________________________________
> From: [email protected]
> To: [email protected]
> CC: [email protected]
> Date: Tue, 3 Jun 2014 23:01:23 -0400
> Subject: Re: Ask about Ray Meta
>
> Dear Sebastien,
>
> On 3 June 2014 23:24, Sébastien Boisvert
> <[email protected]<mailto:[email protected]>>
> wrote:
>
>
> ________________________________
> > From: [email protected]<mailto:[email protected]>
> > To: [email protected]<mailto:[email protected]>
> > Date: Fri, 30 May 2014 21:18:05 -0400
> > Subject: Ask about Ray Meta
> >
> > Dear Sébastien Boisvert,
> >
> > I would like to use Ray Meta in my research.
> > In your paper, you have conducted experiments for 124 human gut
> > microbiomes. I have tried to run Ray Meta for the MH0047
> > dataset(ERS006592), but I got little bit different results with the
> > results written in your paper.
> >
> > For the MH0047 dataset (ERS006592), scaffolds> 500
> > in your paper :
> > N50 = 10,277
> > Number of scaffolds = 9,387
> > Total length = 24,687,275
> >
> > in my experiment
> > N50 = 9,946
> > Number of scaffolds = 9,544
> > Total length = 24,850,660
>
> If you run on 1 rank, the result is deterministic, otherwise, it is not.
>
> What do you mean with running on 1 rank?
mpiexec -n 1 program parameters
>
> >
> > I run the Ray Meta with this commands :
> >
> > mpiexec -n 32 ray-build/Ray -k 31 -i ERR011192mix.fastq -i
> > ERR011193mix.fastq -o MH47Results
> >
> > I would like to make sure, whether my commands are true or not. I am
> > looking forward to hearing from you soon. Thank you very much.
> >
>
> When you downloaded the data from your data source, I suppose
> there were 4 files (11192_1, 11192_2, 11193_1, 11193_2).
>
> Is that correct ?
>
> Yes, there were 4 files (11192_1, 11192_2, 11193_1, 11193_2). I
> created interleaved file for the paired end read files. In my
> case, ERR011192mix.fastq is the interleave file for 11192_1
> and 11192_2.
Our Genome Biology results were generated with the -p option, but that
won't change anything here.
>
> I am looking forward to hearing from you soon.
> Thank you very much.
You are most welcome.
>
> Afia
>
>
> > Best regards,
> > Afiahayati
> > Dept. of Biosciences and Informatics
> > Keio University
> > Japan
>
>
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