Hi Zeran,
this problem is caused by the genome+junctions length being close to the 2^32 boundary.
To avoid this problem you would need to specify more precisely the total number of (collapsed) junctions to be inserted in the genome.
You can find this number in the Log.out file:
Jul 28 10:04:01 Finished SA search: number of new junctions=3292413, old junctions=0
If you specify --limitSjdbInsertNsj 3400000, the error should go away.
Cheers
Alex