Just saw this over at the TopHat site. Perhaps upgrading to latest Tophat may fix your problem.
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Version 2.0.8 is a quick fix release addressing the following issues:
This version correctly handles the newest version of Bowtie2 v2.1.0.
The segment mapping slow-down introduced by some Bowtie2 parameter changes in version 2.0.7 is now corrected
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There is also a new version of bowtie2 (v.2.1.0) available as well.
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