circos CONFIGURATION FILE ERROR
circos CONFIGURATION FILE ERROR
Error parsing the configuration file.
环境
- 系统:Ubuntu 18.04
- 安装 sudo apt install circos
报错
[email protected]:~/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>>
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