error in Genemark-ES

[Niloofar]

I am trying to use Genemark-ES. The installation went well and the program starts working, however, I get an error message:

Can't exec "/home/ubuntu/gmes/gmes/make_mat.v3.0.ini.csh": No such file or directory at /home/ubuntu/gmes/gmes/gm_es.pl line 270.
Died at /home/ubuntu/gmes/gmes/gm_es.pl line 270.

However, I can see that "make_mat.v3.0.ini.csh" is actually there. So I am confused why I am getting this error and how to resolve it.

Can anyone help with this please?

[GenoMax]

You probably have to add execute permissions for the script file. Try this.

$ chmod a+x /home/ubuntu/gmes/gmes/make_mat.v3.0.ini.csh

If you are using a non-admin account then you may need to use "sudo".

[Niloofar]

Dear GenoMax

Thanks a lot for your quick reply.
I did accordingly but I am still getting the same error

[GenoMax]

Does the file have code in it?

[SES]

You probably have to add execute permissions for the script file. Try this.

$ chmod a+x /home/ubuntu/gmes/gmes/make_mat.v3.0.ini.csh

If you are using a non-admin account then you may need to use "sudo".

It's not a permissions issue or Perl would say:

Permission denied at /path/to/gm_es.pl line xx

Or, since the whole script is really just a bunch of shell commands, executing a command with "system" from Perl would produce a similar error from the shell (depending on the default shell):

sh: make_mat.v3.0.ini.csh: Permission denied

But those are not the errors we see, so there must me something funny with this distribution where the paths are incorrect. FWIW, I could never get this program working for different reasons, and looking at the code convinced me not to try.

[Niloofar]

Does the file have code in it?

Sorry GenoMax, I cannot understand the question. As you may have alrady noticed, I am quite new to Linux. Would you please explain which file you mean?

[Niloofar]

It's not a permissions issue or Perl would say:

Permission denied at /path/to/gm_es.pl line xx

Or, since the whole script is really just a bunch of shell commands, executing a command with "system" from Perl would produce a similar error from the shell (depending on the default shell):

sh: make_mat.v3.0.ini.csh: Permission denied

But those are not the errors we see, so there must me something funny with this distribution where the paths are incorrect. FWIW, I could never get this program working for different reasons, and looking at the code convinced me not to try.

Thanks, SES
Yes, I can see on the web that many users have had problems with GeneMark. Thanks for your reply