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  • Votinhkiem90
    Member
    • Sep 2013
    • 30
    #1

    How to run script (csh file) in Glimmer

    tnt@tnt:~$ Downloads/glimmer3.02/sample-run/g3-from-scratch.csh auto_data_31/contigs.fa test
    Step 1 of 4: Finding long orfs for training
    /fs/szgenefinding/Glimmer3/bin/long-orfs: Command not found.
    Failed to find long-orf training set

    Tags: None
  • GenoMax
    Senior Member
    • Feb 2008
    • 7142
    #2
    Originally posted by Votinhkiem90 View Post
    tnt@tnt:~$ Downloads/glimmer3.02/sample-run/g3-from-scratch.csh auto_data_31/contigs.fa test
    Step 1 of 4: Finding long orfs for training
    /fs/szgenefinding/Glimmer3/bin/long-orfs: Command not found.
    Failed to find long-orf training set

    Did you compile the program after downloading the source?

    Code:
    /fs/szgenefinding/Glimmer3/bin/long-orfs: Command not found.
    That seems to indicate that the script is unable to find the "long-orf" program that should be present in /bin after compilation.

    Comment

    • Votinhkiem90
      Member
      • Sep 2013
      • 30
      #3
      Originally posted by GenoMax View Post
      Did you compile the program after downloading the source?

      Code:
      /fs/szgenefinding/Glimmer3/bin/long-orfs: Command not found.
      That seems to indicate that the script is unable to find the "long-orf" program that should be present in /bin after compilation.
      Thank for help, I compiled but have an error.
      * Make Target is all
      ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/Common all #####
      make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/Common'
      make[1]: Nothing to be done for `all'.
      make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/Common'
      ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/ICM all #####
      make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/ICM'
      make[1]: Nothing to be done for `all'.
      make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/ICM'
      ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/Glimmer all #####
      make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/Glimmer'
      make[1]: Nothing to be done for `all'.
      make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/Glimmer'
      ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/Util all #####
      make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/Util'
      make[1]: Nothing to be done for `all'.
      make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/Util'
      * Make Target is all
      ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/Common all #####
      make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/Common'
      make[1]: Nothing to be done for `all'.
      make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/Common'
      ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/ICM all #####
      make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/ICM'
      make[1]: Nothing to be done for `all'.
      make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/ICM'
      ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/Glimmer all #####
      make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/Glimmer'
      make[1]: Nothing to be done for `all'.
      make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/Glimmer'
      ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/Util all #####
      make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/Util'
      make[1]: Nothing to be done for `all'.
      make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/Util'
      * Make Target is all
      ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/Common all #####
      make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/Common'
      make[1]: Nothing to be done for `all'.
      make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/Common'
      ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/ICM all #####
      make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/ICM'
      make[1]: Nothing to be done for `all'.
      make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/ICM'
      ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/Glimmer all #####
      make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/Glimmer'
      make[1]: Nothing to be done for `all'.
      make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/Glimmer'
      ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/Util all #####
      make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/Util'
      make[1]: Nothing to be done for `all'.
      make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/Util'
      tnt@tnt:~/Downloads/glimmer3.02/src$ make
      * Make Target is all
      ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/Common all #####
      make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/Common'
      make[1]: Nothing to be done for `all'.
      make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/Common'
      ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/ICM all #####
      make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/ICM'
      make[1]: Nothing to be done for `all'.
      make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/ICM'
      ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/Glimmer all #####
      make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/Glimmer'
      make[1]: Nothing to be done for `all'.
      make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/Glimmer'
      ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/Util all #####
      make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/Util'
      make[1]: Nothing to be done for `all'.
      make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/Util'
      * Make Target is all
      ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/Common all #####
      make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/Common'
      make[1]: Nothing to be done for `all'.
      make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/Common'
      ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/ICM all #####
      make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/ICM'
      make[1]: Nothing to be done for `all'.
      make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/ICM'
      ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/Glimmer all #####
      make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/Glimmer'
      make[1]: Nothing to be done for `all'.
      make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/Glimmer'
      ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/Util all #####
      make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/Util'
      make[1]: Nothing to be done for `all'.
      make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/Util'
      * Make Target is all
      ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/Common all #####
      make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/Common'
      make[1]: Nothing to be done for `all'.
      make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/Common'
      ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/ICM all #####
      make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/ICM'
      make[1]: Nothing to be done for `all'.
      make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/ICM'
      ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/Glimmer all #####
      make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/Glimmer'
      make[1]: Nothing to be done for `all'.
      make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/Glimmer'
      ##### Making Directory /home/tnt/Downloads/glimmer3.02/src/Util all #####
      make[1]: Entering directory `/home/tnt/Downloads/glimmer3.02/src/Util'
      make[1]: Nothing to be done for `all'.
      make[1]: Leaving directory `/home/tnt/Downloads/glimmer3.02/src/Util'
      tnt@tnt:~/Downloads/glimmer3.02/src$ cd ..
      How to fix?

      Comment

      • GenoMax
        Senior Member
        • Feb 2008
        • 7142
        #4
        I do not see an error in the "make".

        Can you check "/fs/szgenefinding/Glimmer3/bin/" directory to see if it has been populated? You should now be able to run the original program as long as the executables are there in /fs/szgenefinding/Glimmer3/bin/ directory.

        Comment

        • Votinhkiem90
          Member
          • Sep 2013
          • 30
          #5
          Originally posted by GenoMax View Post
          I do not see an error in the "make".

          Can you check "/fs/szgenefinding/Glimmer3/bin/" directory to see if it has been populated? You should now be able to run the original program as long as the executables are there in /fs/szgenefinding/Glimmer3/bin/ directory.
          thanks for help, What should I do? "/fs/szgenefinding/Glimmer3/bin/" directory not populated?

          Comment

          • GenoMax
            Senior Member
            • Feb 2008
            • 7142
            #6
            Originally posted by Votinhkiem90 View Post
            thanks for help, What should I do? "/fs/szgenefinding/Glimmer3/bin/" directory not populated?
            I just realized that you compiled the software in a new location. So the directory you would want to check would be

            /home/tnt/Downloads/glimmer3.02/bin

            Comment

            • Votinhkiem90
              Member
              • Sep 2013
              • 30
              #7
              Originally posted by GenoMax View Post
              I just realized that you compiled the software in a new location. So the directory you would want to check would be
              Yes, I know, but I don't know how to compile it.
              However, all tool in the /glimmer3.02/bin still normally running? when I want to run g3-from,... in Scipts express this error.
              hmm

              Comment

              • Bioinform
                Member
                • May 2013
                • 17
                #8
                -bash: ./g3-from-scratch.csh: Permission denied

                Originally posted by Votinhkiem90 View Post
                Yes, I know, but I don't know how to compile it.
                However, all tool in the /glimmer3.02/bin still normally running? when I want to run g3-from,... in Scipts express this error.
                hmm
                HI,

                I am having a problem with glimmer3.

                -bash: ./g3-from-scratch.csh: Permission denied

                Help would be appreciated

                Thanks

                Comment

                • GenoMax
                  Senior Member
                  • Feb 2008
                  • 7142
                  #9
                  Originally posted by Bioinform View Post
                  HI,

                  I am having a problem with glimmer3.

                  -bash: ./g3-from-scratch.csh: Permission denied

                  Help would be appreciated

                  Thanks
                  You probably do not have execute permissions on that script. Do the following
                  Code:
                  $ chmod u+x ./g3-from-scratch.csh

                  Comment

                  • Rabia Faizan
                    Junior Member
                    • Mar 2018
                    • 2
                    #10
                    i need help

                    Comment

                    • Rabia Faizan
                      Junior Member
                      • Mar 2018
                      • 2
                      #11
                      urgent

                      need help in Glimmer installation please its urgent

                      Comment

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