[mira_talk] Solexa de-novo assembly of paired reads
- From: Tony Travis <a.travis@xxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Mon, 12 Jul 2010 10:29:07 +0100
Hello, Bastien.
I'm trying to assemble about 20,000,000 paired-end Solexa reads using
MIRA V3.0.3 (production version). The job has been running for three
weeks now but has not yet completed the first pass.
I'm running it under 64-bit Linux on a 2GHz Opteron with 16GiB RAM.
During the first phase the system was swapping a lot because MIRA
required about 20GiB RAM. However, even though MIRA is now using about
30GiB RAM there is very little swap activity and the processor is
running at 100% most of the time...
I don't know the fragment sizes for this run, but do you think that MIRA
is taking so long because I didn't include the appropriate fragment sizes?
This is how I'm running the job from a FASTQ file with the default
Solexa read naming convention:
Bye,
Tony.
# @(#)Makefile 2010-06-10 A.J.Travis
#
# MIRA assembly of metagenome
#
PROJECT = meta
READ = $(PROJECT)_in.solexa.fastq
all: $(READ)
mira -project=$(PROJECT) \
-fastq \
-job=denovo,genome,normal,solexa
clean:
clobber: clean
-rm -r $(PROJECT)_assembly
--
Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
mailto:a.travis@xxxxxxxxxx, http://bioinformatics.rri.sari.ac.uk/~ajt
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