Re: [circos] "configuration", "missing", "etc/tracks/scatter.conf"

[Naman Mangukia]

1. If I am not wrong, you are using Linux OS.

2. Do this:

make a directory, suppose at location : "/mnt/d/analyse/Circos/"  and directory name "Run".

Now, copy your "circos.conf" [your circos config file] to this Run folder.

Open command prompt in this Run folder.

Then, run the command.

Assuming your circos is installed at "/usr/bin/",

Your command will be:

/usr/bin/circos -conf circos.conf

If your config file is proper, then your command will run.

Regards,

Naman

On Thu, Oct 28, 2021 at 1:13 PM Y Ish <pneumo...@gmail.com> wrote:

Hello, I'm trying to make a figure with scatter plots.

Error massage said that scatter.conf is not found, but the file is saved in /etc/tracks/ .

What should I do? Please help me...

--------COMMAND and ERROR------------------------------

$ circos -conf /mnt/d/analyse/Circos/circos.conf -outputdir /mnt/d/analyse/Circos/figure/

debuggroup summary 0.10s welcome to circos v0.69-8 15 Jun 2019 on Perl 5.030000

debuggroup summary 0.11s current working directory /etc

debuggroup summary 0.11s command /usr/bin/circos -conf /mnt/d/analyse/Circos/circos.conf -outputdir /mnt/d/analyse/Circos/figure/

debuggroup summary 0.11s loading configuration from file /mnt/d/analyse/Circos/circos.conf

debuggroup summary 0.11s found conf file /mnt/d/analyse/Circos/circos.conf

debuggroup summary 0.20s debug will appear for these features: output,summary

debuggroup summary 0.21s bitmap output image /mnt/d/analyse/Circos/figure/circos.png

debuggroup summary 0.21s SVG output image /mnt/d/analyse/Circos/figure/circos.svg

debuggroup summary 0.21s parsing karyotype and organizing ideograms

debuggroup summary 0.22s karyotype has 39 chromosomes of total size 16,539

debuggroup summary 0.22s applying global and local scaling

debuggroup summary 0.23s allocating image, colors and brushes

debuggroup summary 1.22s drawing 39 ideograms of total size 16,539

debuggroup summary 1.22s drawing highlights and ideograms

Redundant argument in sprintf at /usr/share/perl5/Circos/Error.pm line 364.

  *** CIRCOS ERROR ***

      cwd: /etc

      command: /usr/bin/circos -conf /mnt/d/analyse/Circos/circos.conf

      -outputdir /mnt/d/analyse/Circos/figure/

  CONFIGURATION FILE ERROR

  Circos could not find the configuration file. To run Circos, you need to

  specify this file using the -conf flag. The configuration file contains all

  the parameters that define the image, including input files, image size,

  formatting, etc.

  If you do not use the -conf flag, Circos will attempt to look for a file

  circos.conf in several reasonable places such as . etc/ ../etc

  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/

  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", "missing", "etc/tracks/scatter.conf") called at /usr/share/perl5/Circos/Configuration.pm line 796

        Circos::Configuration::loadconfiguration("etc/tracks/scatter.conf", 1) called at /usr/share/perl5/Circos/Track.pm line 223

        Circos::Track::assign_defaults(ARRAY(0x5606dccd8390), HASH(0x5606e0014940)) called at /usr/share/perl5/Circos/Track.pm line 201

        Circos::Track::make_tracks_v2(HASH(0x5606dd2491c0), HASH(0x5606e0014940)) called at /usr/share/perl5/Circos.pm line 1439

        Circos::run("Circos", "configfile", "/mnt/d/analyse/Circos/circos.conf", "_argv", "-conf /mnt/d/analyse/Circos/circos.conf -outputdir /mnt/d/ana"..., "outputdir", "/mnt/d/analyse/Circos/figure/", "_cwd", ...) called at /usr/bin/circos line 538

---------------etc/tracks-------------------------------

$ ls -l /etc/tracks/

total 48

-rwxr-xr-x 1 root root 220 Jul 20  2019 README

-rwxr-xr-x 1 root root  31 Jul 20  2019 axis.conf

-rwxr-xr-x 1 root root 102 Jul 20  2019 connector.conf

-rwxr-xr-x 1 root root 177 Jul 20  2019 heatmap.conf

-rwxr-xr-x 1 root root 147 Jul 20  2019 highlight.bg.conf

-rwxr-xr-x 1 root root 123 Jul 20  2019 highlight.conf

-rwxr-xr-x 1 root root 118 Jul 20  2019 histogram.conf

-rwxr-xr-x 1 root root 120 Jul 20  2019 line.conf

-rwxr-xr-x 1 root root 172 Jul 20  2019 link.conf

-rwxr-xr-x 1 root root 191 Jul 20  2019 scatter.conf

-rwxr-xr-x 1 root root 488 Jul 20  2019 text.conf

-rwxr-xr-x 1 root root 256 Jul 20  2019 tile.conf

---------MY CIRCOS.CONF------------------------

# circos.conf

karyotype = /mnt/d/analyse/Circos/karyotype_rcrs.txt

<ideogram>

<spacing>

default = 0.002r

</spacing>

radius    = 0.9r

thickness = 50p

fill      = yes

stroke_color = black

stroke_thickness = 5p

show_label     = yes

show_scatter = yes

label_with_tag = yes

label_font     = light

label_radius   = dims(ideogram,radius_outer) + 0.05r

label_center   = yes

label_size     = 24p

label_color    = black

label_parallel = no

label_case     = upper 

</ideogram>

<plots>

<plot>

show  = yes

type  = scatter

file  = /mnt/d/analyse/Circos/level_pb.txt

fill_color = grey

stroke_color     = black

stroke_thickness = 0

glyph            = rectangle

glyph_size       = 8

color            = red

r1    = 0.75r

r0    = 0.90r

max   = 100

min   = 0

<backgrounds>

<background>

color     = vvlgreen

y0        = 74

</background>

<background>

color     = vlgrey

y1        = 74

y0        = 10

</background>

<background>

color     = vvlred

y1        = 10

</background>

</backgrounds>

<axes>

<axis>

color     = lgreen

thickness = 1

spacing   = 0.05r

y0        = 74

</axis>

<axis>

color     = dgreen

thickness = 2

spacing   = 0.1r

y0        = 74

</axis>

<axis>

color     = lgrey

thickness = 1

spacing   = 0.05r

y1        = 74

y0        = 10

</axis>

<axis>

color     = dgrey

thickness = 2

spacing   = 0.1r

y1        = 74

y0        = 10

</axis>

<axis>

color     = lred

thickness = 1

spacing   = 0.05r

y1        = 10

</axis>

<axis>

color     = dred

thickness = 2

spacing   = 0.1r

y1        = 10

</axis>

</axes>

<rules>

<rule>

condition    = var(value) > 74

stroke_color = dgreen

fill_color   = green

glyph        = rectangle

glyph_size   = 8

</rule>

<rule>

condition    = var(value) < 10

stroke_color = dred

fill_color   = red

glyph        = triangle

</rule>

</rules>

</plot>

</plots>

################################################################

# The remaining content is standard and required. It is imported 

# from default files in the Circos distribution.

#

# These should be present in every Circos configuration file and

# overridden as required. To see the content of these files, 

# look in etc/ in the Circos distribution.

<image>

# Included from Circos distribution.

<<include image.conf>>

</image>

# RGB/HSV color definitions, color lists, location of fonts, fill patterns.

# Included from Circos distribution.

<<include colors_fonts_patterns.conf>>

# Debugging, I/O an dother system parameters

# Included from Circos distribution.

<<include housekeeping.conf>>

--
You received this message because you are subscribed to the Google Groups "Circos" group.
To unsubscribe from this group and stop receiving emails from it, send an email to circos-data-visual...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/circos-data-visualization/278c30ad-a783-47db-b0fc-66d6ee76935dn%40googlegroups.com.

[Y Ish]

Thank you for your comment.

Yes, I use ubuntu on Windows 10.

The run folder was something I hadn't tried. 

Eventually, this error was resolved by rewriting housekeeping.conf. so I have deleted this conversation, I'm sorry.

”etc/tracks”→"/etc/tracks"

 But I'm not sure if this is correct or not, so I would like to use the run folder if I have problems again.

Thank you.

2021年10月28日木曜日 18:28:49 UTC+9 Neo Anderson:

[Martin Krzywinski]

> Error massage said that scatter.conf is not found, but the file is saved in /etc/tracks/ .

Circos will not look in /etc for configuration files. 

The software is designed to be installed in a single directory and not across the file system, the way typical UNIX system tools are installed.

Typical installation is something like

/opt/circos/circos-vx.xx/

/usr/local/bin/circos -> /opt/circos/circos-vx.xx/bin/circos

At runtime, the script will scan directories *relative to the binary*, e.g.

/opt/circos/circos-vx.xx/bin/etc

/opt/circos/circos-vx.xx/bin/../etc

for configuration.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

To view this discussion on the web visit https://groups.google.com/d/msgid/circos-data-visualization/26a8f749-0e22-460b-b9ab-728c02f83875n%40googlegroups.com.