[maker-devel] trouble running example

[Emily Wong]

Hello,

I'm a little stuck running the example - wondering if you may have any suggestions?
When I run:
maker -CTL

I get:
which: no RepeatMasker in (/usr/local/bio/staden-linux-x86-1-7-0/linux-x86_64-bin:/usr/lib64/qt-3.3/bin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/home/emily/bin:/home/emily/maker/bin)
which: no augustus in (/usr/local/bio/staden-linux-x86-1-7-0/linux-x86_64-bin:/usr/lib64/qt-3.3/bin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/home/emily/bin:/home/emily/maker/bin)
which: no snap in (/usr/local/bio/staden-linux-x86-1-7-0/linux-x86_64-bin:/usr/lib64/qt-3.3/bin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/home/emily/bin:/home/emily/maker/bin)

But I ignore this as I've specified in the contig maker_opts.ctl that RepeatMasker and SNAP are in home/emily/repeatmasker and /snap respectively (and I am not running augustus).

So then I run:
maker maker_exe.ctl maker_opts.ctl maker_bopts.ctl

I get:
Argument "fly" isn't numeric in division (/) at /home/emily/maker/bin/maker line 1654, <CTL> line 44.
Argument "/usr/local/SNAP" isn't numeric in division (/) at /home/emily/maker/bin/maker line 1654, <CTL> line 44.
Illegal division by zero at /home/emily/maker/bin/maker line 1654, <CTL> line 44            

This is line 44 in maker:
$|  = 1;

Or should I be looking at line 1654?

I'm not sure where "/usr/local/SNAP" is coming from as snap is installed in my home directory 'home/emily/snap'.


Thanks in advance,
Emily



Emily Wong

PhD Student

Faculty of Veterinary Science
The University of Sydney
Room 511, 
Gunn Building (B19), Regimental Crescent
NSW 2006 Australia
Email: emilyw at vetsci.usyd.edu.au
Ph: +61 433 567 288




Emily Wong

PhD Student

Faculty of Veterinary Science
The University of Sydney
Room 511, 
Gunn Building (B19), Regimental Crescent
NSW 2006 Australia
Email: emilyw at vetsci.usyd.edu.au
Ph: +61 433 567 288


-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20080721/2db67938/attachment.html