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  • error in Genemark-ES

    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?

  • #2
    You probably have to add execute permissions for the script file. Try this.

    Code:
    $ 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".

    Comment


    • #3
      Dear GenoMax

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

      Comment


      • #4
        Does the file have code in it?

        Comment


        • #5
          Originally posted by GenoMax View Post
          You probably have to add execute permissions for the script file. Try this.

          Code:
          $ 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:
          Code:
          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):
          Code:
          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.

          Comment


          • #6
            Originally posted by GenoMax View Post
            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?

            Comment


            • #7
              Originally posted by SES View Post
              It's not a permissions issue or Perl would say:
              Code:
              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):
              Code:
              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

              Comment

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