If a read has the chance to align to many different places and the -m parameter is set quite high, bowtie will crash. We've discovered that on 32-bit machines running 1 thread, specifying 1048576 for -m works, but 1048577 will fail. This number is decreased if you add additional threads, and it is increased (but the problem is not eliminated) if you run on a 64-bit machine.
I've attached a sample file that we've used to demonstrate the above conditions. Thanks!
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