Circos

Question

[Ahashan]

I have facing problem in circos genome visualization plot making. The result is below is appearing... Each time I modified the command from chatGPT, but it is not working. Can you please help me in this regard. Command in nano Circos.conf plot:

# Circos configuration file

# Karyotype file
karyotype = karyotype_fixed.txt

# Ideogram configuration (showing contigs)
<ideogram>
  show = yes
  radius = 0.90r
  thickness = 10
  fill = yes
</ideogram>

# Gene plot (using circos_genes.txt)
<plot>
  type = scatter
  file = circos_genes.txt
  r0 = 0.7r
  r1 = 0.9r
  color = red
</plot>

# CDS plot (if you want to include CDS from cleaned_gff.gff or another file)
<plot>
  type = scatter
  file = cleaned_gff.gff
  r0 = 0.5r
  r1 = 0.7r
  color = blue
</plot>

Result:

(circos_env) siam@siampc:~/assembly/siam/PROKKA_11252024$ circos -conf circos.conf
debuggroup summary 0.19s welcome to circos v0.69-8 15 Jun 2019 on Perl 5.032001
debuggroup summary 0.19s current working directory /home/siam/assembly/siam/PROKKA_11252024
debuggroup summary 0.19s command /home/siam/anaconda3/envs/circos_env/bin/circos -conf circos.conf
debuggroup summary 0.19s loading configuration from file circos.conf
debuggroup summary 0.19s found conf file circos.conf
Use of uninitialized value within %Circos::Configuration::CONF in split at /home/siam/anaconda3/envs/circos_env/bin/../lib/Circos/Configuration.pm line 218.
$VAR1 = {
          _argv => '-conf circos.conf',
          _cwd => '/home/siam/assembly/siam/PROKKA_11252024',
          configdir => '.',
          configfile => 'circos.conf',
          counter => {
                       ideogram => 1,
                       plot => 2,
                       scatter => 2
                     },
          debug_group => 'output,summary',
          ideogram => {
                        fill => 1,
                        radius => '0.90r',
                        show => 1,
                        thickness => '10'
                      },
          karyotype => 'karyotype_fixed.txt',
          plot => [
                    {
                      color => 'red',
                      file => 'circos_genes.txt',
                      r0 => '0.7r',
                      r1 => '0.9r',
                      type => 'scatter'
                    },
                    {
                      color => 'blue',
                      file => 'cleaned_gff.gff',
                      r0 => '0.5r',
                      r1 => '0.7r',
                      type => 'scatter'
                    }
                  ]
        };

  *** CIRCOS ERROR ***

      cwd: /home/siam/assembly/siam/PROKKA_11252024

      command: /home/siam/anaconda3/envs/circos_env/bin/circos -conf circos.conf

  CONFIGURATION FILE ERROR

  Configuration parameter [plot] 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/siam/anaconda3/envs/circos_env/bin/../lib/Circos/Error.pm line 425.
    Circos::Error::fatal_error("configuration", "multivalue", "plot", "_root") called at /home/siam/anaconda3/envs/circos_env/bin/../lib/Circos/Configuration.pm line 441
    Circos::Configuration::check_multivalues(HASH(0x61e254b41c28), undef) called at /home/siam/anaconda3/envs/circos_env/bin/../lib/Circos/Configuration.pm line 294
    Circos::Configuration::populateconfiguration("debug_group", "output,summary", "_cwd", "/home/siam/assembly/siam/PROKKA_11252024", "configfile", "circos.conf", "_argv", "-conf circos.conf") called at /home/siam/anaconda3/envs/circos_env/bin/../lib/Circos.pm line 153
    Circos::run("Circos", "_cwd", "/home/siam/assembly/siam/PROKKA_11252024", "_argv", "-conf circos.conf", "configfile", "circos.conf") called at /home/siam/anaconda3/envs/circos_env/bin/circos line 536
(circos_env) siam@siampc:~/assembly/siam/PROKKA_11252024$ 

[dthorbur]

Please don't rely on ChatGPT to write your code for you. The documentation for Circos is great and has extensive examples. You're unlikely to get any help on forums like this if you post ChatGPT code and ask us to debug it for you.

[microfuge]

Typically the structure is

<plots>
<plot></plot>
<plot></plot>
</plots>

Can you try enclosing them in <plots> E.g

# Gene plot (using circos_genes.txt)
<plots>
<plot>
  type = scatter
  file = circos_genes.txt
  r0 = 0.7r
  r1 = 0.9r
  color = red
</plot>

# CDS plot (if you want to include CDS from cleaned_gff.gff or another file)
<plot>
  type = scatter
  file = cleaned_gff.gff
  r0 = 0.5r
  r1 = 0.7r
  color = blue
</plot>
</plots>