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:
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.
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).
Download: | data, images (PNG/SVG) and configuration
# 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 |
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.
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 = { '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 not defined |