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#243 Bowtie fails at high -m on some data sets

open
nobody
bowtie (175)
5
2012-09-20
2012-09-20
Anonymous
No

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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  • A file containing a couple very short reads

     
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