Re: [Bio-bwa-help] bwa mem memory usage

[Rusch, M. <Michael.Rusch@STJUDE.ORG>]

Thanks, the reference is GRCh37-lite (forgot to mention that), but we have seen that for this particular experiment we're getting a disproportionately large number of reads from repeat regions.  So, that's a lead.  I'll tune -c and see what I can do.  Thanks.

Michael

From: Heng Li [mailto:lh...@sa...]
Sent: Sunday, October 13, 2013 8:34 AM
To: Rusch, Michael
Cc: Bio...@li...
Subject: Re: [Bio-bwa-help] bwa mem memory usage. .

Varying read length should not be a problem. I guess this is caused by a highly repetitive reference genome and reads from those highly repetitive regions. For a seed, bwa-mem keeps up to 10000 hits. That may be a lot. You may consider to tune "-c" or use bwa-backtrack.

Heng

On Oct 13, 2013, at 7:19 AM, "Rusch, Michael" <Michael.Rusch@STJUDE.ORG<mailto:Michael.Rusch@STJUDE.ORG>> wrote:


I'm using bwa 0.7.5a.  I have some FASTQs for which bwa mem requires over 44G of memory for single-end alignment.  My files have reads of varying lengths, and I did note that there are a lot of shorter (i.e. < 90bp) reads in the problematic files.  Is that the problem?  I don't know what the actual memory usage will be, as I run on a cluster where I have to set memory limits, and I've only gone up to 44GB so far.

I couldn't find any documentation on bwa mem memory requirements.  Is this normal/expected behavior?

Michael

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