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  • Tophat error

    I'm doing analysis with Solexa data, and I try to use Tophat.
    However, I'm not sure why sometimes the system would throw out the error messages while sometimes it works correctly.

    The error message would be as follows:
    Traceback (most recent call last):
    File "./tophat", line 2347, in ?
    sys.exit(main())
    File "./tophat", line 2252, in main
    params.read_params = check_reads(params.read_params, reads_list)
    File "./tophat", line 1045, in check_reads
    observed_formats = set([])
    NameError: global name 'set' is not defined

    Is it a bug? Or something else?


    Thanks.

  • #2
    Wich is your python version ?
    Code:
    python -V
    Edit: I think you are alternatively using 2 python versions:
    - one older than 2.3 (which haven't the set command)
    - another more recent (works)
    I had a similar problem not so long ago, because in my .bashrc there were a $PATH problem: one path containing an old version of python was called first when I use a bash shell :-/
    Last edited by nicolallias; 03-21-2011, 02:24 AM.

    Comment


    • #3
      Ooops!
      Actually, my .bashrc has a wrong $PATH direction for the Python settings.
      Thanks!

      Comment

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