To draw a subset of chromosomes, you need to change chromosomes_display_default to no.
only to show chromosomes chr1, chr2, chr3
karyotype = ../data/karyotype.5chr.txt
chromosomes_units = 1000000
#chromosomes_display_default = yes
chromosomes_display_default = no
chromosomes = chr1;chr2;chr3
<<include ideogram.conf>>
<<include ../etc/ticks.conf>>
<<include ../../etc/image.conf>>
<<include etc/colors_fonts_patterns.conf>>
<<include etc/housekeeping.conf>>
figure 14
relative ideogram spacing , default = 0.01r
Relative spacing ensures that the fraction of the ideogram circle occupied by spacing is the same, regardless of the total size of ideogram in the figure.
figure 15
Surprise 1:
#reboot the host machine, and switch on the virtual tool, power on the redhat linux sever 7, run the circos , but circos can't be found.
[arthur@localhost 4]$ pwd
/home/arthur/BGA2017/Course_material/June08/circos-course/session/1/4
[arthur@localhost 4]$ ls
circos.png etc
# to confirm if the file has been edited for the new lesson
[arthur@localhost 4]$ cd etc
[arthur@localhost etc]$ ls
circos.conf ideogram.conf
#yeah, the authour has finished the parameters setting of the chromosomes_display_default
[arthur@localhost etc]$ vim circos.conf
[arthur@localhost etc]$ cd ..
# run circos , but failed
[arthur@localhost 4]$ circos
bash: circos: command not found...
#loss of parameters '-conf'? ---NO
[arthur@localhost 4]$ circos -conf etc/circos.conf
bash: circos: command not found...
[arthur@localhost 4]$ whereis circos
circos:[arthur@localhost 4]$ which circos
/usr/bin/which: no circos in (/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin)
# circos distributon example, test circos can work here or not . ----failed again when 'circos' 'circos -conf', the full pathway typed can be useful
[arthur@localhost example]$ ls
circos.png circos.svg data etc README run run.out
[arthur@localhost example]$ circos
bash: circos: command not found...
[arthur@localhost example]$ circos -conf etc/circos.conf
bash: circos: command not found...
[arthur@localhost example]$ ../bin/circos -conf ./etc/circos.conf
debuggroup summary 0.35s welcome to circos v0.69-6 31 July 2017 on Perl 5.016003
debuggroup summary 0.36s current working directory /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example
debuggroup summary 0.36s command ../bin/circos -conf ./etc/circos.conf
debuggroup summary 0.36s loading configuration from file ./etc/circos.conf
debuggroup summary 0.36s found conf file ./etc/circos.conf
debuggroup summary 1.05s debug will appear for these features: output,summary
debuggroup summary 1.05s bitmap output image ./circos.png
debuggroup summary 1.05s SVG output image ./circos.svg
debuggroup summary 1.05s parsing karyotype and organizing ideograms
debuggroup summary 1.65s karyotype has 66 chromosomes of total size 8,540,079,869
debuggroup summary 1.69s applying global and local scaling
debuggroup summary 1.79s allocating image, colors and brushes
debuggroup summary 5.80s drawing 24 ideograms of total size 3,344,416,167
debuggroup summary 5.80s drawing highlights and ideograms
debuggroup summary 9.68s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/link.conf
debuggroup summary 9.69s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/link.conf
debuggroup summary 9.70s process track_0 link /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/rn.bundle.txt
debuggroup summary 10.49s process track_1 link /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/mm.bundle.txt
debuggroup summary 10.79s drawing link track_0 z 0
debuggroup summary 12.14s drawing link track_1 z 0
debuggroup summary 12.31s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/highlight.conf
debuggroup summary 12.32s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/highlight.conf
debuggroup summary 12.32s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/text.conf
debuggroup summary 12.32s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.32s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.33s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.33s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.33s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.33s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.33s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.33s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.33s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.33s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.33s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.34s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.34s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.34s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.34s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.34s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.34s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.34s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.35s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.35s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.35s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.35s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.35s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.35s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.35s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.35s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.36s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.36s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.36s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.36s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.36s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.36s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.36s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.36s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.36s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.37s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.37s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.37s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.37s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.37s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.37s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.37s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.37s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.37s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.38s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.38s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.38s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.38s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/heatmap.conf
debuggroup summary 12.38s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/scatter.conf
debuggroup summary 12.39s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/scatter.conf
debuggroup summary 12.39s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/scatter.conf
debuggroup summary 12.39s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/scatter.conf
debuggroup summary 12.40s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/scatter.conf
debuggroup summary 12.40s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/scatter.conf
debuggroup summary 12.40s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/scatter.conf
debuggroup summary 12.40s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/scatter.conf
debuggroup summary 12.40s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/scatter.conf
debuggroup summary 12.40s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/scatter.conf
debuggroup summary 12.40s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/scatter.conf
debuggroup summary 12.41s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/scatter.conf
debuggroup summary 12.41s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/scatter.conf
debuggroup summary 12.41s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/scatter.conf
debuggroup summary 12.41s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/scatter.conf
debuggroup summary 12.41s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/scatter.conf
debuggroup summary 12.41s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/scatter.conf
debuggroup summary 12.41s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/scatter.conf
debuggroup summary 12.42s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/scatter.conf
debuggroup summary 12.42s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/scatter.conf
debuggroup summary 12.42s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/scatter.conf
debuggroup summary 12.42s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/scatter.conf
debuggroup summary 12.42s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/scatter.conf
debuggroup summary 12.42s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/scatter.conf
debuggroup summary 12.42s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/scatter.conf
debuggroup summary 12.42s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/scatter.conf
debuggroup summary 12.43s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/scatter.conf
debuggroup summary 12.43s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/histogram.conf
debuggroup summary 12.43s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/scatter.conf
debuggroup summary 12.43s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/histogram.conf
debuggroup summary 12.43s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/scatter.conf
debuggroup summary 12.46s processing track_0 highlight /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/highlights.txt
debuggroup summary 12.49s processing track_1 highlight /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/highlights.txt
debuggroup summary 12.53s processing track_2 text /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/genes.txt
debuggroup summary 14.04s processing track_3 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.hs.mm.20e6.txt
debuggroup summary 14.14s processing track_4 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.hs.rn.20e6.txt
debuggroup summary 14.27s processing track_5 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.hs.mm.10e6.txt
debuggroup summary 14.43s processing track_6 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.hs.rn.10e6.txt
debuggroup summary 14.67s processing track_7 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.1.txt
debuggroup summary 14.74s processing track_8 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.2.txt
debuggroup summary 14.80s processing track_9 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.3.txt
debuggroup summary 14.87s processing track_10 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.4.txt
debuggroup summary 14.94s processing track_11 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.5.txt
debuggroup summary 14.98s processing track_12 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.6.txt
debuggroup summary 15.04s processing track_13 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.7.txt
debuggroup summary 15.11s processing track_14 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.8.txt
debuggroup summary 15.17s processing track_15 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.9.txt
debuggroup summary 15.24s processing track_16 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.10.txt
debuggroup summary 15.31s processing track_17 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.11.txt
debuggroup summary 15.37s processing track_18 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.12.txt
debuggroup summary 15.44s processing track_19 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.13.txt
debuggroup summary 15.49s processing track_20 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.14.txt
debuggroup summary 15.56s processing track_21 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.15.txt
debuggroup summary 15.62s processing track_22 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.16.txt
debuggroup summary 15.70s processing track_23 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.17.txt
debuggroup summary 15.77s processing track_24 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.18.txt
debuggroup summary 15.81s processing track_25 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.19.txt
debuggroup summary 15.87s processing track_26 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.20.txt
debuggroup summary 15.94s processing track_27 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.21.txt
debuggroup summary 16.01s processing track_28 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.22.txt
debuggroup summary 16.08s processing track_29 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.rn.5e6.hs.1.txt
debuggroup summary 16.15s processing track_30 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.rn.5e6.hs.2.txt
debuggroup summary 16.24s processing track_31 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.rn.5e6.hs.3.txt
debuggroup summary 16.32s processing track_32 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.rn.5e6.hs.4.txt
debuggroup summary 16.41s processing track_33 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.rn.5e6.hs.5.txt
debuggroup summary 16.50s processing track_34 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.rn.5e6.hs.6.txt
debuggroup summary 16.58s processing track_35 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.rn.5e6.hs.7.txt
debuggroup summary 16.67s processing track_36 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.rn.5e6.hs.8.txt
debuggroup summary 16.76s processing track_37 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.rn.5e6.hs.9.txt
debuggroup summary 16.84s processing track_38 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.rn.5e6.hs.10.txt
debuggroup summary 16.92s processing track_39 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.rn.5e6.hs.11.txt
debuggroup summary 17.01s processing track_40 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.rn.5e6.hs.12.txt
debuggroup summary 17.09s processing track_41 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.rn.5e6.hs.13.txt
debuggroup summary 17.17s processing track_42 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.rn.5e6.hs.14.txt
debuggroup summary 17.26s processing track_43 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.rn.5e6.hs.15.txt
debuggroup summary 17.34s processing track_44 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.rn.5e6.hs.16.txt
debuggroup summary 17.43s processing track_45 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.rn.5e6.hs.17.txt
debuggroup summary 17.50s processing track_46 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.rn.5e6.hs.18.txt
debuggroup summary 17.59s processing track_47 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.rn.5e6.hs.19.txt
debuggroup summary 17.68s processing track_48 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.rn.5e6.hs.20.txt
debuggroup summary 17.74s processing track_49 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.rn.5e6.hs.21.txt
debuggroup summary 17.84s processing track_50 heatmap /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.rn.5e6.hs.22.txt
debuggroup summary 17.92s processing track_51 scatter /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.rn.5e6.hs.1.txt
debuggroup summary 18.00s processing track_52 scatter /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.rn.5e6.hs.2.txt
debuggroup summary 18.08s processing track_53 scatter /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.rn.5e6.hs.3.txt
debuggroup summary 18.19s processing track_54 scatter /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.rn.5e6.hs.4.txt
debuggroup summary 18.27s processing track_55 scatter /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.rn.5e6.hs.5.txt
debuggroup summary 18.37s processing track_56 scatter /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.1.txt
debuggroup summary 18.45s processing track_57 scatter /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.2.txt
debuggroup summary 18.54s processing track_58 scatter /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.3.txt
debuggroup summary 18.63s processing track_59 scatter /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.4.txt
debuggroup summary 18.88s processing track_60 scatter /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.5.txt
debuggroup summary 18.97s processing track_61 scatter /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.6.txt
debuggroup summary 19.06s processing track_62 scatter /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.7.txt
debuggroup summary 19.15s processing track_63 scatter /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.8.txt
debuggroup summary 19.24s processing track_64 scatter /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.9.txt
debuggroup summary 19.29s processing track_65 scatter /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.10.txt
debuggroup summary 19.38s processing track_66 scatter /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.11.txt
debuggroup summary 19.43s processing track_67 scatter /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.12.txt
debuggroup summary 19.51s processing track_68 scatter /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.13.txt
debuggroup summary 19.59s processing track_69 scatter /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.14.txt
debuggroup summary 19.64s processing track_70 scatter /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.15.txt
debuggroup summary 19.67s processing track_71 scatter /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.16.txt
debuggroup summary 19.74s processing track_72 scatter /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.17.txt
debuggroup summary 19.81s processing track_73 scatter /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.18.txt
debuggroup summary 19.89s processing track_74 scatter /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.19.txt
debuggroup summary 19.97s processing track_75 scatter /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.20.txt
debuggroup summary 20.07s processing track_76 scatter /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.21.txt
debuggroup summary 20.15s processing track_77 scatter /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.mm.5e6.hs.22.txt
debuggroup summary 20.23s processing track_78 histogram /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.hs.mm.20e6.txt
debuggroup summary 20.29s processing track_79 scatter /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.hs.mm.5e6.txt
debuggroup summary 20.73s processing track_80 histogram /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.hs.rn.20e6.txt
debuggroup summary 20.83s processing track_81 scatter /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example/data/heatmap.hs.rn.5e6.txt
debuggroup summary 21.22s drawing track_0 highlight z 0 highlights.txt
debuggroup summary 21.22s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 21.35s drawing track_1 highlight z 0 highlights.txt
debuggroup summary 21.35s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 21.42s drawing track_2 text z 0 genes.txt
debuggroup summary 21.54s placing text track data/genes.txt
debuggroup summary 21.54s ... see progress with -debug_group text
debuggroup summary 21.55s ... see placement summary with -debug_group textplace
debuggroup summary 71.40s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 74.13s drawing track_3 heatmap z 0 heatmap.hs.mm.20e6.txt
debuggroup summary 74.16s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 74.42s drawing track_4 heatmap z 0 heatmap.hs.rn.20e6.txt
debuggroup summary 74.45s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 74.65s drawing track_5 heatmap z 0 heatmap.hs.mm.10e6.txt
debuggroup summary 74.69s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 75.17s drawing track_6 heatmap z 0 heatmap.hs.rn.10e6.txt
debuggroup summary 75.22s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 75.68s drawing track_7 heatmap z 0 heatmap.mm.5e6.hs.1.txt
debuggroup summary 75.69s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 75.77s drawing track_8 heatmap z 0 heatmap.mm.5e6.hs.2.txt
debuggroup summary 75.78s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 75.84s drawing track_9 heatmap z 0 heatmap.mm.5e6.hs.3.txt
debuggroup summary 75.85s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 75.89s drawing track_10 heatmap z 0 heatmap.mm.5e6.hs.4.txt
debuggroup summary 75.90s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 75.97s drawing track_11 heatmap z 0 heatmap.mm.5e6.hs.5.txt
debuggroup summary 75.97s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 76.05s drawing track_12 heatmap z 0 heatmap.mm.5e6.hs.6.txt
debuggroup summary 76.06s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 76.14s drawing track_13 heatmap z 0 heatmap.mm.5e6.hs.7.txt
debuggroup summary 76.15s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 76.18s drawing track_14 heatmap z 0 heatmap.mm.5e6.hs.8.txt
debuggroup summary 76.19s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 76.22s drawing track_15 heatmap z 0 heatmap.mm.5e6.hs.9.txt
debuggroup summary 76.22s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 76.30s drawing track_16 heatmap z 0 heatmap.mm.5e6.hs.10.txt
debuggroup summary 76.31s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 76.39s drawing track_17 heatmap z 0 heatmap.mm.5e6.hs.11.txt
debuggroup summary 76.40s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 76.48s drawing track_18 heatmap z 0 heatmap.mm.5e6.hs.12.txt
debuggroup summary 76.48s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 76.56s drawing track_19 heatmap z 0 heatmap.mm.5e6.hs.13.txt
debuggroup summary 76.57s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 76.65s drawing track_20 heatmap z 0 heatmap.mm.5e6.hs.14.txt
debuggroup summary 76.66s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 76.74s drawing track_21 heatmap z 0 heatmap.mm.5e6.hs.15.txt
debuggroup summary 76.74s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 76.82s drawing track_22 heatmap z 0 heatmap.mm.5e6.hs.16.txt
debuggroup summary 76.83s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 76.86s drawing track_23 heatmap z 0 heatmap.mm.5e6.hs.17.txt
debuggroup summary 76.87s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 76.93s drawing track_24 heatmap z 0 heatmap.mm.5e6.hs.18.txt
debuggroup summary 76.93s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 76.98s drawing track_25 heatmap z 0 heatmap.mm.5e6.hs.19.txt
debuggroup summary 76.99s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 77.07s drawing track_26 heatmap z 0 heatmap.mm.5e6.hs.20.txt
debuggroup summary 77.07s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 77.15s drawing track_27 heatmap z 0 heatmap.mm.5e6.hs.21.txt
debuggroup summary 77.16s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 77.23s drawing track_28 heatmap z 0 heatmap.mm.5e6.hs.22.txt
debuggroup summary 77.24s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 77.32s drawing track_29 heatmap z 0 heatmap.rn.5e6.hs.1.txt
debuggroup summary 77.33s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 77.43s drawing track_30 heatmap z 0 heatmap.rn.5e6.hs.2.txt
debuggroup summary 77.44s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 77.53s drawing track_31 heatmap z 0 heatmap.rn.5e6.hs.3.txt
debuggroup summary 77.53s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 77.62s drawing track_32 heatmap z 0 heatmap.rn.5e6.hs.4.txt
debuggroup summary 77.63s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 77.72s drawing track_33 heatmap z 0 heatmap.rn.5e6.hs.5.txt
debuggroup summary 77.73s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 77.83s drawing track_34 heatmap z 0 heatmap.rn.5e6.hs.6.txt
debuggroup summary 77.84s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 77.89s drawing track_35 heatmap z 0 heatmap.rn.5e6.hs.7.txt
debuggroup summary 77.90s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 77.94s drawing track_36 heatmap z 0 heatmap.rn.5e6.hs.8.txt
debuggroup summary 77.94s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 78.01s drawing track_37 heatmap z 0 heatmap.rn.5e6.hs.9.txt
debuggroup summary 78.02s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 78.11s drawing track_38 heatmap z 0 heatmap.rn.5e6.hs.10.txt
debuggroup summary 78.12s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 78.21s drawing track_39 heatmap z 0 heatmap.rn.5e6.hs.11.txt
debuggroup summary 78.22s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 78.31s drawing track_40 heatmap z 0 heatmap.rn.5e6.hs.12.txt
debuggroup summary 78.32s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 78.41s drawing track_41 heatmap z 0 heatmap.rn.5e6.hs.13.txt
debuggroup summary 78.42s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 78.52s drawing track_42 heatmap z 0 heatmap.rn.5e6.hs.14.txt
debuggroup summary 78.53s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 78.62s drawing track_43 heatmap z 0 heatmap.rn.5e6.hs.15.txt
debuggroup summary 78.63s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 78.72s drawing track_44 heatmap z 0 heatmap.rn.5e6.hs.16.txt
debuggroup summary 78.73s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 78.82s drawing track_45 heatmap z 0 heatmap.rn.5e6.hs.17.txt
debuggroup summary 78.83s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 78.89s drawing track_46 heatmap z 0 heatmap.rn.5e6.hs.18.txt
debuggroup summary 78.90s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 78.94s drawing track_47 heatmap z 0 heatmap.rn.5e6.hs.19.txt
debuggroup summary 78.95s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 79.02s drawing track_48 heatmap z 0 heatmap.rn.5e6.hs.20.txt
debuggroup summary 79.03s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 79.12s drawing track_49 heatmap z 0 heatmap.rn.5e6.hs.21.txt
debuggroup summary 79.13s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 79.22s drawing track_50 heatmap z 0 heatmap.rn.5e6.hs.22.txt
debuggroup summary 79.23s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 79.32s drawing track_51 scatter z 0 heatmap.rn.5e6.hs.1.txt orient out
debuggroup summary 79.33s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 79.48s drawing track_52 scatter z 0 heatmap.rn.5e6.hs.2.txt orient out
debuggroup summary 79.49s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 79.54s drawing track_53 scatter z 0 heatmap.rn.5e6.hs.3.txt orient out
debuggroup summary 79.55s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 79.68s drawing track_54 scatter z 0 heatmap.rn.5e6.hs.4.txt orient out
debuggroup summary 79.69s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 79.82s drawing track_55 scatter z 0 heatmap.rn.5e6.hs.5.txt orient out
debuggroup summary 79.83s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 80.07s drawing track_56 scatter z 0 heatmap.mm.5e6.hs.1.txt orient out
debuggroup summary 80.07s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 80.13s drawing track_57 scatter z 0 heatmap.mm.5e6.hs.2.txt orient out
debuggroup summary 80.14s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 80.20s drawing track_58 scatter z 0 heatmap.mm.5e6.hs.3.txt orient out
debuggroup summary 80.21s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 80.26s drawing track_59 scatter z 0 heatmap.mm.5e6.hs.4.txt orient out
debuggroup summary 80.27s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 80.30s drawing track_60 scatter z 0 heatmap.mm.5e6.hs.5.txt orient out
debuggroup summary 80.31s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 80.35s drawing track_61 scatter z 0 heatmap.mm.5e6.hs.6.txt orient out
debuggroup summary 80.35s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 80.40s drawing track_62 scatter z 0 heatmap.mm.5e6.hs.7.txt orient out
debuggroup summary 80.41s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 80.46s drawing track_63 scatter z 0 heatmap.mm.5e6.hs.8.txt orient out
debuggroup summary 80.46s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 80.52s drawing track_64 scatter z 0 heatmap.mm.5e6.hs.9.txt orient out
debuggroup summary 80.52s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 80.58s drawing track_65 scatter z 0 heatmap.mm.5e6.hs.10.txt orient out
debuggroup summary 80.59s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 80.64s drawing track_66 scatter z 0 heatmap.mm.5e6.hs.11.txt orient out
debuggroup summary 80.65s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 80.70s drawing track_67 scatter z 0 heatmap.mm.5e6.hs.12.txt orient out
debuggroup summary 80.71s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 80.77s drawing track_68 scatter z 0 heatmap.mm.5e6.hs.13.txt orient out
debuggroup summary 80.78s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 80.83s drawing track_69 scatter z 0 heatmap.mm.5e6.hs.14.txt orient out
debuggroup summary 80.84s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 80.90s drawing track_70 scatter z 0 heatmap.mm.5e6.hs.15.txt orient out
debuggroup summary 80.90s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 80.96s drawing track_71 scatter z 0 heatmap.mm.5e6.hs.16.txt orient out
debuggroup summary 80.97s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 81.02s drawing track_72 scatter z 0 heatmap.mm.5e6.hs.17.txt orient out
debuggroup summary 81.03s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 81.09s drawing track_73 scatter z 0 heatmap.mm.5e6.hs.18.txt orient out
debuggroup summary 81.09s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 81.15s drawing track_74 scatter z 0 heatmap.mm.5e6.hs.19.txt orient out
debuggroup summary 81.15s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 81.22s drawing track_75 scatter z 0 heatmap.mm.5e6.hs.20.txt orient out
debuggroup summary 81.23s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 81.27s drawing track_76 scatter z 0 heatmap.mm.5e6.hs.21.txt orient out
debuggroup summary 81.28s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 81.33s drawing track_77 scatter z 0 heatmap.mm.5e6.hs.22.txt orient out
debuggroup summary 81.34s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 81.40s drawing track_78 histogram z 0 heatmap.hs.mm.20e6.txt orient out
debuggroup summary 81.41s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 82.56s drawing track_79 scatter z 0 heatmap.hs.mm.5e6.txt orient out
debuggroup summary 82.66s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 83.44s drawing track_80 histogram z 0 heatmap.hs.rn.20e6.txt orient in
debuggroup summary 83.47s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup summary 84.02s drawing track_81 scatter z 0 heatmap.hs.rn.5e6.txt orient in
debuggroup summary 84.12s found conf file /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/../etc/tracks/axis.conf
debuggroup output 84.88s generating output
debuggroup output 86.88s created PNG image ./circos.png (3648 kb)
debuggroup output 86.88s created SVG image ./circos.svg (2379 kb)
debuggroup timer 86.88s report circos 86.526 s
debuggroup timer 86.88s report color 3.668 s
debuggroup timer 86.88s report colorcache 0.039 s
debuggroup timer 86.88s report colordefinitions 1.330 s
debuggroup timer 86.88s report colorfetch 0.190 s
debuggroup timer 86.88s report colorlists 0.052 s
debuggroup timer 86.88s report colorlookups 0.013 s
debuggroup timer 86.88s report colortransparency 1.923 s
debuggroup timer 86.88s report dataparams 2.495 s
debuggroup timer 86.88s report datarules 4.580 s
debuggroup timer 86.88s report graphic_png_polygon 1.207 s
debuggroup timer 86.88s report graphic_slice 3.726 s
debuggroup timer 86.88s report graphic_slice_polygon_coord 0.790 s
debuggroup timer 86.88s report graphic_slice_polygon_svg 1.216 s
debuggroup timer 86.88s report graphic_slice_preprocess 0.323 s
debuggroup timer 86.88s report highlights 0.000 s
debuggroup timer 86.88s report ideograms_draw 3.854 s
debuggroup timer 86.88s report ideograms_processing 0.047 s
debuggroup timer 86.88s report ideograms_ticks_draw 2.960 s
debuggroup timer 86.88s report ideograms_zoom 0.087 s
debuggroup timer 86.88s report io 1.092 s
debuggroup timer 86.88s report karyotype 0.597 s
debuggroup timer 86.88s report parameter_seek 7.714 s
debuggroup timer 86.88s report track_heatmap 3.309 s
debuggroup timer 86.88s report track_highlight 0.136 s
debuggroup timer 86.88s report track_histogram 1.023 s
debuggroup timer 86.88s report track_preprocess 1.056 s
debuggroup timer 86.88s report track_scatter 2.473 s
debuggroup timer 86.88s report track_text_ashift 37.445 s
debuggroup timer 86.88s report track_text_ashiftiter 19.898 s
debuggroup timer 86.88s report track_text_draw 2.453 s
debuggroup timer 86.88s report track_text_place 49.844 s
debuggroup timer 86.88s report track_text_preashift 10.617 s
debuggroup timer 86.88s report track_text_preprocess 0.871 s
debuggroup timer 86.88s report track_text_refine 0.006 s
debuggroup timer 86.88s report unitconvert 0.063 s
debuggroup timer 86.88s report unitconvert_decision 0.007 s
debuggroup timer 86.88s report unitconvert_delegate 0.020 s
debuggroup timer 86.88s report unitparse 0.233 s
debuggroup summary,timer 86.88s image took more than 30 s to generate. Component timings are shown above. To always show them, use -debug_group timer. To adjust the time cutoff, change debug_auto_timer_report in etc/housekeeping.conf.
[arthur@localhost example]$ ls -l
total 5948
-rw-r--r--. 1 arthur arthur 3648086 Nov 23 10:52 circos.png
-rw-r--r--. 1 arthur arthur 2379254 Nov 23 10:52 circos.svg
drwxr-xr-x. 2 arthur arthur 4096 Jun 4 2017 data
drwxr-xr-x. 2 arthur arthur 4096 Jun 4 2017 etc
-rw-r--r--. 1 arthur arthur 1476 Jun 4 2017 README
-rwxr-xr-x. 1 arthur arthur 202 Jun 4 2017 run
-rw-r--r--. 1 arthur arthur 37130 Jun 4 2017 run.out
[arthur@localhost example]$ eog circos.png
#check the /etc/profile
#export PATH="/home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin:$PATH"
#nothing seems wrong, then go to the example, to run circos again. -----failed
[arthur@localhost example]$ circos
bash: circos: command not found...
#edit the export,
#export PATH="$PATH:/home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin"
#save and exit, run 'source /etc/profile 'make it work, this time everything goes on #well
[arthur@localhost example]$ ../bin/circos -conf etc/circos.conf
debuggroup summary 0.26s welcome to circos v0.69-6 31 July 2017 on Perl 5.016003
debuggroup summary 0.27s current working directory /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example
debuggroup timer 84.82s report unitparse 0.196 s
debuggroup summary,timer 84.82s image took more than 30 s to generate. Component timings are shown above. To always show them, use -debug_group timer. To adjust the time cutoff, change debug_auto_timer_report in etc/housekeeping.conf.
[arthur@localhost example]$ ls
circos.png circos.svg data etc README run run.out
[arthur@localhost example]$ ls -l
total 7656
-rw-r--r--. 1 arthur arthur 3648086 Nov 23 10:58 circos.png
-rw-r--r--. 1 arthur arthur 2379254 Nov 23 10:58 circos.svg
drwxr-xr-x. 2 arthur arthur 4096 Jun 4 2017 data
drwxr-xr-x. 2 arthur arthur 4096 Jun 4 2017 etc
-rw-r--r--. 1 arthur arthur 1476 Jun 4 2017 README
-rwxr-xr-x. 1 arthur arthur 202 Jun 4 2017 run
-rw-r--r--. 1 arthur arthur 37130 Jun 4 2017 run.out
[arthur@localhost example]$ eog circos.png
^C
[arthur@localhost example]$ eog circos.svg
[root@localhost example]# pwd
/home/arthur/BGA2017/Course_material/circos/circos-0.69-6/example
[root@localhost 4]# circos
debuggroup summary 0.27s welcome to circos v0.69-6 31 July 2017 on Perl 5.016003
debuggroup summary 0.27s current working directory /home/arthur/BGA2017/Course_material/June08/circos-course/session/1/4
debuggroup summary 0.27s command /home/arthur/BGA2017/Course_material/circos/circos-
debuggroup output 4.50s created PNG image ./circos.png (39 kb)
[root@localhost 4]# ls
circos.png etc
[root@localhost 4]# ls -l
total 40
-rw-r--r--. 1 arthur arthur 38862 Nov 23 11:15 circos.png
drwxr-xr-x. 2 arthur arthur 44 Nov 23 10:46 etc
[root@localhost 4]# eog circos.png
(eog:6308): dconf-WARNING **: failed to commit changes to dconf: The connection is closed
(eog:6308): dconf-WARNING **: failed to commit changes to dconf: The connection is closed
^C
[arthur@localhost 4]$ circos
debuggroup summary 0.25s welcome to circos v0.69-6 31 July 2017 on Perl 5.016003
debuggroup summary 0.25s current working directory /home/arthur/BGA2017/Course_material/June08/circos-course/session/1/4
debuggroup output 3.23s created PNG image ./circos.png (39 kb)
surprise 2
#root can't use the command 'eog', but the arthur can
[arthur@localhost 4]$ eog circos.png
[arthur@localhost 4]$ su root
Password:
[root@localhost 4]# eog circos.png
No protocol specified
** (eog:11087): WARNING **: Could not open X display
No protocol specified
Cannot open display:
Run 'eog --help' to see a full list of available command line options.
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