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  • Help! submit jobs about Corona Lite

    There were some errors when I submit the matching jobs.

    Here is the error message:
    Code:
    [zhan@head mapping_F_25_2]$ submit_scripts_to_PBS.pl -j JOB_LIST.txt &
    [1] 17307
    [zhan@head mapping_F_25_2]$
    Parse a job list file containing script names and run them on PBS.
    
    SUBMIT: output_ALIGN_1_1: /home/zhan/solid/bifxTrainingData_10panels_auto/mappin                                                                                      g_F_25_2/scripts/output_ALIGN_1_1.sh
    qsub: illegal -N value
    Use of uninitialized value in concatenation (.) or string at /data/tools/Corona/                                                                                      lib/perl/PBSJob.pm line 102.
    [ERROR] qsub: (17308):
    
     --
    Sleeping 5 seconds and retrying
    [zhan@head mapping_F_25_2]$ qsub: illegal -N value
    Use of uninitialized value in concatenation (.) or string at /data/tools/Corona/lib/perl/PBSJob.pm line 102.
    [ERROR] qsub: (17336):
    
     --
    Sleeping 10 seconds and retrying
    qsub: illegal -N value
    Use of uninitialized value in concatenation (.) or string at /data/tools/Corona/lib/perl/PBSJob.pm line 102.
    [ERROR] qsub: (17385):
    
     --
    [FATAL]: Submission of job failed after 3 retries
    Job submission output_ALIGN_1_1 failed.
    There was openPBS patched on my cluster.

    Code:
    [zhan@head mapping_F_25_2]$ qmgr
    Max open servers: 4
    Qmgr: p s
    #
    # Create queues and set their attributes.
    #
    #
    # Create and define queue workq
    #
    create queue workq
    set queue workq queue_type = Execution
    set queue workq enabled = True
    set queue workq started = True
    #
    # Create and define queue tracking
    #
    create queue tracking
    set queue tracking queue_type = Execution
    set queue tracking enabled = True
    set queue tracking started = True
    #
    # Create and define queue secondary
    #
    create queue secondary
    set queue secondary queue_type = Execution
    set queue secondary enabled = True
    set queue secondary started = True
    #
    # Set server attributes.
    #
    set server scheduling = True
    set server default_queue = workq
    set server log_events = 511
    set server mail_from = adm
    set server query_other_jobs = True
    set server resources_default.nodect = 1
    set server resources_default.nodes = 1
    set server scheduler_iteration = 600
    set server node_pack = False
    Want some helps, thanks

  • #2
    tracking queue and secondary queue have been created

    the other tasks could be completed by PBS (such as Iprscan)

    How can I do ...

    Comment


    • #3
      Check whether the name of your job exceeds 15 characters or not.
      Xi Wang

      Comment


      • #4
        Originally posted by Xi Wang View Post
        Check whether the name of your job exceeds 15 characters or not.
        Thank you.

        However, this is the standard submitting procedure according to the instructions in Documents.

        I think Job name is set by default.

        Comment


        • #5
          Originally posted by skblazer View Post
          Thank you.

          However, this is the standard submitting procedure according to the instructions in Documents.

          I think Job name is set by default.
          Yes, I thinks so. I dont know if it is a bug of Corona. I also encountered this problem days ago, and I solved this problem by replacing the names of job to shorter ones. I edited the perl script.
          Xi Wang

          Comment


          • #6
            Originally posted by Xi Wang View Post
            Yes, I thinks so. I dont know if it is a bug of Corona. I also encountered this problem days ago, and I solved this problem by replacing the names of job to shorter ones. I edited the perl script.
            Ah...

            So can you tell me which perl script should be edited?

            The version I used is 4.2.2

            Thank you.

            Comment


            • #7
              Originally posted by skblazer View Post
              Ah...

              So can you tell me which perl script should be edited?

              The version I used is 4.2.2

              Thank you.
              My version is 4.0r2.0.

              In the file "matching_large_genomes_cmap_save_script.pl", search "$jobname", make sure all the "$jobname"s are of length less than 15.
              Xi Wang

              Comment


              • #8
                Hi.. Xi Wang
                I have a question.

                some error when I submit the matching jobs on SGE
                -----------------------------------------------------------
                [ngs@bio matching_F3]$ submit_scripts_to_SGE.pl -j JOB_LIST.txt

                Parse a job list file containing script names and run them on SGE.

                Submitting job ALIGN_1_1
                WARNING: No job number. This message was received:

                Failed to submit job ALIGN_1_1
                [ngs@bio matching_F3]$

                [ngs@bio matching_F3]$ cat JOB_LIST.txt
                1 /home/ngs/testData_corona/matching_F3/scripts/output_ALIGN_1_1.sh
                2 /home/ngs/testData_corona/matching_F3/scripts/output_ALIGN_2_1.sh
                3 /home/ngs/testData_corona/matching_F3/scripts/output_ALIGN_3_1.sh
                4 /home/ngs/testData_corona/matching_F3/scripts/output_ALIGN_4_1.sh
                5 echo "wait for matching jobs to finish" 1,2,3,4
                6 /home/ngs/testData_corona/matching_F3/scripts/output_POST_MATCHING_BY_SETS_1.sh
                7 echo "wait for post_matching_by_sets jobs to finish" 6
                8 /home/ngs/testData_corona/matching_F3/scripts/output_POST_MATCHING_BY_CHR_1.sh
                9 /home/ngs/testData_corona/matching_F3/scripts/output_POST_MATCHING_BY_CHR_2.sh
                10 /home/ngs/testData_corona/matching_F3/scripts/output_POST_MATCHING_BY_CHR_3.sh
                11 /home/ngs/testData_corona/matching_F3/scripts/output_POST_MATCHING_BY_CHR_4.sh
                12 echo "wait for post_matching_by_sets jobs to finish" 8,9,10,11
                13 /home/ngs/testData_corona/matching_F3/scripts/output_POST_MATCHING_CONCAT_MATCH_FILES.sh
                13 echo "wait for post_matching_concat_match_files jobs to finish" 13
                14 /home/ngs/testData_corona/matching_F3/scripts/output_POST_MATCHING_FINAL.sh
                15 /home/ngs/testData_corona/matching_F3/scripts/output_POST_MATCHING_MAKING_INDEX.sh
                -----------------------------------------------------------

                Do I need to modify a script(submit_scripts_to_SGE.pl or matching_large_genomes_cmap_save_script.pl) ?
                Last edited by luckyjin; 11-02-2009, 12:27 AM.

                Comment


                • #9
                  Originally posted by luckyjin View Post
                  Hi.. Xi Wang
                  I have a question.

                  some error when I submit the matching jobs on SGE
                  -----------------------------------------------------------
                  [ngs@bio matching_F3]$ submit_scripts_to_SGE.pl -j JOB_LIST.txt

                  Parse a job list file containing script names and run them on SGE.

                  Submitting job ALIGN_1_1
                  WARNING: No job number. This message was received:

                  Failed to submit job ALIGN_1_1
                  [ngs@bio matching_F3]$

                  [ngs@bio matching_F3]$ cat JOB_LIST.txt
                  1 /home/ngs/testData_corona/matching_F3/scripts/output_ALIGN_1_1.sh
                  2 /home/ngs/testData_corona/matching_F3/scripts/output_ALIGN_2_1.sh
                  3 /home/ngs/testData_corona/matching_F3/scripts/output_ALIGN_3_1.sh
                  4 /home/ngs/testData_corona/matching_F3/scripts/output_ALIGN_4_1.sh
                  5 echo "wait for matching jobs to finish" 1,2,3,4
                  6 /home/ngs/testData_corona/matching_F3/scripts/output_POST_MATCHING_BY_SETS_1.sh
                  7 echo "wait for post_matching_by_sets jobs to finish" 6
                  8 /home/ngs/testData_corona/matching_F3/scripts/output_POST_MATCHING_BY_CHR_1.sh
                  9 /home/ngs/testData_corona/matching_F3/scripts/output_POST_MATCHING_BY_CHR_2.sh
                  10 /home/ngs/testData_corona/matching_F3/scripts/output_POST_MATCHING_BY_CHR_3.sh
                  11 /home/ngs/testData_corona/matching_F3/scripts/output_POST_MATCHING_BY_CHR_4.sh
                  12 echo "wait for post_matching_by_sets jobs to finish" 8,9,10,11
                  13 /home/ngs/testData_corona/matching_F3/scripts/output_POST_MATCHING_CONCAT_MATCH_FILES.sh
                  13 echo "wait for post_matching_concat_match_files jobs to finish" 13
                  14 /home/ngs/testData_corona/matching_F3/scripts/output_POST_MATCHING_FINAL.sh
                  15 /home/ngs/testData_corona/matching_F3/scripts/output_POST_MATCHING_MAKING_INDEX.sh
                  -----------------------------------------------------------

                  Do I need to modify a script(submit_scripts_to_SGE.pl or matching_large_genomes_cmap_save_script.pl) ?
                  Sorry, I've never used SGE before. Does anybody else know it?

                  I think you should check the job number manually when you submit a job to SGE. And it would be a problem in the script submit_scripts_to_SGE.pl .
                  Xi Wang

                  Comment


                  • #10
                    Originally posted by Xi Wang View Post
                    My version is 4.0r2.0.

                    In the file "matching_large_genomes_cmap_save_script.pl", search "$jobname", make sure all the "$jobname"s are of length less than 15.
                    Thank you very much.

                    I have solved it according to your suggestion.

                    Comment


                    • #11
                      what is exact solution

                      Originally posted by skblazer View Post
                      Thank you very much.

                      I have solved it according to your suggestion.
                      I have the same problem but i dont know how to solve exactly . so please tell me where to change

                      Comment


                      • #12
                        Originally posted by sarwar View Post
                        I have the same problem but i dont know how to solve exactly . so please tell me where to change
                        Do you have a file named: matching_large_genomes_cmap_save_script.pl?
                        If yes, please edit this file. You can search for "$jobname", and delete some letters of its value.
                        If you can give me some more detailed info, I may help you with more details.
                        Xi Wang

                        Comment


                        • #13
                          Originally posted by Xi Wang View Post
                          Do you have a file named: matching_large_genomes_cmap_save_script.pl?
                          If yes, please edit this file. You can search for "$jobname", and delete some letters of its value.
                          If you can give me some more detailed info, I may help you with more details.
                          when we submit the job through submit_script_SGE.pl then it says like following in terminal:
                          ###############################################
                          warning : no job number .this message was received:
                          qsub: illigal -c value
                          failed to submit job ALIGN_1_1
                          ####################################

                          ofcourse i have file matching_large_genome..._cmap_save_script.pl
                          so please help me out .
                          thanks in advance
                          Last edited by sarwar; 05-10-2010, 03:43 AM. Reason: adding more information

                          Comment


                          • #14
                            Originally posted by sarwar View Post
                            when we submit the job through submit_script_SGE.pl then it says like following in terminal:
                            ###############################################
                            warning : no job number .this message was received:
                            qsub: illigal -c value
                            failed to submit job ALIGN_1_1
                            ####################################

                            so please help me out .
                            thanks in advance
                            Sorry, I've no idea about the problem regarding SGE. Hope others can help you.
                            Xi Wang

                            Comment


                            • #15
                              Originally posted by Xi Wang View Post
                              Sorry, I've never used SGE before. Does anybody else know it?

                              I think you should check the job number manually when you submit a job to SGE. And it would be a problem in the script submit_scripts_to_SGE.pl .

                              is this problem solved?

                              i have the same problem
                              please help me out ..

                              Comment

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