Re: [Bio-bwa-help] keep bwa index in memory

[Ross W. <ros...@nc...>]

Heng,
Thanks for the quick response! I have not found any mention of that
preloading option in the Bowtie2 web manual, but will keep looking.
Regards,
Ross


________________________________________________________
|      Ross Whetten
|      Professor, Department of Forestry & Environmental Resources
|      North Carolina State University, Raleigh NC 27695-8008, USA

On Tue, Oct 14, 2014 at 4:49 PM, Heng Li <lh...@me...> wrote:

> Yes, loading the index for a 22Gb genome takes a while. I am afraid that
> there are no good solutions. Bowtie2 and STAR both support preloading the
> index into RAM for repeated use. I have thought about the feature but
> haven’t got time to implement it.
>
> Heng
>
> On Oct 14, 2014, at 16:45, Ross Whetten <ros...@nc...> wrote:
>
> > Hi all,
> > We are using BWA mem to align paired-end reads for each of a few hundred
> samples to a large genome (22 Gb). When the program starts, memory usage
> increases but no output appears until about 40 Gb of RAM is occupied, then
> alignment results begin appearing on STDOUT. It seems that the program goes
> through this 'lag phase' (loading the index into RAM?) for each invocation,
> so when using a bash loop to process hundreds of files in series, the total
> time taken up by this process is significant. Is there a better way to
> align each of several hundred separate samples, or a command-line option
> that tells BWA mem to keep the index in memory for the next cycle through
> the loop?
> >
> > Thanks,
> > Ross
> >
> >
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