CONFIGURATION FILE ERROR

[Assa Yeroslaviz]

Hi,

I guess this is a regular problem with people posting here, but I tried and didn't find any solution to my specific problem.

I try to run circos with a specific configuration file:
command:
~/software/circos-0.64/bin/circos -silent -conf circos/circos_svg.conf

But if I add these line:

anglestep       = 0.1
minslicestep    = 2
beziersamples   = 40
debug           = no
warnings        = no
imagemap        = no

# don't touch!
units_ok        = bupr
units_nounit    = n

I get a configuration error massage like that:

  *** 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, use this tutorial to learn how
  to use the debugging facility

      http://www.circos.ca/tutorials/lessons/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 /home/AYeroslaviz/software/circos-0.64/bin/../lib/Circos/Error.pm line 354
    Circos::Error::fatal_error('configuration', 'multivalue', 'debug', '_root') called at /home/AYeroslaviz/software/circos-0.64/bin/../lib/Circos/Configuration.pm line 397
    Circos::Configuration::check_multivalues('HASH(0xa8a62b4)', undef) called at /home/AYeroslaviz/software/circos-0.64/bin/../lib/Circos/Configuration.pm line 251
    Circos::Configuration::populateconfiguration('configfile', 'circos/circos_svg.conf', 'silent', 1) called at /home/AYeroslaviz/software/circos-0.64/bin/../lib/Circos.pm line 202
    Circos::run('Circos', 'configfile', 'circos/circos_svg.conf', 'silent', 1) called at /home/AYeroslaviz/software/circos-0.64/bin/circos line 300


at the bottom I copy-pasted my complete config file

I would appreciate your help.

thanks
Assa

config file:

# Chromosome name, size and color definition
karyotype = multChr/circos/multChr_karyotype.conf

# The <ideogram> block defines the position, size, labels and other
# properties of the segments on which data are drawn. These segments
# are usually chromosomes, but can be any integer axis.

<ideogram>

<spacing>
# Spacing between ideograms. Suffix "r" denotes a relative value. It
# is relative to circle circumference (e.g. space is 0.5% of
# circumference).
default = 10u

# You can increase the spacing between specific ideograms.
#<pairwise hsY;hs1>
#spacing = 20r
#</pairwise>

</spacing>

# Ideogram position, thickness and fill.
#
# Radial position within the image of the ideograms. This value is
# usually relative ("r" suffix).
radius         = 0.65r

# Thickness of ideograms, which can be absolute (e.g. pixels, "p"
# suffix) or relative ("r" suffix). When relative, it is a fraction of
# image radius.
thickness        = 40p

# Ideograms can be drawn as filled, outlined, or both. When filled,
# the color will be taken from the last field in the karyotype file,
# or set by chromosomes_colors. Color names are discussed in
#
# http://www.circos.ca/documentation/tutorials/configuration/configuration_files
#
# When stroke_thickness=0p or if the parameter is missing, the ideogram is
# has no outline and the value of stroke_color is not used.

fill             = yes 
stroke_color     = black # dgrey
stroke_thickness = 2p  

</ideogram>

chromosomes_units           = 1000000
chromosomes_display_default = yes

anglestep       = 0.1
minslicestep    = 2
beziersamples   = 40
debug           = no
warnings        = no
imagemap        = no

# don't touch!
units_ok        = bupr
units_nounit    = n

################################################################
# The remaining content is standard and required. It is imported from
# default files in the Circos distribution.
#
# These should be present in every Circos configuration file and
# overridden as required. To see the content of these files,
# look in etc/ in the Circos distribution.
#
# It's best to include these files using relative paths. This way, the
# files if not found under your current directory will be drawn from
# the Circos distribution.
#
# As always, centralize all your inputs as much as possible.

#<image>
# Included from Circos distribution.
#<<include etc/image.conf>>               
#</image>
<image>
    dir = multChr
    file  = multChr_circos.svg
    24bit = yes
    #png = yes
    #svg = yes
    # radius of inscribed circle in image
    radius         = 320p
    background     = white
    # by default angle=0 is at 3 o'clock position
    angle_offset   = -90
    #angle_orientation = counterclockwise
   
    auto_alpha_colors = yes
    auto_alpha_steps  = 5
</image>

<links>
    z      = 0
    crest  = 1
    color  = grey
    bezier_radius_purity = 0.5

    <<include multChr_inter_links.conf>>
    <<include multChr_intra_links.conf>>
</links>

# RGB/HSV color definitions, color lists, location of fonts, fill
# patterns. Included from Circos distribution.
#
# In older versions of Circos, colors, fonts and patterns were
# included individually. Now, this is done from a central file. Make
# sure that you're not importing these values twice by having
#
# *** DO NOT DO THIS ***
# <colors>
# <<include etc/colors.conf>>
# <colors>
# **********************
<<include etc/colors_fonts_patterns.conf>>

# Debugging, I/O an dother system parameters
# Included from Circos distribution.
<<include etc/housekeeping.conf>>

[Martin Krzywinski]

Don't add those lines! These parameters are already in etc/housekeeping.conf.

It looks like you're using an old configuration file, that's been hacked a little. Please look at the quick start tutorials

http://www.circos.ca/documentation/tutorials/quick_start/

to see how configuration files look for the latest versions.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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