Use of uninitialized value $norm[0] in join or string at /usr/bin/circos-0.56/bin/../lib/Circos/Unit.pm line 187, <F> line 1310.

[Olga Botvinnik]

Hello,

I am working my way through circos-course-0.03 and I'm having trouble with session 3, lesson 2 (aka 3/2). The *.conf files are attached.

(On Mac OS 10.6.8, Perl 5.12.4)

localhost:2 olgabotvinnik$ $CIRCOS/bin/circos -conf etc/circos.conf

debuggroup conf 0.11s welcome to circos 0.56

debuggroup conf 0.11s loading configuration from file etc/circos.conf

debuggroup conf 0.11s looking for conf file etc/circos.conf

debuggroup conf 0.11s found conf file etc/circos.conf

debuggroup summary 0.34s debug will appear for these features: summary

debuggroup summary 0.34s parsing karyotype and organizing ideograms

debuggroup summary 0.52s applying global and local scaling

Use of uninitialized value $norm[0] in join or string at /usr/bin/circos-0.56/bin/../lib/Circos/Unit.pm line 187, <F> line 1310.

Use of uninitialized value within %Circos::Error::GROUPERROR in uc at /usr/bin/circos-0.56/bin/../lib/Circos/Error.pm line 249, <F> line 1310.

  *** CIRCOS ERROR ***

  Unable to convert a value [_undef_] from one unit [n] to another [b]. The

  following from->to combinations were expected: r->b u->b

  If you are having trouble debugging this error, use this tutorial to learn how

  to use the debugging facility

      http://www.circos.ca/tutorials/lessons/configuration/debugging

  If you're still stumped, get support in the Circos Google Group

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

  Stack trace:

 at /usr/bin/circos-0.56/bin/../lib/Circos/Error.pm line 277

Circos::Error::fatal_error('unit', 'conversion_fail', undef, 'n', 'b', 'r->b u->b') called at /usr/bin/circos-0.56/bin/../lib/Circos/Unit.pm line 224

Circos::Unit::unit_convert('from', undef, 'to', 'b', 'factors', 'HASH(0x100fc0d20)') called at /opt/local/lib/perl5/5.12.4/Memoize.pm line 247

Memoize::_memoizer(undef, 'from', undef, 'to', 'b', 'factors', 'HASH(0x100fc0d20)') called at /usr/bin/circos-0.56/bin/../lib/Circos.pm line 6502

Circos::ideogram_spacing('HASH(0x100fb1cc0)', 'HASH(0x100fb1ee8)') called at /opt/local/lib/perl5/5.12.4/Memoize.pm line 247

Memoize::_memoizer(undef, 'HASH(0x100fb1cc0)', 'HASH(0x100fb1ee8)') called at /usr/bin/circos-0.56/bin/../lib/Circos.pm line 547

Circos::run('Circos', 'configfile', 'etc/circos.conf') called at /usr/bin/circos-0.56/bin/circos line 229

Also, the symlinks for ticks.conf and ideogram.conf haven't worked for me, so I've been copying the files over. They point to circos-course-0.03/../../1/etc/ticks.conf (for example), which doesn't exist since the Circos directory is not in the current folder, plus for some of them, when I trace my way back to where the original file is supposed to be, it's not even there. A suggestion is to have redundant files in all the lesson directories, or to link them to the session directories, which seem to work fine.

[Martin Krzywinski]

Hi Olga,

The course files are old and out of date. I'm going to be posting Circos v0.60 and new course files in the next day or so, for next week's class in Naples.

Sorry for these incompatibility problems. You're not doing anything wrong.

Meanwhile, use the tutorials.

Martin

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