circos.conf not found error

[Roland Nagel]

Hi, I'm getting a circos.conf not found error when I run this command. I'm just trying to run an example to make sure everything is working for now.  

> (circos) rasika~$circos -conf /home/rasika/circos.conf 

If I'm reading the debugging error below correctly, it's finding the .conf file but maybe there is a probelm with the example .conf file? Apologies, newbie here. 

 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/rasika/miniconda3/envs/circos/bin/../lib/Circos/Error.pm line 425.
        Circos::Error::fatal_error("configuration", "bad_command_line_options", "") called at /home/rasika/miniconda3/envs/circos/bin/circos line 533
(circos) rasika:~$ circos -conf /home/rasika/circos.conf
debuggroup summary 0.15s welcome to circos v0.69-8 15 Jun 2019 on Perl 5.032001
debuggroup summary 0.16s current working directory /home/rasika
debuggroup summary 0.16s command /home/rasika/miniconda3/envs/circos/bin/circos -conf /home/rasika/circos.conf
debuggroup summary 0.16s loading configuration from file /home/rasika/circos.conf
debuggroup summary 0.16s found conf file /home/rasika/circos.conf

  *** CIRCOS ERROR ***

      cwd: /home/rasika

      command: /home/rasika/miniconda3/envs/circos/bin/circos -conf
      /home/rasika/circos.conf

  CONFIGURATION FILE ERROR

  Error parsing the configuration file. You used an <<include FILE>> directive,
  but the FILE could not be found. This FILE is interpreted relative to the
  configuration file in which the <<include>> directive is used. Circos lookd
  for the file in these directories

  /home/rasika

  /home/rasika

  /home/rasika/etc

  /home/rasika/miniconda3/envs/circos/bin/etc

  /home/rasika/miniconda3/envs/circos/bin/../etc

  /home/rasika/miniconda3/envs/circos/bin/..

  /home/rasika/miniconda3/envs/circos/bin

  The Config::General module reported the error

  Config::General The file "circos.image.conf" does not exist within ConfigPath:
  /home/rasika./home/rasika./home/rasika/etc./home/rasika/miniconda3/envs/circos/bin/etc./home/rasika/miniconda3/envs/circos/bin/../etc./home/rasika/miniconda3/envs/circos/bin/.../home/rasika/miniconda3/envs/circos/bin!
  at /home/rasika/miniconda3/envs/circos/bin/../lib/Circos/Configuration.pm line
  819.

this is the conf file. 

karyotype = circos.sequences.txt
chromosomes_units = 1000000

<ideogram>
<spacing>
default = 0.010r
</spacing>
radius    = 0.75r
thickness = 50p
fill      = yes
show_label       = yes
label_font       = default
label_size       = 14
label_parallel   = no
</ideogram>

show_ticks       = yes
show_tick_labels = yes

<ticks>
radius           = 1r
color            = black
thickness        = 4p
multiplier       = 1e-3
format           = %d
<tick>
spacing        = 0.05u
size           = 20p
show_label     = yes
label_size     = 14p
label_offset   = 10p
</tick>
</ticks>

<colors>
chr1* = red
chr2* = green
chr3* = blue
chr4* = orange
</colors>

<links>
crest = 1
bezier_radius = 0.3r
bezier_radius_purity = 1.0
<link>
show = yes
ribbon = yes
stroke_color = vdgrey
stroke_thickness = 2
file   = circos.segdup.txt
radius        = 0.99r
#color         = red_a4
thickness     = 15
</link>
</links>

################################################################
# 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.

<image>
<<include circos.image.conf>>
</image>

# RGB/HSV color definitions, color lists, location of fonts, fill patterns.
# Included from Circos distribution.
<<include etc/colors_fonts_patterns.conf>>

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

<highlights>
fill_color = green
<highlight>
file = circos.highlight.txt
ideogram = yes
fill_color = blue_a3
stroke_color = black
stroke_thickness = 4
</highlight>
<highlight>
file = circos.highlight1.txt
ideogram = no
fill_color = blue_a3
stroke_color = black
stroke_thickness = 4
r0 = 1r +100p
r1 = 1r +150p
</highlight>
<highlight>
file = circos.highlight2.txt
ideogram = no
fill_color = blue_a3
stroke_color = black
stroke_thickness = 4
r0 = 1r +175p
r1 = 1r +225p
</highlight>
<highlight>
file = circos.highlight3.txt
ideogram = no
fill_color = blue_a3
stroke_color = black
stroke_thickness = 4
r0 = 1r +250p
r1 = 1r +300p
</highlight>
<highlight>
file = circos.highlight4.txt
ideogram = no
fill_color = blue_a3
stroke_color = black
stroke_thickness = 4
r0 = 1r +325p
r1 = 1r +375p
</highlight>
</highlights>
<ideogram>
label_radius = 1r + 400p
</ideogram>