A circos problem
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Entering edit mode
7.0 years ago

Hello everyone.

I'm new to circos and want have a easy try to plot a pic. And it reported a problem as follows. Could someone helps me, any advice and suggestions will be greatly appreciated !

debuggroup summary 0.11s welcome to circos v0.69-5 2 May 2017 on Perl 5.022000
debuggroup summary 0.11s current working directory /home/sxuan/anaconda3/pkgs/circos-0.69.5-pl5.22.0_0/example/etc/circos_test
debuggroup summary 0.11s command /home/sxuan/anaconda3/bin/circos -conf circos.conf
debuggroup summary 0.11s loading configuration from file circos.conf
debuggroup summary 0.11s found conf file circos.conf
debuggroup summary 0.22s debug will appear for these features: output,summary
debuggroup summary 0.22s bitmap output image ./circos.png
debuggroup summary 0.22s SVG output image ./circos.svg
debuggroup summary 0.22s parsing karyotype and organizing ideograms
debuggroup summary 0.22s karyotype has 2 chromosomes of total size 3,928,791
debuggroup summary 0.22s applying global and local scaling
Use of uninitialized value $norm[0] in join or string at /home/sxuan/anaconda3/bin/../lib/Circos/Unit.pm line 196, <F> line 3.
The 'from' parameter (undef) to Circos::Unit::unit_convert was an 'undef', which is not one of the allowed types: scalar
 at /home/sxuan/anaconda3/bin/../lib/Circos/Unit.pm line 203, <F> line 3.
        Circos::Unit::unit_convert("from", undef, "to", "b", "factors", HASH(0x51a55f0)) called at /home/sxuan/anaconda3/lib/perl5/5.22.0/Memoize.pm line 245
        Memoize::_memoizer(CODE(0x47c91e8), "from", undef, "to", "b", "factors", HASH(0x51a55f0)) called at (eval 84) line 1
        Memoize::__ANON__("from", undef, "to", "b", "factors", HASH(0x51a55f0)) called at /home/sxuan/anaconda3/bin/../lib/Circos.pm line 5576
        Circos::ideogram_spacing(HASH(0x51a34f8), HASH(0x51a3180), 0) called at /home/sxuan/anaconda3/bin/../lib/Circos.pm line 538
        Circos::run("Circos", "_cwd", "/home/sxuan/anaconda3/pkgs/circos-0.69.5-pl5.22.0_0/example/e"..., "configfile", "circos.conf", "_argv", "-conf circos.conf") called at /home/sxuan/anaconda3/bin/circos line 535

the circos.conf is here:

  1 <<include etc/colors_fonts_patterns.conf>>
  2 
  3 <image>
  4 <<include etc/image.conf>>
  5 </image>
  6 
  7 karyotype=karyotype.txt
  8 chromosomes_units=100000
  9 chromosomes_display_default=yes
 10 
 11 <ideogram>
 12 <spacing>
 13 defalut=0.005r
 14 </spacing>
 15 radius=0.80r
 16 thickness=6p
 17 fill=yes
 18 fill_color=deepskyblue
 19 stroke_color=black
 20 stroke_thickness=1p
 21 show_label=yes
 22 label_font=light
 23 label_radius=30
 24 label_size=30
 25 label_parallel=yes
 26 </ideogram>
 27 
 28 <<include etc/housekeeping.conf>>

and here is the plot data:

  1 chr - scaffold1 1 0 1102171 deepskyblue
  2 chr - scaffold2 2 0 2826618 red
software error • 2.4k views
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Is the karyotype.txt file the same genome and range of chromosomes as your input data?

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