Genemark: Can't exec make_mat.v3.0.ini.csh: No such file or directory

Question

[Rob Syme]

A common error when running genemark on a fresh Ubuntu install is for gm_es.pl to fail with an error like:

Can't exec "/opt/genemark/gmes_bp_linux_64/gmes/make_mat.v3.0.ini.csh": No such file or directory at /opt/genemark/current/gmes/gm_es.pl line 270.

The paths may be slightly different, but the error will be the same. Why is this error occurring and what can be done to fix it?

Answer 1

[Rob Syme]

The error is most likely because the c shell (csh) is not installed on your system. If this is the case and you are on Ubuntu, try:

sudo apt-get install csh

If you have csh installed in a location other than /bin/csh, you will need to change the first line of the make_mat.v3.0.ini.csh script to point to your installation, or make a symbolic link to your installation like so:

sudo ln -s /path/to/csh /bin/csh

Another cause might be that the make_mat.v3.0.ini.csh script is no longer executable. If that is the case, try

chmod +x /path/to/make_mat.v3.0.ini.csh