ERROR:CONFIGURATION FILE ERROR

[Taehyuk Kang]

It seems a common error, so I have tried to resolve this problem by my self using your tutorials. But, I cannot figure it out.. I am attaching my error message at below. Please help me.

Many thanks,

Taehyuk

-----------------------------------------------------------------------------------------------------

Taehyuks-MacBook-Pro:~ Taehyuk$ circos -version
circos | v 0.67-7 | 16 Mar 2015 | Perl 5.018002
Taehyuks-MacBook-Pro:~ Taehyuk$ circos -modules
ok       1.29 Carp
ok       0.36 Clone
ok       2.61 Config::General
ok       3.40 Cwd
ok      2.145 Data::Dumper
ok       2.52 Digest::MD5
ok       2.84 File::Basename
ok       3.40 File::Spec::Functions
ok       0.23 File::Temp
ok       1.51 FindBin
ok       0.39 Font::TTF::Font
ok       2.53 GD
ok        0.2 GD::Polyline
ok       2.39 Getopt::Long
ok       1.16 IO::File
ok       0.33 List::MoreUtils
ok       1.38 List::Util
ok       0.01 Math::Bezier
ok      1.998 Math::BigFloat
ok       0.06 Math::Round
ok       0.08 Math::VecStat
ok       1.03 Memoize
ok       1.32 POSIX
ok       1.08 Params::Validate
ok       1.61 Pod::Usage
ok       2.04 Readonly
ok 2013031301 Regexp::Common
ok       2.64 SVG
ok       1.16 Set::IntSpan
ok     1.6611 Statistics::Basic
ok       2.41 Storable
ok       1.17 Sys::Hostname
ok       2.02 Text::Balanced
ok       0.59 Text::Format
ok     1.9725 Time::HiRes
Taehyuks-MacBook-Pro:~ Taehyuk$ circos -conf circos.conf
debuggroup summary 0.10s welcome to circos v0.67-7 16 Mar 2015 on Perl 5.018002
debuggroup summary 0.10s loading configuration from file circos.conf

  *** CIRCOS ERROR ***

  CONFIGURATION FILE ERROR

  Circos could not find the configuration file. To run Circos, you need to
  specify this file using the -conf flag. The configuration file contains all
  the parameters that define the image, including input files, image size,
  formatting, etc.

  If you do not use the -conf flag, Circos will attempt to look for a file
  circos.conf in several reasonable places such as . etc/ ../etc

  To see how configuration files work, create the example image, whose
  configuration and data are found in example/. From the Circos distribution
  directory,

      cd example

      ../bin/circos -conf ./circos.conf

  or use the 'run' script (UNIX only).

  Configuration files are described here

      http://circos.ca/tutorials/lessons/configuration/configuration_files/

  and the use of command-line flags, such as -conf, is described here

      http://circos.ca/tutorials/lessons/configuration/runtime_parameters/

  Windows users unfamiliar with Perl should read

      http://circos.ca/tutorials/lessons/configuration/unix_vs_windows/

  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 /Users/Taehyuk/software/circos/circos-0.67-7/bin/../lib/Circos/Error.pm line 418.
    Circos::Error::fatal_error('configuration', 'missing') called at /Users/Taehyuk/software/circos/circos-0.67-7/bin/../lib/Circos/Configuration.pm line 796
    Circos::Configuration::loadconfiguration('circos.conf') called at /Users/Taehyuk/software/circos/circos-0.67-7/bin/../lib/Circos.pm line 141
    Circos::run('Circos', 'configfile', 'circos.conf') called at /Users/Taehyuk/software/circos/circos-0.67-7/bin/circos line 382
Taehyuks-MacBook-Pro:~ Taehyuk$

[wzx1...@gmail.com]

Hello, I have the same problem. Anyone can help us! Thanks, zhixong

在 2016年6月7日星期二 UTC-4下午7:01:49，Taehyuk Kang写道：

[Martin Krzywinski]

You're seeing this error because Circos cannot find the configuration file.

When you're using -conf FILE, make sure that the FILE exists.

If your file is elsewhere, use the full path to the file, e.g.

circos -conf /home/user/projects/01/circos.conf

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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