I've downloaded the latest version of Bowtie2 for Windows (bowtie2-2.2.3-mingw-win64.zip), and added the executables directory to PATH. Whenever I try to run something via Bowtie2 I immediately get errors. If I just type 'bowtie2' I already get 'bowtie2-align-s.exe' has stopped working: (ERR): Description of arguments failed! Exiting now ... I've also tried commands which work perfectly with an older version of Bowtie2, same problem occurs.
Anyone knows what is going on?