Warnings or Errors were seen
ERROR PARSING YOUR TABLE FILE problem: Cell value (data) for (data,data) is not numeric. 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/kfqgweusamp/results/circos-table-kfqgweusamp-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: Cell value (data) for (data,data) is not numeric. 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/kfqgweusamp
debuggroup summary 0.22s command CIRCOS_DIR/bin/circos -param random_string=kfqgweusamp -conf WORKING_DIR/kfqgweusamp/etc/circos.conf
debuggroup summary 0.22s guessing configuration file
debuggroup summary 0.22s found conf file /var/tmp/tableviewer/kfqgweusamp/etc/circos.conf
*** CIRCOS ERROR ***
cwd: /var/tmp/tableviewer/kfqgweusamp
command: CIRCOS_DIR/bin/circos
-param random_string=kfqgweusamp -conf
WORKING_DIR/kfqgweusamp/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/kfqgweusamp/etc
/var/tmp/tableviewer/kfqgweusamp/etc
/var/tmp/tableviewer/kfqgweusamp/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/kfqgweusamp/etc./var/tmp/tableviewer/kfqgweusamp/etc./var/tmp/tableviewer/kfqgweusamp/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
# Small 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
| data | data | 255,136,0 | 186,255,0 | 104,152,178 | 38,82,153 |
| data | data | A | B | C | D |
| 255,136,0 | A | 10 | 10 | 10 | 10 |
| 186,255,0 | B | 20 | 20 | 20 | 20 |
| 200,200,200 | E | 30 | 30 | 40 | 40 |
| 150,150,150 | F | 50 | 50 | 60 | 60 |
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
7.29 s
draw
0.70 s
resize1
0.00 s
resize2
0.13 s
parse
0.26 s
conf
0.22 s
fileprep
1.26 s
archive
0.13 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 localparams
$VAR1 = { 'sample' => '1', 'tablefile' => 'table-20.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-20.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-20.txt |
| REMOTE_ADDR | 18.188.242.160 |
| REMOTE_PORT | 53102 |
| REQUEST_METHOD | GET |
| REQUEST_SCHEME | https |
| REQUEST_URI | /tableviewer/?sample=1&tablefile=table-20.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 | ZxHuzjLU_gAUnkPQIIatowAAAEw |
cookie
| cookie not defined |