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  • REPET denovo BLASTER step

    Hi,
    I am troubleshooting the software REPET https://urgi.versailles.inra.fr/Tools/REPET , and I got to the step 2 of TEdenovo.py analysis:

    In
    Code:
    TEdenovo.py -P DmelChr4 -C TEdenovo.cfg -S 2 -s Blaster
    the python script start to work, give you an output folder (DmelChr4_Blaster, with two additional config files), then python is no longer called and it never finish from this terminal output:

    Code:
    START TEdenovo.py (2016-06-23 17:21:44)
    version 2.5
    project name = DmelChr4
    project directory = /users/work/DmelChr4_TEdenovo
    beginning of step 2
    self-alignment with Blaster
    The copy option is: True
    Anyone working with it before and having similar issues. Thanks
    Last edited by cascoamarillo; 06-24-2016, 06:45 AM.

  • #2
    Hi, I had exactly the same problem. When I went into the mysql database manually and deleted the tables TEdenovo.py had created (named 'jobs' and 'info_tables' I think) then ran step 2 again it got farther. The mysql query I used was

    DROP TABLE jobs;
    DROP TABLE info_tables;

    Comment


    • #3
      Thank you!
      OK, now stuck on step 3.....

      Comment

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