visualize settings samples about

Warnings or Errors were seen

ERROR PARSING YOUR TABLE FILE
 
problem: Column size (data) is not numeric. You have specified that a row with column sizes exists, but it doesn't seem that way. Are you sure that your setting of col_size_row=yes is correct?
 
Died at /home/martink/work/circos/svn/tools/tableviewer/bin/parse-table line 1752, <FILE> line 13.
Circos image output (/home/martink/www/htdocs/tableviewer/tmp/qgweciqsamp/results/circos-table-qgweciqsamp-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: Column size (data) is not numeric. You have specified that a row with column sizes exists, but it doesn't seem that way. Are you sure that your setting of col_size_row=yes is correct?
 
Died at /home/martink/work/circos/svn/tools/tableviewer/bin/parse-table line 1752, <FILE> line 13.

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

  *** CIRCOS ERROR ***

      cwd: /var/tmp/tableviewer/qgweciqsamp

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

  /var/tmp/tableviewer/qgweciqsamp/etc

  /var/tmp/tableviewer/qgweciqsamp/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/qgweciqsamp/etc./var/tmp/tableviewer/qgweciqsamp/etc./var/tmp/tableviewer/qgweciqsamp/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


# Medium tab-delimited table with mixed row and column labels.
#
# + column size (first row)
# + row size (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	 [x] col with row size	  [x] row with col size
# color	 [ ] col with row colors  [ ] row with col colors









data
data
3000
2750
2500
2500
750
1250
1500




data
data
A
B
C
D
E
F
G




3000
A
105
450
92
96
5
301
195




2750
B
20
46
78
33
53
28
83




2500
C
118
553
94
317
25
89
287




2500
D
100
18
108
104
105
25
173




1250
H
23
83
123
342
98
48
205




2000
I
173
428
103
325
82
215
23




1500
J
305
173
138
49
81
258
207

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.
  • Data contains row containing column segment size.
  • 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
8.27 s
draw
0.73 s
resize1
0.00 s
resize2
0.20 s
parse
0.30 s
conf
0.25 s
fileprep
1.65 s
archive
0.27 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 = {
  'columns' => 'col_size',
  'sample' => '1',
  'tablefile' => 'table-07.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?columns=col_size&sample=1&tablefile=table-07.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 columns=col_size&sample=1&tablefile=table-07.txt
REMOTE_ADDR 18.222.98.201
REMOTE_PORT 55258
REQUEST_METHOD GET
REQUEST_SCHEME https
REQUEST_URI /tableviewer/?columns=col_size&sample=1&tablefile=table-07.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 Ztz8tz8ymABCcauuJVKQfgAAAIA

cookie

cookie not defined