circos报错处理：Error parsing the configuration file

circos： Error parsing the configuration file

环境

• 系统：Ubuntu 18.04
• 安装 sudo apt install circos

报错

lzn@lzn-PC:~/CKX/gene_duplication/circos$ circos -conf circos.conf

debuggroup summary 0.12s welcome to circos v0.69-6 31 July 2017 on Perl 5.026001
debuggroup summary 0.12s current working directory /home/lzn/CKX/gene_duplication/circos
debuggroup summary 0.12s command circos -conf circos.conf
debuggroup summary 0.13s loading configuration from file circos.conf
debuggroup summary 0.13s found conf file circos.conf

*** CIRCOS ERROR ***

  cwd: /home/lzn/CKX/gene_duplication/circos

  command: /usr/bin/circos -conf 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

/etc/circos

.

./etc

/usr/bin/etc

/usr/bin/…/etc

/usr/bin/…

/usr/bin

The Config::General module reported the error

Config::General The file “etc/fonts/fonts.conf” does not exist within
ConfigPath:
/etc/circos…/etc./usr/bin/etc./usr/bin/…/etc./usr/bin/…/usr/bin! at
/usr/share/perl5/Circos/Configuration.pm line 820.

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 /usr/share/perl5/Circos/Error.pm line 425.
Circos::Error::fatal_error(“configuration”, “cannot_find_include”, “/etc/circos\x{a}.\x{a}./etc\x{a}/usr/bin/etc\x{a}/usr/bin/…/etc\x{a}/usr/bin/…\x{a}”…, “Config::General The file “etc/fonts/fonts.conf” does not exis”…) called at /usr/share/perl5/Circos/Configuration.pm line 826
Circos::Configuration::loadconfiguration(“circos1.txt”) called at /usr/share/perl5/Circos.pm line 148
Circos::run(“Circos”, “_argv”, “-conf circos1.txt”, “configfile”, “circos1.txt”, “_cwd”, “/home/lzn/CKX/gene_duplication/circos”) called at /usr/bin/circos line 538

报错原因

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

中文大概意思是：解析配置文件失败。你使用的<<include FILE>>找不到。该文件对于使用<<include>>指令的配置文件进行解释。

<<include FILE>>是在你画circos图的配置文件（本文中的circos.conf）中指定的。

circos.conf中的具体内容：

chromosomes_units=1000000
<ideogram>
fill=yes
label_font=default
label_parallel=yes
label_radius=dims(image,radius)-60p
label_size=45
radius=0.90r

​ …

</ticks>
<colors>
<<include etc/colors.conf>> #找不到
<<include etc/brewer.conf>> #找不到
#<<include etc/colors_fonts_patterns.conf>> #找不到
#<< include colors.ucsc.conf>>
#<< include colors.hsv.conf>>
</colors>

<fonts>
<<include etc/fonts.conf>> #找不到
</fonts>

<image>
<<include etc/image.conf>> #找不到
</image>
<<include etc/housekeeping.conf>> #找不到

解决办法

因为找不到<<include FILE>>文件。同时提示：circos在如下目录：

/etc/circos

.

./etc

/usr/bin/etc

/usr/bin/…/etc

/usr/bin/…

/usr/bin

中查找文件。这些<<include FILE>>都在 /etc/circos文件夹中，所以只需将配置文件中的路径改为/etc/circos内即可。例如：

</ticks>
<colors>
<<include /etc/circos/colors.conf>>
<<include /etc/circos/brewer.conf>>
#<<include /etc/circos/colors_fonts_patterns.conf>>
#<< include colors.ucsc.conf>>
#<< include colors.hsv.conf>>
</colors>

<fonts>
<<include /etc/circos/fonts.conf>>
</fonts>

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