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

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?

maker annotation genemark
• 2,877 views • link
updated by Ram Ram • written by Rob Syme Rob Syme

1 answer

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
• 0 views • link
updated by Ram Ram • written by Rob Syme Rob Syme

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