Tophat Error

[ercfrtz]

I have been using tophat and it has been running fine, but I recently started receiving the following error. I checked my install version and saw it was a version behind and installed the newest version and get the same error.

File "/shared/local/tophat-1.4.1.Linux_x86_64/tophat", line 650
except getopt.error, msg:
^
SyntaxError: invalid syntax


Does anyone know what would be causing this issue?

[peromhc]

Can you provide us with the command you supplied to tophat? the getopt.error suggests to me that something abut your command is wrong.

[ercfrtz]

/shared/local/tophat-1.4.1.Linux_x86_64/tophat -r 100 -o /storage/isu/reecy_lab/tmp_eric/new.Lee.data/kph /storage/isu/reecy_lab/tmp_eric/index/b_taurus/umd3.1/mitoy/bos_taurus_all /storage/isu/reecy_lab/tmp_eric/new.Lee.data/kph/all.animals_1.fq /storage/isu/reecy_lab/tmp_eric/new.Lee.data/kph/all.animals_2.fq

That is the command I used. I was using it just a few days ago and it worked fine.

Edit:

I also tried just calling tophat with no options or input to get the help to display and I get the same error.

[ercfrtz]

I discovered what the issue was. It appears that when we upgraded our python instance from 2.X to 3.X, tophat no longer worked. We re-installed python 2.X as /usr/local/bin/python2 and then I edited the tophat code itself on the line that has
#!/usr/bin/env python

to

#!/usr/bin/env python2

It appears to be working again after making these adjustments.

[blancha]

I just had exactly the same problem.
Luckily, I found this post immediately, and was able to fix the problem in just a few seconds.

How is the bioinformatics community going to move on from Python 2 to Python 3 if these problems keep occurring?

I have moved on. I now write all my pipelines in Python 3.
I'd just switched my environment to Python 3 when this initially perplexing problem occurred.

We should all agree to dump Python 2 and move on to Python 3.
(Or just give up on Python 3 and stick to Python 2)
Otherwise, these #!!?? bugs will keep on popping up.

[blancha]

I don't know if Cole, Daehwan or Geo read this forum.
If any of you do, you should just add a 2 to the shebang line for the tophat script as ercfrtz suggested.

#!/usr/bin/env python2
instead of
#!/usr/bin/env python

I think there is a larger problem between Python 2 and Python 3, but I'm sure this simple temporary fix will avoid many frustrations as more and more users switch their default environment from Python 2 to Python 3.