome/circos-0.69-9/Escherichia") called at /home/phagegenome/miniconda3/bin/circos line 536
phagegenome@DESKTOP-QQBHUA8:~/circos-0.69-9/Escherichia$ I need a solution for this problem 

[Martin]

>Configuration parameter [svg_font_scale] in parent block [_root] has been
> defined more than once in the block shown above, and has been interpreted as a

> list. This is not allowed. Did you forget to comment out an old value of the
> parameter?

You have defined this parameter twice in the root of the config (i.e., not inside a <block>...</block>). 

Check your config. 

If you've used <<include FILE>> then it might be that the parameter is defined in both the the included file.

e.g.

svg_font_scale = 1

<<include file.conf>>

#file.conf

...

svg_font_scale =1