Compatibility of Bowtie1 (v1.2.0 or later) with Tophat2

[rason81]

bowtie1 with versions greater than 1.2.0 are not compatible with Tophat (v2.1.1), reporting things like "./SeqAn-1.4.2/seqan/basic/basic_exception.h:236 FAILED! (Uncaught exception of type St11logic_error: basic_string::_S_construct NULL not valid)".
Possibly this issue is related to generation of *_genome.bwt.samheader.sam, because recent bowtie versions cannot generate sam headers with the empty input.
Although there is alternative for Tophat, it is still at some point the optimal one.
So, how to fix this issue?

[yuanlizhanshi]

i encountered the same problem, how did you slove this?