5 circos绘制基因组共线性图绘图命令运行问题

老师您好!根据老师前几日给出的建议采用circos进行基因组共线性分析。link,text,genome文件按照老师课程中的格式准备。config1.txt 用的是老师给的参考资料中的文件,仅修改了输入文件。最后运行绘图命令时出现如下报错,请问老师这个是哪里出问题了呀?要怎么解决呢?谢谢老师~

attachments-2019-02-CE6kBbP95c690264c8f2e.jpgattachments-2019-02-hRrefZ5O5c69026e6e019.jpg

  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/share1/cir/config1.txt') called at /biosoft/circos/circos-0.69-6/bin/../lib/Circos/Configuration.pm line 796

Circos::Configuration::loadconfiguration('/home/manager/share1/cir/config1.txt') called at /biosoft/circos/circos-0.69-6/bin/../lib/Circos.pm line 148

Circos::run('Circos', 'outputdir', '/home/manager/share1/cir/result', '_cwd', '/home/manager/share1/gene_duplication/cir', '_argv', '-conf /home/manager/share1/cir/config1.txt -outputdir /home/m...', 'outputfile', 'test1', ...) called at /biosoft/circos/circos-0.69-6/bin/circos line 536

attachments-2019-02-MV4uaJRP5c6902eb2a4ee.jpgattachments-2019-02-4kXF2uDp5c6902f293e09.jpg
chromosomes_units=1000000
#chromosomes_reverse=/chr[01]/
<ideogram>
    fill=yes
    label_font=default
    label_parallel=yes
    label_radius=dims(image,radius)-60p
    label_size=45
    radius=0.90r
    show_label=yes
    <spacing>
        default=0.005r
    </spacing>
    stroke_color=dgrey
    stroke_thickness=2p
    thickness=0.03r
</ideogram>
karyotype=/home/manager/share1/cir/chr.info
<links>
    bezier_radius=0r
    bezier_radius_purity=0.75
    color=black
    crest=0.5
    <link>
        bezier_radius=0r
        bezier_radius_purity=0.75
        color=set2-8-qual-1
        crest=0.5
        file=/home/manager/share1/cir/new_link.txt
        radius=0.88r
        <rules>
            <rule>
                color=red
                condition=var(intrachr)
            </rule>
            <rule>
                color=red
                condition=var(interchr)
            </rule>
        </rules>
        thickness=6
        z=20
    </link>
    <link>
        bezier_radius=0r
        bezier_radius_purity=0.75
        color=230,230,230,0.2
        crest=0.5
        ribbon=yes
        file=/home/manager/share1/cir/genome.txt
        radius=0.88r
        <rules>
            <rule>
                condition=var(intrachr)
            </rule>
            <rule>
                condition=var(interchr)
            </rule>
        </rules>
        thickness=1
        z=15
    </link>
    radius=0.40r
    thickness=1
</links>
<plots>
    <plot>
        color=set2-8-qual-2
        file=/home/manager/share1/cir/nwe_text.txt
        label_font=light
        link_color=black
        link_dims=0p,2p,5p,2p,2p
        link_thickness=2p
        r0=0.88r
        r1=0.99r
        rpadding=5p
        show_links=no
        type=text
    </plot>
    type=histogram
</plots>
show_tick_labels=yes
show_ticks=yes
spacing=10u
<ticks>
    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>
<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>>

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2 个回答

omicsgene - 生物信息
擅长:重测序,遗传进化,转录组,GWAS

怀疑你的路径写错错了,你检查一下:

attachments-2019-02-i7jDtEce5c695cdb1e285.jpg

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安生水
擅长:perl,基因家族,linux,chip-seq

使用pwd命令,看一下你当前目录是否在/home/manager/share1/cir/ 下。

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