error

[Lara]

Hi,

I got this error executing circos: 

lara:~$ /usr/bin/circos-0.69-9/bin/circos -conf /mnt/d/Circos/circos.conf
debuggroup summary 0.36s welcome to circos v0.69-8 15 Jun 2019 on Perl 5.034000
debuggroup summary 0.37s current working directory /home/lara
debuggroup summary 0.37s command /usr/bin/circos-0.69-9/bin/circos -conf /mnt/d/Circos/circos.conf
debuggroup summary 0.37s loading configuration from file /mnt/d/Circos/circos.conf
debuggroup summary 0.38s found conf file /mnt/d/Circos/circos.conf

  *** CIRCOS ERROR ***

      cwd: /home/lara

      command: /usr/bin/circos-0.69-9/bin/circos -conf /mnt/d/Circos/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

  /mnt/d/Circos

  /mnt/d/Circos

  /mnt/d/Circos/etc

  /usr/bin/circos-0.69-9/bin/etc

  /usr/bin/circos-0.69-9/bin/../etc

  /usr/bin/circos-0.69-9/bin/..

  /usr/bin/circos-0.69-9/bin

  The Config::General module reported the error

  Config::General The file "inc/colors.ucsc.conf" does not exist within
  ConfigPath:
  /mnt/d/Circos./mnt/d/Circos./mnt/d/Circos/etc./usr/bin/circos-0.69-9/bin/etc./usr/bin/circos-0.69-9/bin/../etc./usr/bin/circos-0.69-9/bin/.../usr/bin/circos-0.69-9/bin!
  at /usr/bin/circos-0.69-9/bin/../lib/Circos/Configuration.pm line 819.

  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/bin/circos-0.69-9/bin/../lib/Circos/Error.pm line 425.
        Circos::Error::fatal_error("configuration", "cannot_find_include", "/mnt/d/Circos\x{a}/mnt/d/Circos\x{a}/mnt/d/Circos/etc\x{a}/usr/bin/circos"..., "Config::General The file \"inc/colors.ucsc.conf\" does not exis"...) called at /usr/bin/circos-0.69-9/bin/../lib/Circos/Configuration.pm line 825
        Circos::Configuration::loadconfiguration("/mnt/d/Circos/circos.conf") called at /usr/bin/circos-0.69-9/bin/../lib/Circos.pm line 148
        Circos::run("Circos", "_cwd", "/home/lara", "_argv", "-conf /mnt/d/Circos/circos.conf", "configfile", "/mnt/d/Circos/circos.conf") called at /usr/bin/circos-0.69-9/bin/circos line 536

Using this .conf generated with vim and tried with nano too:

karyotype = hap1_scaf.circos.tsv, hap2_scaf.circos.tsv
chrominfo = hap1_scaf.chrom.txt, hap2_scaf.chrom.txt

<<include inc/colors.ucsc.conf>>

hap1_scaf = hap1_scaf
hap2_scaf = hap2_scaf

options {
    chroms = hap1_scaf,hap2_scaf
}

tracks {
    <tracks hap1_scaf>
        <track type="link">
            <options>
                link_type = "identity"
                link_color = "black"
                link_density = 0.5
            </options>
            file = hap_circos_alignment.txt
        </track>
    </tracks>
}

Has anyone an idea whats wrong? It somehow seems like the line break is a problem, but I don't get it. Is there an option, that something is wrong with my circos installation, but I did it as described in the instruction. 

[Martin]

Your configuration file doesn't look like a Circos config. Circos doesn't use syntax like

options {

...

} 

This config file might be for a tool that itself generates a Circos config. I'm not sure.

Please check the tutorials

https://circos.ca/documentation/tutorials/configuration/

for what Circos expects from its config files.

m