manager@bl8vbox[laccasecircos] /biosoft/circos/circos-0.69-6/bin/circos -conf /home/manager/share/laccasefamily/laccasecircos/config3.txt -outputdir ./ -outputfile ABRE3a

debuggroup summary 0.43s welcome to circos v0.69-6 31 July 2017 on Perl 5.018002

debuggroup summary 0.43s current working directory /home/manager/share/laccasegenefamily/laccasecircos

debuggroup summary 0.43s command /biosoft/circos/circos-0.69-6/bin/circos -conf /home/manager/share/laccasefamily/laccasecircos/config3.txt -outputdir ./ -outputfile ABRE3a

debuggroup summary 0.43s loading configuration from file /home/manager/share/laccasefamily/laccasecircos/config3.txt

  *** CIRCOS ERROR ***

      cwd: /home/manager/share/laccasegenefamily/laccasecircos

      command: /biosoft/circos/circos-0.69-6/bin/circos -conf

      /home/manager/share/laccasefamily/laccasecircos/config3.txt -outputdir ./

      -outputfile ABRE3a

  CONFIGURATION FILE ERROR

  Circos could not find the configuration file

  [/home/manager/share/laccasefamily/laccasecircos/config3.txt]. 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 where Circos looks for the file, use

      circos -debug_flag io

  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/

  This error can also be produced if supporting configuration files, such as

  track defaults, cannot be read.

  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 /biosoft/circos/circos-0.69-6/bin/../lib/Circos/Error.pm line 425.

Circos::Error::fatal_error('configuration', 'missing', '/home/manager/share/laccasefamily/laccasecircos/config3.txt') called at /biosoft/circos/circos-0.69-6/bin/../lib/Circos/Configuration.pm line 796

Circos::Configuration::loadconfiguration('/home/manager/share/laccasefamily/laccasecircos/config3.txt') called at /biosoft/circos/circos-0.69-6/bin/../lib/Circos.pm line 148

Circos::run('Circos', 'outputdir', './', 'outputfile', 'ABRE3a', '_argv', '-conf /home/manager/share/laccasefamily/laccasecircos/config3...', '_cwd', '/home/manager/share/laccasegenefamily/laccasecircos', ...) called at /biosoft/circos/circos-0.69-6/bin/circos line 536

chromosomes_units=1000000    #刻度单位Mb

#chromosomes_reverse=/[12345678910]/   #染色体反转

karyotype=./laccasechr.info  #染色体信息配置文件

show_tick_labels=yes

show_ticks=yes

spacing=10u

<ticks>  #设置染色体刻度

    color=black

    format=%d

    multiplier=1e-6

    radius=1r

    thickness=2p

    <tick>

        size=10p

        spacing=5u

    </tick>

    <tick>

        color=black

        format=%d

        label_offset=10p

        label_size=25p

        show_label=yes

        size=15p

        spacing=25u

        thickness=4p

    </tick>

</ticks>

<ideogram> #染色体绘制设置

    fill=yes   #是否填充颜色

    label_font=default

    label_parallel=yes

    label_radius=dims(image,radius)-60p

    label_size=45

    radius=0.8r  #设置半径，以免基因名称过长超出显示范围

    show_label=yes

    <spacing>

        default=0.005r

    </spacing>

    stroke_color=dgrey

    stroke_thickness=2p

    thickness=0.03r

</ideogram>

<links>  #设置连线

    bezier_radius=0r

    bezier_radius_purity=0.75

    color=black

    crest=0.5

    <link>  #基因家族共线性

        bezier_radius=0r

        bezier_radius_purity=0.75

        color=set2-8-qual-1

        crest=0.5

        file=./ABRE3a.link.txt

        radius=0.98r

        <rules>

            <rule>

                color=red

                condition=var(intrachr)

            </rule>

            <rule>

                color=red

                condition=var(interchr)

            </rule>

        </rules>

        thickness=8

        z=20   #层数

    </link>

    <link>  #全基因组共线性

        bezier_radius=0r

        bezier_radius_purity=0.75

        color=230,230,230,0.2

        crest=0.5

        ribbon=yes

        file=./genome.blocklink.txt

        radius=0.98r

        thickness=1

        z=15

    </link>

    radius=0.40r

    thickness=1

</links>

<plots>

    <plot>

        color=black

        file=./ABRE3a.text.txt

        label_font=condensed

        label_size=24p

        link_color=red

        link_dims=0p,0p,50p,0p,10p

        link_thickness=2p

        r0=1r

        r1=1r+200p

        rpadding=0p

        padding=0p

        show_links=yes

        type=text

    </plot>

    type=histogram

</plots>

<colors>

<<include etc/colors.conf>>

<<include etc/brewer.conf>>

#<<include etc/colors_fonts_patterns.conf>>

#<<include colors.ucsc.conf>>

#<<include colors.hsv.conf>>

</colors>

<fonts>

<<include etc/fonts.conf>>

</fonts>

<image>

<<include etc/image.conf>>

</image>

<<include etc/housekeeping.conf>>