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Old 03-19-2011, 08:31 AM   #1
Location: Taiwan

Join Date: Jan 2010
Posts: 17
Default 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 ?
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?

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Old 03-21-2011, 02:16 AM   #2
Location: France

Join Date: Jan 2010
Posts: 23

Wich is your python version ?
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 at 02:24 AM.
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Old 03-30-2011, 01:13 AM   #3
Location: Taiwan

Join Date: Jan 2010
Posts: 17

Actually, my .bashrc has a wrong $PATH direction for the Python settings.
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