circos plots not created when running example command.

[asifzubair]

Hi, I checked that all circos requirements are satisfied by running:

./test.modules which output:

ok   Carp
ok   Config::General
ok   Cwd
ok   Data::Dumper
ok   Digest::MD5
ok   File::Basename
ok   File::Spec::Functions
ok   File::Temp
ok   FindBin
ok   GD
ok   GD::Image
ok   GD::Polyline
ok   Getopt::Long
ok   IO::File
ok   List::MoreUtils
ok   List::Util
ok   Math::Bezier
ok   Math::BigFloat
ok   Math::Round
ok   Math::VecStat
ok   Memoize
ok   POSIX
ok   Params::Validate
ok   Pod::Usage
ok   Readonly
ok   Regexp::Common
ok   Set::IntSpan
ok   Storable
ok   Sys::Hostname
ok   Text::Format
ok   Time::HiRes

However, after running the example command:
perl mitoSeek.pl -i Examples/brca_tumor.bam -j Examples/brca_normal.bam -t 4 -sb 0 -hp 1 -d 5 -str 4 -sp 1 -sa 0
I find that there are no .png files in my brca_tumor/circos folder.
Is there some way I could trouble shoot this ? Thanks !

[tanovsky]

same problem.. :S please help!

[tanovsky]

were u using ubuntu too? solved with advice from http://davetang.org/muse/2012/05/08/installing-circos/

[asifzubair]

Thanks! I think I tried this on Mac - but I'll look at the link you provided.

[xapata83]

Hi,

I was having the same problem till earlier today (running this on debian). It's an issue with the env variable pointing to the bin folder. As root, ln -s /usr/bin/env /bin/env worked for me. If you don't have root access, you can manually edit the files in the /Resources/circos/bin directory as described in the circos README file (located in the Resources/circos directory).