Entering edit mode
9.4 years ago
Whoknows
▴
960
Hi friends
I installed Tophat2 with all dependencies (bowtie2, Boost, Samtools) but when I want to run tophat, it shows this error:
File "/home/tophat-2.0.14/bin/tophat", line 1003
except getopt.error, msg: ^
SyntaxError: invalid syntax
My python version is 3.4 , how can I fix this problem?
Thanks
What Devon said. Tophat is not Python 3 clean, so Python 2 is required.
Hi Whoknows, did Devon's suggestion work for you?
Yes, tophat has problem with python 2, I had to reinstall linux with python2
Please accept his answer if that's the case, so this question would be marked as solved by the system.
Yes it was because python 3 in changed to python 2
Click the green check mark you see on the left panel of his answer, near the number of votes.