This is a bug in version 2.3.1.
Can you try a previous version ?
From: Zain A Alvi [zain.a...@student.shu.edu]
Sent: Friday, May 08, 2015 7:21 AM
To: denovoassembler-users@lists.sourceforge.net
Subject: [Denovoassembler-users] Ray Assembler Chunk Size Error Proble
> From: plat...@sbcglobal.net
> To: sebastien.boisver...@ulaval.ca
> Date: Thu, 21 Aug 2014 10:47:37 -0400
> Subject: Re: [Denovoassembler-users] Ray assembler
>
> Hi Seb
>
Hi Adrian,
> I know you're no longer actively devel
You need to recompile Ray with MAXKMERLENGTH=something larger than 32.
> From: eforoo...@nigeb.ac.ir
> To: sebastien.boisver...@ulaval.ca
> Date: Thu, 21 Aug 2014 05:30:58 -0400
> Subject: Ray assembler
>
>
> hello dear Sébastien,
> I am a phd student and I
On 20/11/13 12:49 AM, madhu bioinfo wrote:
> hello sebastin,
Hi,
Please use the mailing list.
> Am having illumina paired data of bacteria i would like to do the ray
> assembly and i have tried the assembly with default parameters but it dint
> give me
> the expected results
What was the expe
Hello,
On 04/04/13 04:57 PM, Hung-Ying Lin wrote:
> Dear Dr. Boisvert,
I am not a doctor.
>
> Please allow me to introduce myself. I'm Hung-Ying, currently a PhD
> student in Genetics program at Iowa State University and I am conducting a
> project that compares
> performances among
> [again, please CC the list as Ray is a community effort]
Sorry about that.
>
> How much memory do you have collectively with these 16 MPI ranks ?
512 G.
Christina
>
> On 11/01/2012 03:06 PM, Christina Boucher wrote:
>> Hi Sebastien,
>>
>> I believe that Ray chocked on my data also. In
> 512 G.
OK, you have 512 GiB, and you launched 16 Ray MPI processes.
If I do the maths, this gives a 32 GiB per process, assuming you don't
have a swap partition and assuming that you are alone on the machine.
You said that Ray is running out of memory at the place below:
> Estimated remaining
> [again, please CC the list]
Sorry, I'll make sure I do that.
>
> On 11/01/2012 02:48 PM, Christina Boucher wrote:
>> Hi Adrain and Sebastien,
>>
>> Nice to hear from McGill folk since that is my alma mater ;)
>>
>
> So you are Canadian then ?
I am ;)
>> However, spades seem to choke on t
[again, please CC the list]
On 11/01/2012 02:48 PM, Christina Boucher wrote:
> Hi Adrain and Sebastien,
>
> Nice to hear from McGill folk since that is my alma mater ;)
>
So you are Canadian then ?
> I mainly work on plant pathogen data and Arabidopsis. In the future, we plan
> on looking at B
Regarding the way Ray is run, soon Ray will be able to run on MPI only, MPI +
pthread, or
even pthread only:
As you may know, Ray ships with a library called RayPlatform, which abstracts
all the parallel stuff from the programmer. In Ray v2.0.0 and v2.1.0, the
associated RayPlatform library (ve
Hello,
You should CC the mailing list as I am sure that numerous people in
the genomics community would be interested by plant genome de novo assembly !
People at McGill University did some work on plant genomes with Ray too.
They posted their results on the list I think.
So you have something
Hello,
On 10/31/2012 03:48 PM, Christina Boucher wrote:
> MPI is already installed on my server… see:
> oak # rpm -qa | grep openmpi
> openmpi-devel-1.5.4-5.fc17.1.x86_64
> openmpi-1.5.4-5.fc17.1.x86_64
>
This is something specific to Fedora 17 (which I happen to be using on my
laptop).
My answ
Hello,
> make[1]: mpicxx: Command not found
To install Ray, you need an MPI library. You don't have one installed.
For example, on Fedora, the packages are openmpi, openmpi-devel, gcc-c++.
> In addition, is the the max kmer length 32? Most people are using upwards to
> 55….?
The maximum k-mer
>>
>> I am trying to use your Ray assembler. I've been using Spades (mainly
>> because I am formerly
>> from Pavel Pevzner's lab) but running out of memory on a large dataset.
>
> Maybe processing your large dataset is more amenable with a distributed
> assembler.
Spades group released a new
Hello,
On 10/29/2012 04:02 PM, Christina Boucher wrote:
> Hi,
>
> I am trying to use your Ray assembler. I've been using Spades (mainly
> because I am formerly
>from Pavel Pevzner's lab) but running out of memory on a large dataset.
Maybe processing your large dataset is more amenable with a di
Hello,
The -show-* options actually show more information in the standard output.
I think though that the -show-memory-usage is enabled by default.
What you describe would be the behavior for an option called -quiet, but
at the moment such an option is not implemented.
Sébastien
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