[mira_talk] Re: (no subject)
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 11 Feb 2011 22:33:11 +0100
On Friday 11 February 2011 00:56:52 Rob Good wrote:
> I'm trying to assemble 5 million solexa reads against a drosophila ref.
>
> mira -fastq -job=mapping,genome,accurate,solexa -project=DGRP-712
>
>
> I get an unceremonious killed with no log output apart from what's on the
> screen. I only have 12 Gb RAM but thought I'd try it after reading the
> optimistic words from Bastein on 3.2.1.5 regarding memory improvements Am
> I being too hopeful
Well, for backbone assemblies you still need quite some space because how MIRA
internally works with long sequences is that it maps them to artificial smaller
sequences ... and with 120mb and Solexa reads as data one needs 24m of these
internal reads, and there you need probably something like ~30 GiB for the
whole thing.
Sorry.
B.
PS: PS: I know, for really large genomes > 100mb MIRA is perhaps not the most
suited tool to do mapping.
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