Error: Circos Plot Creating In Windows Perl (First Time User Problem)

Question

[John]

I am using the activeperl in my windows. I am trying to repeat a tutorial exercise to make myself confidence that I can do myself after some extra days effort.

cd   c:\Perl64\bin\

c:\Perl64\bin perl -conf C:\Users\Owner\Desktop\circos\ circos.2.conf 
 -outputdir C:\Users\Owner\Desktop\circos\     -outputfile firsttrial.png

perl.exe is under the dictory C:\Perl64\bin. the circos.2.conf file is the directory specified above.

I created "circos.2.conf" by coping the text from the circos website. I just changed " data/6/histogram.txt" to "Users\Owner\Desktop\circos\histogram.txt" to meet my interest and the file is stored in the same folder as circos.2.conf. I am not sure where I need to use "/" or "\" for directory - linux or windows convention.

<colors>
<<include etc/colors.conf>>
</colors>

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

<<include ideogram.2.conf>>
<<include ticks.2.conf>>

karyotype = Users\Owner\Desktop\circos\karyotype.human.txt

<image>
dir = /tmp
file  = circos-tutorial.png
# radius of inscribed circle in image
radius         = 1500p
background     = white
angle_offset   = -90
</image>

chromosomes_units = 1000000

chromosomes_display_default = yes

#chromosomes = hs1;hs2;hs3;hs4;hs5;hs6

<plots>

<plot>

file = Users\Owner\Desktop\circos\histogram.txt
type = histogram

r0 = 0.8r
r1 = 0.9r

min=0.15
max=0.3

color     = black
fill_under = yes
fill_color = green
thickness = 2

extend_bin = no

axis           = yes
axis_color     = lgrey
axis_thickness = 2
axis_spacing   = 0.1

background       = yes
background_color = lgreen
background_stroke_color = black
background_stroke_thickness = 2

</plot>

<plot>

file = Users\Owner\Desktop\circos\histogram.txt
type = histogram

r0 = 0.6r
r1 = 0.7r

min=-0.3
max=-0.15

color     = black
fill_under = yes
fill_color = red
thickness = 2

extend_bin = no

axis           = yes
axis_color     = lgrey
axis_thickness = 2
axis_spacing   = 0.1

background       = yes
background_color = lred
background_stroke_color = black
background_stroke_thickness = 2

</plot>

<plot>

file = Users\Owner\Desktop\circos\histogram.txt
type = histogram

r0 = 0.7r
r1 = 0.8r

min=-0.15
max=0.15

color     = black
fill_under = yes
fill_color = orange
thickness = 2

extend_bin = no

axis           = yes
axis_color     = lgrey
axis_thickness = 2
axis_spacing   = 0.1

background       = yes
background_color = lorange
background_stroke_color = black
background_stroke_thickness = 2

</plot>

</plots>

anglestep       = 0.5
minslicestep    = 10
beziersamples   = 40
debug           = no
warnings        = no
imagemap        = no

# don't touch!
units_ok        = bupr
units_nounit    = n

Thus my directory has following files: conf file, histogram.txt and karyotype.human.

c:\Perl64\bin>perl -conf C:\Users\Owner\Desktop\circos\    circos.2.conf -output
dir C:\Users\Owner\Desktop\circos\     -outputfile firsttrial.png

EROR MESSAGE !!!!

Unrecognized switch: -onf  (-h will show valid options).

What is this message ? I did not get any output to my C:\Users\Owner\Desktop\circos\, am I close ???? sorry for basic question

[Michael]

looks like u simply forgot to load enter the perl script on your command line, and the error means that perl doesn't have the -conf option (I think the perl script is named circos, or circos.pl) : perl circos -conf C:UsersOwnerDesktopcircoscircos.2.conf -output dir C:UsersOwnerDesktopcircos -outputfile firsttrial.png

[Dataminer]

Why don't you use CIRCOS online http://mkweb.bcgsc.ca/tableviewer/

[John]

good suggestion, is every type of CIRCOS plot possible online ?? that is my motivation to learn it ...

[Obi Griffith]

Paraphrasing from the Circos Table Viewer website: the visualizations shown there are created by the tableviewer utility script, which is included in Circos. The web page provides a limited interface to the tableviewer (and Circos). For full functionality you need to download it and run it locally.

[John]

thanks for the suggestions, see my recent edits ...looks like the program is running but there is file deficiency, I do not know where I can find it

[John]

I tried to edit the question, but could not so please see the edits as answer ..."ideogram.2.conf" is not available ...i do not know where I can find it

Answer 1

[John]

I could not edit my question, so here is partial solution, but there is still bug remaining

c:\Perl64\bin>perl  C:\circos\circos-0.55\circos-0.55\bin\circos -conf C:\Users\
Owner\Desktop\circos\circos.2.conf -outputdir C:\Users\Owner\Desktop\circos\ -ou
tputfile firsttrial.png

Config::General The file "ideogram.2.conf" does not exist within ConfigPath: C:\
Users\Owner\Desktop\circos\.C:\Users\Owner\Desktop\circos.C:\Users\Owner\Desktop
\circos/etc.C:/circos/circos-0.55/circos-0.55/bin/etc.C:/circos/circos-0.55/circ
os-0.55/bin/../etc.C:/circos/circos-0.55/circos-0.55/bin/...C:/circos/circos-0.5
5/circos-0.55/bin! at C:/circos/circos-0.55/circos-0.55/bin/../lib/Circos/Config
uration.pm line 381

[John]

I found the following notes interesting

http://genomevisualization.net/tutorials/course/handouts/circos-s2.pdf

[John]

I found the ideogram.2.conf file.

http://mkweb.bcgsc.ca/template/circos/tutorials/lessons/2d_tracks/histograms/configuration/