Circos does not run under Unix in a cluster

[e.b...@tum.de]

Hi all,

I am new to Circos and try to use it in a Unix cluster. Circos v0.67 was installed in the general software folder for all users (where users have no write rights) and in my personal user folder (/data/home/lu23boh/software/). I checked for the required Perl modules and that seems to be fine (ok for all).

When I run it with my own conf file I get the following:

lu23boh@tuwzz7x-slph5:~/4circos> circos -conf /data/home/lu23boh/4circos/etc/conf_zm_karyotype_and_layout2EB.conf
debuggroup summary 0.20s welcome to circos v0.67-4 27 Nov 2014 on Perl 5.010000
debuggroup summary 0.20s loading configuration from file /data/home/lu23boh/4circos/etc/conf_zm_karyotype_and_layout2EB.conf
debuggroup summary 0.20s found conf file /data/home/lu23boh/4circos/etc/conf_zm_karyotype_and_layout2EB.conf
debuggroup summary 0.73s debug will appear for these features: output,summary
debuggroup summary 0.73s bitmap output image /data/home/lu23boh/4circos/mydata/ZM_test.png
debuggroup summary 0.73s parsing karyotype and organizing ideograms
WARNING *** Bands for chromosome [Zm10] do not cover entire chromosome
WARNING *** Circos produced a warning and quit because you are running it in paranoid mode. The warning does not nececessarily mean that something is wrong - Circos was likely trying to guess a parameter or massage data to fit the figure.
To change this setting, use -noparanoid flag or change the 'paranoid' parameter in etc/housekeeping.conf to 'paranoid=no'.
 at /data/home/lu23boh/software/circos-0.67/circos-0.67-4/bin/../lib/Circos/Error.pm line 418
        Circos::Error::fatal_error('warning', 'paranoid') called at /data/home/lu23boh/software/circos-0.67/circos-0.67-4/bin/../lib/Circos/Debug.pm line 395
        Circos::Debug::printwarning('Bands for chromosome [Zm10] do not cover entire chromosome') called at /data/home/lu23boh/software/circos-0.67/circos-0.67-4/bin/../lib/Circos/Karyotype.pm line 238
        Circos::Karyotype::validate_karyotype('karyotype', 'HASH(0x28253c0)') called at /data/home/lu23boh/software/circos-0.67/circos-0.67-4/bin/../lib/Circos.pm line 212
        Circos::run('Circos', 'configfile', '/data/home/lu23boh/4circos/etc/conf_zm_karyotype_and_layout2E...') called at /data/home/lu23boh/bin/circos line 382

Then I tried:
lu23boh@tuwzz7x-slph5:~/4circos> circos -conf /data/home/lu23boh/4circos/etc/conf_zm_karyotype_and_layout2EB.conf -noparanoid
debuggroup summary 0.19s welcome to circos v0.67-4 27 Nov 2014 on Perl 5.010000
debuggroup summary 0.19s loading configuration from file /data/home/lu23boh/4circos/etc/conf_zm_karyotype_and_layout2EB.conf
debuggroup summary 0.19s found conf file /data/home/lu23boh/4circos/etc/conf_zm_karyotype_and_layout2EB.conf
debuggroup summary 0.71s debug will appear for these features: output,summary
debuggroup summary 0.71s bitmap output image /data/home/lu23boh/4circos/mydata/ZM_test.png
debuggroup summary 0.71s parsing karyotype and organizing ideograms
debuggroup summary 0.72s karyotype has 10 chromosomes of total size 2,058,582,563
debuggroup summary 0.73s applying global and local scaling
debuggroup summary 0.74s allocating image, colors and brushes
debuggroup summary 2.34s drawing 10 ideograms of total size 2,058,582,563
debuggroup summary 2.34s drawing highlights and ideograms
Speicherzugriffsfehler
"Speicherzugriffsfehler" seems to be "segmentation fault" in English.

If I try to run the example data from my user folder /data/home/lu23boh/software/ I get:
lu23boh@tuwzz7x-slph5:~/4circos> circos -conf /data/home/lu23boh/software/circos-0.67/circos-0.67-4/example/etc/circos.conf
debuggroup summary 0.71s welcome to circos v0.67-4 27 Nov 2014 on Perl 5.010000
debuggroup summary 0.71s loading configuration from file /data/home/lu23boh/software/circos-0.67/circos-0.67-4/example/etc/circos.conf
debuggroup summary 0.71s found conf file /data/home/lu23boh/software/circos-0.67/circos-0.67-4/example/etc/circos.conf
debuggroup summary 1.96s debug will appear for these features: output,summary
Use of uninitialized value in pattern match (m//) at /data/home/lu23boh/software/circos-0.67/circos-0.67-4/bin/../lib/Circos.pm line 156.
Use of uninitialized value in pattern match (m//) at /data/home/lu23boh/software/circos-0.67/circos-0.67-4/bin/../lib/Circos.pm line 157.
fileparse(): need a valid pathname at /data/home/lu23boh/software/circos-0.67/circos-0.67-4/bin/../lib/Circos.pm line 160

I am afraid I am not too familiar with Unix. I would appreciate any help which helps me to get Circos running. It is really a great tool for visualizing genome data.

If any other information is needed, please let me know.

Cheers,
Eva

[Martin Krzywinski]

The last error is unusual, making me think something is amiss. 

Run the example from the example directory

> cd /data/home/lu23boh/software/circos-0.67/circos-0.67-4/example

> circos

The error you're seeing seems to be due to some parameters not being imported from configuration files that are called by circos.conf. Try this

lu23boh@tuwzz7x-slph5:~/4circos> circos -conf /data/home/lu23boh/software/circos-0.67/circos-0.67-4/example/etc/circos.conf -cdump image

This will report the parameters in the <image> block at runtime. Post it here.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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[Eva]

Dear Martin,

I used the option you indicated below and the result is:

lu23boh@tuwzz7x-slph5:~/software/circos-0.67/circos-0.67-4> circos -conf /data/home/lu23boh/software/circos-0.67/circos-0.67-4/example/etc/circos.conf -cdump image
debuggroup summary 0.32s welcome to circos v0.67-4 27 Nov 2014 on Perl 5.010000
debuggroup summary 0.32s loading configuration from file /data/home/lu23boh/software/circos-0.67/circos-0.67-4/example/etc/circos.conf
debuggroup summary 0.32s found conf file /data/home/lu23boh/software/circos-0.67/circos-0.67-4/example/etc/circos.conf
$CONFimage1 = {
                '24bit' => 1,
                angle_offset => -90,
                auto_alpha_colors => 1,
                auto_alpha_steps => '5',
                background => 'white',
                dir => '.',
                file => 'circos.png',
                image_map_file => undef,
                image_map_missing_parameter => undef,
                image_map_name => undef,
                image_map_use => undef,
                png => 1,
                radius => '1500p',
                svg => 1
              };
lu23boh@tuwzz7x-slph5:~/software/circos-0.67/circos-0.67-4>


Any idea how to proceed?

Best regards,
Eva

p.s.: And sorry for having posted twice the same problem. I did not realize that postings have to be cleared by the administrator and I did not see my first posting. You could delete the other thread.

[Eva]

Here is the solution:

It seems that it was not an installation problem, but something maybe trivial for those of you who only work on unix systems and are more familiar with that.
The input files and conf files were edited under Windows. I converted them now using the dos2unix command and now it seems to work.

Now I can spend lots of time creating colourful circos plots :)

Cheers,
Eva

Am Dienstag, 16. Dezember 2014 17:33:03 UTC+1 schrieb Eva:

[Martin Krzywinski]

Yes, anytime you edit files in Windows and use them in UNIX you'll come across the end-of-line encoding incompatibility.

There's a good article about this at

http://stackoverflow.com/questions/7175977/how-to-replace-m-with-a-new-line-in-perl

that shows you how dos2unix, mac2unix and unix2dos work.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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[yas...@mibi03.meb.uni-bonn.de]

On Thursday, April 30, 2015 at 20:20, yassin wrote:

 

I installed circos. How can I check that my installation is okay? I have a genome sequence of a bacterium. How I can work with it using circos.

Thank you

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[Martin Krzywinski]

You can check that things are working by generating the example image that comes with the distribution.

Check example/README

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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