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Old 05-07-2014, 10:11 AM   #38
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707
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Quote:
Originally Posted by WhatsOEver View Post
Dear Brian,

I tested bbmap successfully on a small dataset and so far I'm very happy with the results
However, I'm running into some memory problems using my real dataset:

...

To me it looks like a bug within the memory detection or am I missing something?
WhatsOEver,

Normally, "Reducing threads from 16 to 15 due to low system memory." only occurs if you are right at the edge of the memory limits. It would be helpful to know:
1) The amount of physical memory available (it looks like 64GB, is that correct?)
2) The size of the reference you are using.
3) Whether you are mapping with bbmap.sh or mapPacBio8k.sh
4) The complete stack trace that comes after the error message "java.lang.RuntimeException: java.lang.OutOfMemoryError: Java heap space". Actually, the entire standard error output would be helpful.

You can reduce the amount of memory BBMap needs by reducing the number of threads (e.g. "t=8" to drop it to 8 threads). But that normally will only help with pacbio modes which need much more memory per thread (100s of megs), not with standard bbmap which only uses around 25MB per thread.

Assuming you do have 64GB, I would try with the flag -Xmx58g and see if that works. But regardless, it would help if you could post the above details.

Thanks,
Brian
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