Warnings or Errors were seen

ERROR PARSING YOUR TABLE FILE
 
problem: Duplicate column name (50,50,50) found. Please makes sure that all column names in the header are different.
 
Died at /home/martink/work/circos/svn/tools/tableviewer/bin/parse-table line 1752, <FILE> line 15.
Circos image output (/home/martink/www/htdocs/tableviewer/tmp/vtgmlcysamp/results/circos-table-vtgmlcysamp-large.png) could not be found.

Don't panic. Read the error reports below and the hint section that explains what might be going wrong.

ERROR PARSING YOUR TABLE FILE
 
problem: Duplicate column name (50,50,50) found. Please makes sure that all column names in the header are different.
 
Died at /home/martink/work/circos/svn/tools/tableviewer/bin/parse-table line 1752, <FILE> line 15.

debuggroup summary 0.22s welcome to circos v0.68-pre1 7 Apr 2015 on Perl 5.032001
debuggroup summary 0.23s current working directory /var/tmp/tableviewer/vtgmlcysamp
debuggroup summary 0.23s command CIRCOS_DIR/bin/circos -param random_string=vtgmlcysamp -conf WORKING_DIR/vtgmlcysamp/etc/circos.conf
debuggroup summary 0.23s guessing configuration file
debuggroup summary 0.23s found conf file /var/tmp/tableviewer/vtgmlcysamp/etc/circos.conf

  *** CIRCOS ERROR ***

      cwd: /var/tmp/tableviewer/vtgmlcysamp

      command: CIRCOS_DIR/bin/circos
      -param random_string=vtgmlcysamp -conf
      WORKING_DIR/vtgmlcysamp/etc/circos.conf

  CONFIGURATION FILE ERROR

  Error parsing the configuration file. You used an <<include FILE>> directive,
  but the FILE could not be found. This FILE is interpreted relative to the
  configuration file in which the <<include>> directive is used. Circos lookd
  for the file in these directories

  /var/tmp/tableviewer/vtgmlcysamp/etc

  /var/tmp/tableviewer/vtgmlcysamp/etc

  /var/tmp/tableviewer/vtgmlcysamp/etc/etc

  CIRCOS_ROOT/circos-0.68-pre1/bin/etc

  CIRCOS_ROOT/circos-0.68-pre1/bin/../etc

  CIRCOS_ROOT/circos-0.68-pre1/bin/..

  CIRCOS_ROOT/circos-0.68-pre1/bin

  The Config::General module reported the error

  Config::General The file "data/colors.conf" does not exist within ConfigPath:
  /var/tmp/tableviewer/vtgmlcysamp/etc./var/tmp/tableviewer/vtgmlcysamp/etc./var/tmp/tableviewer/vtgmlcysamp/etc/etc.CIRCOS_ROOT/circos-0.68-pre1/bin/etc.CIRCOS_ROOT/circos-0.68-pre1/bin/../etc.CIRCOS_ROOT/circos-0.68-pre1/bin/...CIRCOS_ROOT/circos-0.68-pre1/bin!
  at
  CIRCOS_ROOT/circos-0.68-pre1/bin/../lib/Circos/Configuration.pm
  line 819.

  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. Please
  include this error and all your configuration and data files.

      http://groups.google.com/group/circos-data-visualization

  Stack trace:

Hints

If your data file contains order, size and/or color information for rows and/or columns please check off the appropriate options in the upload form. If you forget to check off the options, you'll probably get an error about duplicate column names. If you have set these options, make sure that your data file has the required information.

If the error refers to -ribbon_variable, then you have ratio layout on (see data samples section to read about data format requirements.

Before uploading a data file, check the samples gallery to make sure that your data format is compatible.

File must be plain text.
Data values must be non-negative integers. If all are <1, multiply them by a fixed factor.
Data must be space-separated (one or more tab or space, which will be collapsed).
No two rows or columns may have the same name.
Column and row names must begin with a letter (e.g. 'A', 'A0', 'A-0') and can only contain letters, numbers and _. No punctuation! No double underscores.
Maximum number of rows × columns is 30 × 30. To visualize larger tables email me (name, institution, use case) and I'll provide you with an access code to remove this restriction. Alternatively, you can install Circos and run the tableviewer scripts without limitations.
If you are using order, size and color rows/columns in combination they must appear in that order.

If you do not adhere to these rules, expect errors.

Need help? Post questions to the Circos Google Group.

You can try again or write to me (attach your file and the error report).

Your table image is ready!

Download: | data, images (PNG/SVG) and configuration

table data used for figure


# Large tab-delimited table with mixed row and column labels.
#
# + column color (first row)
# + row color (first column)
#
# When uploading this file, make sure you check off the fields shown below.
# 
# order	 [ ] col with row order	  [ ] row with col order
# size	 [ ] col with row size	  [ ] row with col size
# color	 [x] col with row colors  [x] row with col colors
#
# This data set uses custom colors to draw focus to specific rows and/or columns.
# All rows and columns are dark grey RGB=(50,50,50) except for row C1 (orange) and C2 (blue).



data
data
50,50,50
50,50,50
50,50,50
50,50,50
50,50,50
50,50,50
50,50,50
50,50,50
50,50,50
50,50,50
50,50,50
50,50,50
50,50,50
50,50,50
50,50,50


data
data
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O


50,50,50
A
91
558
96
113
109
125
57
109
115
102
92
89
42
51
45


50,50,50
B
21
1
21
21
18
18
8
25
17
20
16
21
11
8
10


236,28,36
C1
75
652
93
232
290
278
291
332
99
109
101
97
54
50
48


28,145,236
C2
104
22
100
940
120
109
52
958
112
116
92
96
49
50
45


50,50,50
E
97
22
122
86
112
102
47
104
81
898
79
101
55
54
47


50,50,50
F
83
23
103
96
114
483
46
95
97
94
93
92
50
51
52


50,50,50
G
12
2
10
10
8
10
0
8
10
8
9
9
6
5
247


50,50,50
H
96
20
109
102
106
107
48
117
98
88
94
111
44
46
48


50,50,50
I
100
21
98
87
97
95
45
92
119
111
86
106
50
57
49


50,50,50
J
101
18
81
83
777
111
52
115
100
100
109
99
44
48
45


50,50,50
K
96
19
96
97
400
105
43
86
103
112
92
86
52
52
48


50,50,50
L
100
19
122
70
97
90
41
110
94
85
97
98
60
46
47


50,50,50
M
45
9
49
42
280
47
28
50
47
40
49
50
25
22
29


50,50,50
N
81
16
80
1159
78
77
38
773
66
73
64
80
35
41
37


50,50,50
O
8
2
8
9
9
12
312
11
9
9
9
8
4
6
5

display options

Maximum table size is row × col = 50 × 50
Row/column segments in descending order.
Row/column segments ordered alphabetically by label.
Row ribbons placed first.
Segment color is interpolated by segment count.
Ribbon colour sorce is set to row.
Ribbon transparency set to 1/5.
Ribbon fade transparency set to 0/5.
Larger ribbons on top.

You can change the settings at any time. If you require finer control over the image, you should download Circos and use the bundled tableviewer utility.

total

9.18 s

draw

0.80 s

resize1

0.00 s

resize2

0.19 s

parse

0.47 s

conf

0.45 s

fileprep

2.13 s

archive

0.20 s

Cookie version [NO_VERSION].
Wrong cookie version [NO_VERSION] but needed [0.63-10]. Making new cookie.
access_code 
color_ribbons_by_value 0
contribution_tracks   
encoding 
fade_transparency 0
format        
intra_segment 
label_segment_color vvvdgrey
label_segment_font normal
label_segment_font_size 24
label_segment_on_segment 
label_segment_parallel 1
label_tick_color vvvdgrey
label_tick_font light
label_tick_font_size 16
label_tick_parallel 0
min_percentile 0
normalize 0
placement_order row,col
q1ribbonc inherit
q1ribbons 1
q1ribbont inherit
q1ribbonuse 
q2ribbonc inherit
q2ribbons 1
q2ribbont inherit
q2ribbonuse 
q3ribbonc inherit
q3ribbons 1
q3ribbont inherit
q3ribbonuse 
q4ribbonc inherit
q4ribbons 1
q4ribbont inherit
q4ribbonuse 
ratio_layout 
reverse_ribbons 
ribbon_bundle_order native
ribbon_caps   
ribbon_color_source row
ribbon_layer_order size_asc
segment_color_interpolation count
segment_color_order ascii
segment_order ascii
segment_order_progression size_desc
segment_radius 0.75
segment_spacing 0.0075r
segment_thickness 35p
transparency 1
version 0.63-10
Baking new cookie.
connection local
params
$VAR1 = {
  'sample' => '1',
  'tablefile' => 'table-09.txt'
};

cookie
$VAR1 = {
  'access_code' => [
    ''
  ],
  'color_ribbons_by_value' => [
    0
  ],
  'contribution_tracks' => [
    '',
    '',
    ''
  ],
  'encoding' => [
    ''
  ],
  'fade_transparency' => [
    0
  ],
  'format' => [
    '',
    '',
    '',
    '',
    '',
    '',
    '',
    ''
  ],
  'intra_segment' => [
    ''
  ],
  'label_segment_color' => [
    'vvvdgrey'
  ],
  'label_segment_font' => [
    'normal'
  ],
  'label_segment_font_size' => [
    24
  ],
  'label_segment_on_segment' => [
    ''
  ],
  'label_segment_parallel' => [
    1
  ],
  'label_tick_color' => [
    'vvvdgrey'
  ],
  'label_tick_font' => [
    'light'
  ],
  'label_tick_font_size' => [
    16
  ],
  'label_tick_parallel' => [
    0
  ],
  'min_percentile' => [
    0
  ],
  'normalize' => [
    0
  ],
  'placement_order' => [
    'row,col'
  ],
  'q1ribbonc' => [
    'inherit'
  ],
  'q1ribbons' => [
    1
  ],
  'q1ribbont' => [
    'inherit'
  ],
  'q1ribbonuse' => [
    ''
  ],
  'q2ribbonc' => [
    'inherit'
  ],
  'q2ribbons' => [
    1
  ],
  'q2ribbont' => [
    'inherit'
  ],
  'q2ribbonuse' => [
    ''
  ],
  'q3ribbonc' => [
    'inherit'
  ],
  'q3ribbons' => [
    1
  ],
  'q3ribbont' => [
    'inherit'
  ],
  'q3ribbonuse' => [
    ''
  ],
  'q4ribbonc' => [
    'inherit'
  ],
  'q4ribbons' => [
    1
  ],
  'q4ribbont' => [
    'inherit'
  ],
  'q4ribbonuse' => [
    ''
  ],
  'ratio_layout' => [
    ''
  ],
  'reverse_ribbons' => [
    ''
  ],
  'ribbon_bundle_order' => [
    'native'
  ],
  'ribbon_caps' => [
    '',
    '',
    ''
  ],
  'ribbon_color_source' => [
    'row'
  ],
  'ribbon_layer_order' => [
    'size_asc'
  ],
  'segment_color_interpolation' => [
    'count'
  ],
  'segment_color_order' => [
    'ascii'
  ],
  'segment_order' => [
    'ascii'
  ],
  'segment_order_progression' => [
    'size_desc'
  ],
  'segment_radius' => [
    '0.75'
  ],
  'segment_spacing' => [
    '0.0075r'
  ],
  'segment_thickness' => [
    '35p'
  ],
  'transparency' => [
    1
  ],
  'version' => [
    '0.63-10'
  ]
};

CGI Param

ENV
CONTEXT_DOCUMENT_ROOT	/home/martink/www/htdocs
CONTEXT_PREFIX
DOCUMENT_ROOT	/home/martink/www/htdocs
GATEWAY_INTERFACE	CGI/1.1
HTTPS	on
HTTP_ACCEPT	*/*
HTTP_ACCEPT_ENCODING	gzip, br, zstd, deflate
HTTP_CACHE_CONTROL	max-age=0
HTTP_CONNECTION	keep-alive
HTTP_HOST	mk.bcgsc.ca
HTTP_REFERER	https://mk.bcgsc.ca/tableviewer?sample=1&tablefile=table-09.txt
HTTP_SURROGATE_CAPABILITY	proxy11.dmz.bcgsc.ca="Surrogate/1.0 ESI/1.0"
HTTP_USER_AGENT	Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)
HTTP_VIA	1.1 proxy11.dmz.bcgsc.ca (squid/5.5)
MOD_PERL	mod_perl/2.0.12
MOD_PERL_API_VERSION	2
PATH	/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin
QUERY_STRING	sample=1&tablefile=table-09.txt
REMOTE_ADDR	3.137.167.185
REMOTE_PORT	37410
REQUEST_METHOD	GET
REQUEST_SCHEME	https
REQUEST_URI	/tableviewer/?sample=1&tablefile=table-09.txt
SCRIPT_FILENAME	/home/martink/www/htdocs/tableviewer/index.mhtml
SCRIPT_NAME	/tableviewer/index.mhtml
SCRIPT_URI	https://mk.bcgsc.ca/tableviewer/
SCRIPT_URL	/tableviewer/
SERVER_ADDR	10.9.208.135
SERVER_ADMIN	martink@bcgsc.ca
SERVER_NAME	mk.bcgsc.ca
SERVER_PORT	443
SERVER_PROTOCOL	HTTP/1.1
SERVER_SIGNATURE
SERVER_SOFTWARE	Apache/2.4.53 (Rocky Linux) OpenSSL/3.0.7 mod_apreq2-20101207/2.8.1 mod_perl/2.0.12 Perl/v5.32.1
UNIQUE_ID	Ztz6mw7gGH_ord3G4bKHUgAAAM4

cookie

cookie not defined

data	data	50,50,50	50,50,50	50,50,50	50,50,50	50,50,50	50,50,50	50,50,50	50,50,50	50,50,50	50,50,50	50,50,50	50,50,50	50,50,50	50,50,50	50,50,50
data	data	A	B	C	D	E	F	G	H	I	J	K	L	M	N	O
50,50,50	A	91	558	96	113	109	125	57	109	115	102	92	89	42	51	45
50,50,50	B	21	1	21	21	18	18	8	25	17	20	16	21	11	8	10
236,28,36	C1	75	652	93	232	290	278	291	332	99	109	101	97	54	50	48
28,145,236	C2	104	22	100	940	120	109	52	958	112	116	92	96	49	50	45
50,50,50	E	97	22	122	86	112	102	47	104	81	898	79	101	55	54	47
50,50,50	F	83	23	103	96	114	483	46	95	97	94	93	92	50	51	52
50,50,50	G	12	2	10	10	8	10	0	8	10	8	9	9	6	5	247
50,50,50	H	96	20	109	102	106	107	48	117	98	88	94	111	44	46	48
50,50,50	I	100	21	98	87	97	95	45	92	119	111	86	106	50	57	49
50,50,50	J	101	18	81	83	777	111	52	115	100	100	109	99	44	48	45
50,50,50	K	96	19	96	97	400	105	43	86	103	112	92	86	52	52	48
50,50,50	L	100	19	122	70	97	90	41	110	94	85	97	98	60	46	47
50,50,50	M	45	9	49	42	280	47	28	50	47	40	49	50	25	22	29
50,50,50	N	81	16	80	1159	78	77	38	773	66	73	64	80	35	41	37
50,50,50	O	8	2	8	9	9	12	312	11	9	9	9	8	4	6	5