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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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