I am getting the following error with tophat:

Error in tophat:

[2012-12-27 15:08:40] Beginning TopHat run (v2.0.5)
[2012-12-27 15:08:40] Checking for Bowtie
Traceback (most recent call last):
  File "/usr/bin/tophat", line 4035, in <module>
  File "/usr/bin/tophat", line 3836, in main
  File "/usr/bin/tophat", line 1473, in check_bowtie
    bowtie_version = get_bowtie_version(params.bowtie2)
  File "/usr/bin/tophat", line 1351, in get_bowtie_version
    bowtie_version = [int(x) for x in ver_numbers[:3]] +
IndexError: list index out of range

   I tried Tophat and Tophat2 a couple times and always giving me the same
error. The reads I am trying to map are from small RNA sequencing project.
I am trying to map the unannotated reads back to the genome. I am not sure
what is causing this problem, any help will be appreciated.

Thank you.

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