Ok, I'll do try that, thanks!
Best regards,
Ino
On Fri, May 16, 2014 at 4:04 PM, Boisvert, Sebastien <boisv...@anl.gov>wrote:
> Graph traversal takes place in parallel, so it is usual that
> the same path is obtained in more than one copy.
>
>
> But the code in
> https://github.com/sebhtml/ray/blob/master/code/FusionTaskCreator/FusionWorker.cpp
> collapse these into one copy.
>
> If you add the option -debug-fusions, you may see the underlying issue and
> perhaps find a solution.
>
> > From: ino4presid...@gmail.com [ino4presid...@gmail.com] on behalf of
> Ino de Bruijn [ino.debru...@scilifelab.se]
> > Sent: Friday, May 16, 2014 8:59 AM
> > To: Boisvert, Sebastien
> > Cc: denovoassembler-users@lists.sourceforge.net
> > Subject: Re: [Denovoassembler-users] Duplicate contigs?
> >
> >
> >
> >
> > Hi,
> >
> > Hmm interesting. This is indeed the reverse-complement. But you don't
> output those normally right?
> >
> >
> > There are also some where they are exactly the same:
> >
> > 1 825006 1 825006 825006 825006 100.00 825006 825006
> 100.00 100.00 contig-859 contig-539
> >
> >
> >
> > Best regards,
> > Ino
> >
> >
> >
> > On Fri, May 16, 2014 at 3:44 PM, Boisvert, Sebastien
> > <boisv...@anl.gov> wrote:
> >
> > > From: Ino de Bruijn [ino.debru...@scilifelab.se]
> > > Sent: Friday, May 16, 2014 7:31 AM
> > > To:
> > denovoassembler-users@lists.sourceforge.net
> > > Subject: [Denovoassembler-users] Duplicate contigs?
> >
> > >
> > >
> > >
> > >
> > > Bonjour,
> > >
> > > I have assembled a simulated metagenome of 20 genomes. I have 64 pairs
> each containing 23,5M pairs. I have been using Ray v2.3.1 using 2048 cores.
> > >
> > > For one of the genomes I seem to be getting duplicate contigs.
> > >
> > >
> > > I have mapped the assembly against itself using MUMmer and found out
> that some of the contigs are exactly the same. MUMmer shows these kind of
> hits:
> > >
> > >
> > > [S1] [E2] [S2] [E2] [LEN 1] [LEN 2] [% IDY] [LEN R] [LEN Q] [COV R]
> [COV Q] [REF] [QRY]
> > >
> > >
> > > 1 825006 825006 1 825006 825006 100.00 825006 825006
> 100.00 100.00 contig-859 contig-717
> > >
> > >
> > > For an explanation of the format:
> > >
> > http://mummer.sourceforge.net/manual/#coords
> > >
> >
> >
> > I have seen cases where there was a significant overlap between two
> contigs and for which Ray
> > failed to merge them.
> >
> > I have not seen the case where there are 2 identical contigs (in your
> case, one is the reverse-complement of
> > the other).
> >
> >
> > >
> > > Do you have any idea how this might happen?
> > >
> > >
> > > Best regards,
> > > Ino
> > >
> > >
> > >
> > >
> > >
> >
> >
> >
> >
> >
>
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