I just came acorss this from the manual. I not sure what mmap and allocate is? it mentiones ""If mmap not available and allocate not chosen, then will use fileio (very slow)"" Is the case happening here? Computation options

-B, --batch=INT Batch mode (default = 2)

                             Mode     Offsets       Positions       Genome

                               0      see note      mmap            mmap

                               1      see note      mmap & preload  mmap

                  (default)2      see note      mmap & preload  mmap & preload
                               3      see note      allocate        mmap & preload
                               4      see note      allocate        allocate
                               5      expand        allocate        allocate
                       Note: For a single sequence, all data structures use mmap
                       If mmap not available and allocate not chosen, then will use fileio (very slow)
                   Note about --batch and offsets: Expansion of offsets can be controlled
                   independently by the --expand-offsets flag.  The --batch=5 option is equivalent
                   to --batch=4 plus --expand-offsets=1

Have you tried minimap2? Fast and can do spliced alignment.

Asking why X program is taking too long has no good answers as long as the program is still running/producing output. Since you are likely running this for the first time you have no reference to compare (past results) either. It could be your data, hardware and/or any options that you may be missing/misusing (mmap case).