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Old 03-08-2017, 05:44 AM   #1
LarsB
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Question 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.
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Old 03-08-2017, 06:01 AM   #2
GenoMax
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For reference cross-posted (and potentially answered): https://www.biostars.org/p/240853
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Old 03-08-2017, 06:08 AM   #3
LarsB
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Thanks, GenoMax. Didn't think of this. I posted it here and in biostars.
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Old 03-08-2017, 06:14 AM   #4
GenoMax
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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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