I am not aware of any updated build script to generate the desired files from
the new input files.
From: Marc P. Hoeppner [m.hoepp...@ikmb.uni-kiel.de]
Sent: Monday, June 29, 2015 9:05 AM
To: denovoassembler-users@lists.sourceforge.net
Subject: [Denovoassem
The signal 9 is SIGKILL.
It is hard to tell the exact reason why your process received this signal
with the information you provided.
From: Alma Parada [alma.par...@gmail.com]
Sent: Saturday, June 27, 2015 9:50 AM
To: denovoassembler-users@lists.sourceforge.net
Su
The reads are numbered using their ordering when concatenating
the input files.
From: Namrata Patel [namratapatel...@gmail.com]
Sent: Tuesday, June 09, 2015 11:48 PM
To: Boisvert, Sebastien
Subject: About Read Names in Ray Meta
Hello Sir,
I am Trying to run Ray
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
15).
http://bioinformatics.oxfordjournals.org/content/early/2015/01/19/bioinformatics.btv033.abstract
From: Sinha, Rohini [rs3...@cumc.columbia.edu]
Sent: Thursday, May 21, 2015 11:55 AM
To: Boisvert, Sebastien
Subject: Ray Meta
Hi Sébastien,
I am a bioinformatician a
MEGAHIT is an excellent advancement in the field.
The section 4 of the supplementary information of the MEGAHIT paper specifically
discusses memory requirements:
http://bioinformatics.oxfordjournals.org/content/31/10/1674/suppl/DC1
From: Hornung, Bastian [
> From: Casey,Richard [richard.ca...@colostate.edu]
> Sent: Monday, January 19, 2015 1:01 PM
> To: Boisvert, Sebastien
> Subject: Ray on GPU's
>
>
>
> Hello Sebastien,
> Are there any plans to GPU-enable the Ray algorithm
> (http://denovoassembler.sourcefo
> From: Doyle, Jacqueline R M [jmdo...@purdue.edu]
> Sent: Friday, January 02, 2015 6:01 PM
> To: denovoassembler-users@lists.sourceforge.net
> Subject: [Denovoassembler-users] assembly w/ TruSeq synthetic reads?
>
>
>
> Hi! I’m working on an assembly of a non-model avian genome.
> We currentl
>
> From: John Damm Sørensen [joh...@cbs.dtu.dk]
> Sent: Thursday, November 27, 2014 3:42 AM
> To: Boisvert, Sebastien
> Subject: Request for Ray improvement
> Hi Sebastien,
> I am writing to you
> regarding the usage of the endl s
That did not come out right.
It should read:
The changes are described in section "From Ray to Ray Meta" in the paper
http://genomebiology.com/2012/13/12/R122
and
There is no specific option.
>
> From: Sébastien Boisvert [sebastien.boisver...@ulaval.ca
> From: Deborah Triant [dtri...@virginia.edu]
> Sent: Wednesday, November 05, 2014 5:20 PM
> To: denovoassembler-users@lists.sourceforge.net
> Subject: [Denovoassembler-users] assembly error during taxon loading
>
>
> Hi,
>
> I've been trying to use Ray to assemble a diploid plant genome with Il
> From: Gunning, Don [don.gunn...@intel.com]
> Sent: Thursday, November 13, 2014 11:13 AM
> To: Jacques Corbeil
> Cc: Boisvert, Sebastien
> Subject: RE: Ray
>
>
>
> Jacques
>
> Good to hear that the project is continuing.
I CC'ing this to the list.
>
> From: Jacques Corbeil [jacques.corb...@crchudequebec.ulaval.ca]
> Sent: Thursday, November 13, 2014 10:57 AM
> To: Gunning, Don
> Cc: Boisvert, Sebastien
> Subject: Re: Ray
>
>
> Hello Don,
>
> Very much so! We are trying to port in on basespace at Illum
> From: Bart Nijsse [bart.nij...@wur.nl]
> Sent: Thursday, October 09, 2014 9:42 AM
> To: denovoassembler-users@lists.sourceforge.net
> Subject: [Denovoassembler-users] Critical exception... memory exceeds the
> CHUNK_SIZE
>
>
>
>
> Dear Ray developers,
>
> I am trying to do a denovo assembly
>
> From: Deborah Triant [dtri...@virginia.edu]
> Sent: Tuesday, September 30, 2014 7:36 PM
> To: denovoassembler-users@lists.sourceforge.net
> Subject: [Denovoassembler-users] using checkpoints
> Hi,
> I am using the Ray assembler and hit the walltime on my
re using on your supercomputer, using only 48 MPI
ranks may only use the first
4 nodes (4 * 12 = 48). If that's the case, the 6 other nodes are not being used.
From: Wilhelm, Roland [rwilh...@mail.ubc.ca]
Sent: Monday, September 15, 2014 5:58 PM
To: Boisvert,
>
> From: Louis Letourneau [louis.letourn...@mail.mcgill.ca]
> Sent: Tuesday, August 26, 2014 8:52 AM
> To: denovoassembler-us...@lists.sf.net
> Subject: [Denovoassembler-users] Ray for HLA analysis
> I was wondering if someone would have ideas/insight on ho
though.
From: zg...@nmu.edu [zg...@nmu.edu]
Sent: Wednesday, August 27, 2014 10:27 PM
To: Boisvert, Sebastien
Subject: Compiling Ray
Dear Dr. Boisvert,
I would like to use Ray to produce a genome assembly of an avian genome we
had sequenced, but am very new
Can you try without this:
-mini-ranks-per-rank \
12 \
From: Wilhelm, Roland [rwilh...@mail.ubc.ca]
Sent: Friday, August 22, 2014 7:53 PM
To: Boisvert, Sebastien
Cc: denovoassembler-us...@lists.sf.net
Subject: RE: RAY on Compute Canada server (Parallel
Friday, August 22, 2014 12:47 AM
> To: Boisvert, Sebastien
> Subject: RAY on Compute Canada server (Parallel)
>
>
>
> Good Morning Dr. Boisvert!
>
> I wouldn't be writing you if I didn't think this might require quick and easy
> advice from someone with your kno
> From: Egon Ozer [e-o...@fsm.northwestern.edu]
> Sent: Monday, July 21, 2014 9:30 AM
> To: denovoassembler-us...@lists.sf.net
> Cc: Boisvert, Sebastien
> Subject: Version-dependent performance of Ray
>
>
>
> Hi Sebastien,
>
> Apologies in advance for the long ema
> From: Sulbha Choudhari [sul...@scarletmail.rutgers.edu]
> Sent: Monday, August 18, 2014 1:26 PM
> To: Boisvert, Sebastien
> Subject: Ray Meta
>
>
>
> Hello Dr. Boisvert,
> I would be thankful if you could help me in the software, Ray Meta generated
> by yo
Dear de novo assembler users:
Just to be open, I wish to inform you that I started to work on a new
distributed assembler focusing on
metagenomics. It's called spate [spate]. spate runs on top of the thorium
distributed actor engine and is built
using reusable actor components from the biosal (
> From: Lee Bergstrand [lee.h.bergstr...@gmail.com]
> Sent: Monday, July 21, 2014 1:41 AM
> To: Boisvert, Sebastien
> Subject: Ray Meta Memory Usage For Large Datasets
>
>
> Hello Sébastien,
>
> I was asked contact you by one of my lab-mates, Roli Wilhelm, a
>
> From: Cyril Frantzen [cyril.frant...@nmbu.no]
> Sent: Friday, July 04, 2014 7:32 AM
> To: Boisvert, Sebastien
> Subject: Some questions about your Ray assembler
> Hello,
> We've recently begun experimenting with your Ray
Please use the mailing list at
https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
> From: matteo brilli [matteo.bri...@fmach.it]
> Sent: Monday, May 19, 2014 6:58 AM
> To: Boisvert, Sebastien
> Subject: technical information
>
>
>
>
> Dear Sebastie
> From: Adrian Pelin [apeli...@gmail.com]
> Sent: Sunday, May 18, 2014 6:59 PM
> To: Denovoassembler-users@lists.sourceforge.net
> Subject: Re: [Denovoassembler-users] Assembling polyploid genomes
>
>
>
> Hello,
>
> I am working with a tetraploid dataset, and most assemblies generate
> redunda
> From: ino4presid...@gmail.com [ino4presid...@gmail.com] on behalf of Ino de
> Bruijn [ino.debru...@scilifelab.se]
> Sent: Sunday, May 18, 2014 4:06 AM
> To: Boisvert, Sebastien
> Cc: denovoassembler-users@lists.sourceforge.net
> Subject: Re: [Denovoassembler-users]
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.ne
> 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
>
] wrote:
> To: Boisvert, Sebastien
> Subject: problème ouverture de fichiers avec Ray
>
> Bonjour ,
> je suis actuellement en train d'utiliser votre logiciel ray, sur le
> cluster colosse.
> Cependant, j'ai un léger souci que je n'arrive pas a résoudre.
> J'ai
I don't think so, there is no -d parameter.
> From: Ino de Bruijn [ino.debru...@scilifelab.se]
> Sent: Thursday, May 15, 2014 9:59 AM
> To: denovoassembler-users@lists.sourceforge.net
> Subject: [Denovoassembler-users] Ray -d parameter
>
>
>
>
> Hello,
>
>
> I have accidentally added an extr
The problem is probably a bug in the code related to long reads.
> From: dricamfr...@gmail.com
> To: sebastien.boisver...@ulaval.ca
> Date: Tue, 15 Apr 2014 21:34:13 -0400
> Subject: Re: RE : Assembler panic
>
> Hi Sebastien,
>
> I am sending some sequences of t
You can use Assembly/BiologicalAbundances/_DeNovoAssembly/Contigs.tsv.
The column "Colored k-mers" tells how many k-mers in the contig are colored. 0
means that the
contig is unassigned.
> From: anna.sandion...@unimib.it
> Date: Thu, 3 Apr 2014 12:34:44 +0200
>
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