Unable to move pass error -" Use of uninitialized value $norm[0] in join or string" and doubts in plotting multiple genomes.

[amit babu]

Dear Martin,

I am a researcher in an Indian University and I am trying to plot the chromosomes of a yeast strain S288C. Right now, I am only trying to plot the karyotype.txt file,but I am encountering an error. It is as follows:

Use of uninitialized value $norm[0] in join or string at C:/circos-0.69-9/bin/../lib/Circos/Unit.pm line 196, <F> line 17.
The 'from' parameter (undef) to Circos::Unit::unit_convert was an 'undef', which is not one of the allowed types: scalar
 at C:/circos-0.69-9/bin/../lib/Circos/Unit.pm line 203, <F> line 17.
        Circos::Unit::unit_convert("from", undef, "to", "b", "factors", HASH(0x597d788)) called at C:/Strawberry/perl/lib/Memoize.pm line 249
        Memoize::_memoizer(CODE(0x51b9170), "from", undef, "to", "b", "factors", HASH(0x597d788)) called at (eval 137) line 1
        Memoize::__ANON__("from", undef, "to", "b", "factors", HASH(0x597d788)) called at C:/circos-0.69-9/bin/../lib/Circos.pm line 5589
        Circos::ideogram_spacing(HASH(0x5aebcb8), HASH(0x5ae11f8), 0) called at C:/circos-0.69-9/bin/../lib/Circos.pm line 543
        Circos::run("Circos", "_cwd", "C:/circos-0.69-9/bin", "configfile", "circos2.conf", "_argv", "-conf circos2.conf") called at circos line 536

I have pasted the karyotype and the config file down below. 

I look forward to hearing from you. 

S28CC_karyotype.txt-

chr - chr1 chr1 1 229761 color=black
chr - chr2 chr2 3666 813101 color=black
chr - chr3 chr3 193 316620 color=black
chr - chr4 chr4 11 1531931 color=black
chr - chr5 chr5 1 576871 color=black
chr - chr6 chr6 1 270161 color=black
chr - chr7 chr7 1 1090940 color=black
chr - chr8 chr8 3 562541 color=black
chr - chr9 chr9 1 439888 color=black
chr - chr10 chr10 2 745751 color=black
chr - chr11 chr11 1 666816 color=black
chr - chr12 chr12 1 1078177 color=black
chr - chr13 chr13 1 924430 color=black
chr - chr14 chr14 1 783698 color=black
chr - chr15 chr15 1 1091291 color=black
chr - chr16 chr16 1 948066 color=black
chr - ref|NC_001224| ref|NC_001224|.1 1 85779 color=black

config2.conf-

<<include etc/colors_fonts_patterns.conf>>

<image>
<<include etc/image.conf>>
</image>

karyotype = S28CC_karyotype.txt
chromosomes_color = /./=var(chr)
chromosomes_units=1000
size = 60

<ideogram>
radius = 0.80r
thickness = 30p
fill = yes
fill_color = grey
stroke_thickness = 2p
stroke_color = black
show_label = yes
label_font = bold
label_size = 36p
label_color = black
label_parallel = yes
show_bands = yes
fill_bands = yes
</ideogram>

<<include etc/housekeeping.conf>>

Also, my main objective is to plot the genomic rearrangements between 2 or 3 strains of yeast. I have an alignment file amongst these strains obtained from BLAST. I would like to plot a circular genomic plot for this, where the rearrangements in the genome between these 2 or 3 strains are linked. How would my config file and my input files(link.txt, karyotype.txt, and other files.) look in this case? I am not able to figure it out from the documentation

- Amit Babu