incredible high memory consumption of bwa-mem on small amplicon dataset

LarsB · 03-08-2017, 05:44 AM

Hi all, I am working with Human amplicon data and have been using bwa mem (0.7.15) up to now. Unfortunately, on some datasets the memory consumption exceeds the 8GB RAM I have at spare.

Can someone tell me why this is the case?

I have already tried to modify the parameter (-c or -t) but none of them made it able to run it. Could it be caused by parts of the data aligning to repeat regions/low complexity regions?

If I cannot find a solution to it, I will switch to an alternative aligner that does not need that really high amount of RAM.

GenoMax · 03-08-2017, 06:01 AM

For reference cross-posted (and potentially answered): https://www.biostars.org/p/240853

LarsB · 03-08-2017, 06:08 AM

Thanks, GenoMax. Didn't think of this. I posted it here and in biostars.

GenoMax · 03-08-2017, 06:14 AM

It is fine to cross-post at SeqAnswers. I only linked the other thread to provide reference (for anyone wanting to provide an answer here).

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03-08-2017, 05:44 AM	#1
LarsB Junior Member Location: France Join Date: Feb 2013 Posts: 9	incredible high memory consumption of bwa-mem on small amplicon dataset Hi all, I am working with Human amplicon data and have been using bwa mem (0.7.15) up to now. Unfortunately, on some datasets the memory consumption exceeds the 8GB RAM I have at spare. Can someone tell me why this is the case? I have already tried to modify the parameter (-c or -t) but none of them made it able to run it. Could it be caused by parts of the data aligning to repeat regions/low complexity regions? If I cannot find a solution to it, I will switch to an alternative aligner that does not need that really high amount of RAM.

03-08-2017, 06:01 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,091	For reference cross-posted (and potentially answered): https://www.biostars.org/p/240853

03-08-2017, 06:08 AM	#3
LarsB Junior Member Location: France Join Date: Feb 2013 Posts: 9	Thanks, GenoMax. Didn't think of this. I posted it here and in biostars.

03-08-2017, 06:14 AM	#4
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,091	It is fine to cross-post at SeqAnswers. I only linked the other thread to provide reference (for anyone wanting to provide an answer here).