你的基因组组装到染色体了吗?
没有组装到染色体会有很多scaffold,把那些短scaffold多删除一些,试试;
老师您好,重测序中绘制circos图出现问题,查阅其他同学的提问但是没看懂怎么解决,尝试将ref文件中的fai文件的其他不相关染色体给删掉后还是出现这样的情况,其中有个问题老师您回答“基因组没有组装到染色体 ,这个图绘制会报错”,没理解什么意思,麻烦老师抽空解答,麻烦您了。
*** CIRCOS ERROR ***
cwd: /work/my_reseq/8.circos
command: /share/work/biosoft/circos/latest/bin//circos -conf
/work/my_reseq/8.circos/circos.conf -outputdir /work/my_reseq/8.circos
-outputfile circos
CONFIGURATION FILE ERROR
Could not parse value for configuration parameter [max] in block [plot]. The
location in the configuration is shown above.
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 /share/work/biosoft/circos/circos-0.69-9/bin/../lib/Circos/Error.pm line 425.
Circos::Error::fatal_error("configuration", "undefined_string", "max", "plot") called at /share/work/biosoft/circos/circos-0.69-9/bin/../lib/Circos/Configuration.pm line 649
Circos::Configuration::parse_field(undef, "max", "plot", HASH(0x3c9cdb0), HASH(0x3cb0000)) called at /share/work/biosoft/circos/circos-0.69-9/bin/../lib/Circos/Configuration.pm line 615
Circos::Configuration::repopulateconfiguration(HASH(0x3c9cdb0), "plot", HASH(0x3c9cba0), HASH(0x3ca9120), 1) called at /share/work/biosoft/circos/circos-0.69-9/bin/../lib/Circos/Configuration.pm line 600
Circos::Configuration::repopulateconfiguration(HASH(0x3c9cba0), "plots", HASH(0x2f278c8), HASH(0x3911f90), 1) called at /share/work/biosoft/circos/circos-0.69-9/bin/../lib/Circos/Configuration.pm line 594
Circos::Configuration::repopulateconfiguration(HASH(0x2f278c8), undef, undef, undef, 1) called at /share/work/biosoft/circos/circos-0.69-9/bin/../lib/Circos/Configuration.pm line 290
Circos::Configuration::populateconfiguration("_argv", "-conf /work/my_reseq/8.circos/circos.conf -outputdir /work/my"..., "configfile", "/work/my_reseq/8.circos/circos.conf", "debug_group", "output,summary", "_cwd", "/work/my_reseq/8.circos", ...) called at /share/work/biosoft/circos/circos-0.69-9/bin/../lib/Circos.pm line 153
Circos::run("Circos", "configfile", "/work/my_reseq/8.circos/circos.conf", "_cwd", "/work/my_reseq/8.circos", "_argv", "-conf /work/my_reseq/8.circos/circos.conf -outputdir /work/my"..., "outputdir", ...) called at /share/work/biosoft/circos/latest/bin//circos line 536