Can you check whether the directory where the sequence files are
located is writable by the compute node and has enough space to store
the sorted seed (k-mer) list? progressiveMauve does not use TMPDIR to
store those, they go in a file with the same name as the sequence file,
with a .sslist extension added. They require approximately 4.25
bytes/base, so in your case around 6GB for both sequences. That seems
like the most likely problem, but if that's not it then it would be
helpful if you could send me the sequence files somehow (google drive?
dropbox?) so I can check whether there's some kind of unexpected file
format parsing problem.
-Aaron
On Fri, 2017-02-10 at 10:50 +0100, sebastien letort wrote:
> Hi Aaron,
>
> I have 190 GB of ram and more than 1TB of disk space available.
> I redefined TMPDIR to have enough space here too.
> The program fail again, at the same stage.
>
> I only used one cultivar against its reference with default
> parameter.
>
> Here are the last output lines of vmstat -S M -tn 1 before the prog
> did end.
> procs -----------memory---------- ---swap-- -----io---- --system--
> -----cpu------ ---timestamp---
> 2 0 621 191889 33 60193 0 0 0 0
> 2618 198 5 0
> 95 0 0 2017-02-10 09:59:06 CET
> 2 0 621 191886 33 60196 0 0 0 0
> 2637 211 5 0
> 95 0 0 2017-02-10 09:59:07 CET
> 2 0 621 191882 33 60200 0 0 0 0
> 2595 151 5 0
> 95 0 0 2017-02-10 09:59:08 CET
> 2 0 621 191879 33 60203 0 0 0 0
> 2607 182 5 0
> 95 0 0 2017-02-10 09:59:09 CET
> 2 0 621 192553 33 59538 0 0 0 0 4518
> 1093 4 0
> 95 0 0 2017-02-10 09:59:10 CET
>
> besst,
> Sébastien
>
> Le 10/02/2017 à 02:31, Aaron Darling a écrit :
> >
> > 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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Aaron E. Darling, Ph.D.
Associate Professor, ithree institute
University of Technology Sydney
Australia
http://darlinglab.org
twitter: @koadman
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