Hi,
Didn't manage to finish in time with the debugging option. Our Cray XE6
cluster only allows jobs for 24h unfortunately. I had it running with 2,048
cores, but no luck. I'll see if I can recreate the problem by only using
reads from the one genome that is causing the problem.
I was wondering, completely lost as to how this works. If one increases the
number of cores, do you think it might be able to finish? Or could it be
that collecting the debug output from all the different ranks is actually
limiting and increasing the number of cores only increases the queue for
output collecting.
Best reagrds,
Ino
On Fri, May 16, 2014 at 4:09 PM, Ino de Bruijn
<ino.debru...@scilifelab.se>wrote:
> 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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