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 > > > > > > > > > > > > > > > ------------------------------------------------------------------------------ "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available Simple to use. Nothing to install. Get started now for free." http://p.sf.net/sfu/SauceLabs _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
