Hi Sébastien,
It's certainly possible to align genomes of that size with
progressiveMauve, but your computer will need enough RAM and disk
space, and you will need some patience. I would suggest using entirely
default parameters at first (--seed-family will use extra RAM & compute
time), and it would be well worth ordering the contigs in your draft
genomes against the reference before trying to compute a 3-way
alignment. In terms of RAM you are likely to need 60-100GB available,
with similar amounts of free disk space. The point at which your run
failed is where it's trying to allocate a large block of RAM, so I
suggest checking that first.
Best,
-Aaron
On Thu, 2017-02-09 at 14:07 +0100, sebastien letort wrote:
> Hi everybody,
>
> First try with progressiveMauve, and I got this error.
>
> I'm trying to align two de novo assembly genome of Brassica napus on
> its
> reference (850 MB).
> It seems that something goes wrong on the first steps.
>
> ./progressiveMauve --seed-family --seed-weight 41 $REF_FASTA
> $ASS_PATH/aviso.fa $ASS_PATH/tower.fa > run.log 2> run.err
>
> This list makes reference to memory or version pb for this error.
> I launched the command on a cluster with a lot of memory.
>
> ./progressiveMauve --version
> progressiveMauve build date Feb 13 2015 at 05:57:13
>
> I tried with default size for seed-weight, it didn't change the
> error.
>
> Any help ?
> Sébastien
>
> ------
> run.log
> Storing raw sequence at /tmp/rawseq11609.000
> Sequence loaded successfully.
> Brassica_napus_v4.1.chromosomes.fasta 850292103 base pairs.
> Storing raw sequence at /tmp/rawseq11609.001
> Sequence loaded successfully.
> aviso.fa 699132284 base pairs.
> Storing raw sequence at /tmp/rawseq11609.002
> Sequence loaded successfully.
> tower.fa 690335263 base pairs.
> Creating sorted mer list
> ****
> run.err
> Error creating sorted mer list
> terminate called after throwing an instance of 'genome::gnException'
>
> (code error 134)
>
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--
Aaron E. Darling, Ph.D.
Associate Professor, ithree institute
University of Technology Sydney
Australia
http://darlinglab.org
twitter: @koadman
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