Question: Need help debugging Circos output.
0
gravatar for maxwells_daemon
17 months ago by
maxwells_daemon10 wrote:

Howdy, I am running my Circos .conf file on MacOS, and this is the output I am receiving. Can anyone help me out with understanding why I am having issues with my Circos conf file specifically with regards to the housekeeping.conf file? I also am not sure where the parent block has been defined. Please feel free not to answer this question as I will look at the conf file again.

...

  *** CIRCOS ERROR ***
  CONFIGURATION FILE ERROR
  Configuration parameter [debug] 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
  Stack trace:
 at /usr/local/Cellar/circos/0.67-7/libexec/bin/../lib/Circos/Error.pm line 418.
    Circos::Error::fatal_error('configuration', 'multivalue', 'debug', '_root') called at /usr/local/Cellar/circos/0.67-7/libexec/bin/../lib/Circos/Configuration.pm line 441
    Circos::Configuration::check_multivalues('HASH(0x7fa0a2dd6c78)', undef) called at /usr/local/Cellar/circos/0.67-7/libexec/bin/../lib/Circos/Configuration.pm line 294
    Circos::Configuration::populateconfiguration('debug_group', 'output,summary') called at /usr/local/Cellar/circos/0.67-7/libexec/bin/../lib/Circos.pm line 146
    Circos::run('Circos') called at /usr/local/Cellar/circos/0.67-7/libexec/bin/circos line 382
circos visualization genome • 490 views
ADD COMMENTlink modified 17 months ago • written 17 months ago by maxwells_daemon10

Hello maxwells_daemon,

please use the code button (the one wit 101 010) to format your output. This makes it much more readable.

The problem is stated out in the error message:

CONFIGURATION FILE ERROR Configuration parameter [debug] 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.

Have you checked this? For more debugging you should post your config file as well.

fin swimmer

ADD REPLYlink written 17 months ago by finswimmer12k

As already suggested by finswimmer I added code markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

101010 Button

ADD REPLYlink written 17 months ago by WouterDeCoster41k
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