Hi,
Ray v2.0.0-rc7 was just released today.
Le 2012-05-17 09:46, Egon Ozer a écrit :
Is there a way for me to turn off / disable GenomeNeighbourhood in
2.0-rc5 or do I need to wait for the next release?
- Egon
On May 16, 2012, at 1:17 PM, Sébastien Boisvert wrote:
Hi !
Although Ray 2.0 brings metagenomics features, such as de novo
assembly, taxonomy profiling
and gene ontology profiling, the other change is Ray's software
architecture. Ray now utilises RayPlatform.
RayPlatform is a development framework to ease the creation of
massively distributed high performance computing applications.
All the new stuff since January 2012 was done using RayPlatform, and
all the old stuff was ported
to RayPlatform. Porting was easy because the code was already modular.
The disabled plugin reports which contigs are nearby another one in
the de Bruijn graph.
This can be useful in many case, like designing primers to validate
the order
of 2 contigs that are not scaffolded.
It is disabled at the moment because it is slow.
In any Ray run, there is a directory called 'Plugins' that contains
the plugins loaded
in RayPlatform.
It contains runtime information about plugins.
Here is a list of plugins loaded by Ray v2.0-rc7-devel:
Name: Amos
Description: Writes the assembly in the Amos format
Name: CoverageGatherer
Description: Sends coverage depth frequencies
Name: EdgePurger
Description: Deals with invalid edges
Name: FusionData
Description: This plugin propagates paths
Name: FusionTaskCreator
Description: Contained paths are dumped
Name: GeneOntology
Description: Get a ontology view on the sample.
Name: GenomeNeighbourhood
Description: Get a sophisticated bird's-eye view of a sample's DNA
Name: JoinerTaskCreator
Description: Similar paths are joined
Name: KmerAcademyBuilder
Description: Filter out almost all sequencing errors with a Bloom
filter and an academy
Name: Library
Description: Obtains an estimation of library lengths
Name: MachineHelper
Description: Legacy plugin for some master modes
Name: MessageProcessor
Description: Legacy plugin for message tags
Name: MessageRouter
Description: message router for large jobs (bundled with RayPlatform)
Name: MessagesHandler
Description: MPI wrapper with round-robin policy (bundled with
RayPlatform)
Name: NetworkTest
Description: This is a plugin used to test the network latency.
Name: Partitioner
Description: A plugin that counts sequences in files in parallel
Name: PhylogenyViewer
Description: Get a taxonomy view of the sample.
Name: Scaffolder
Description: Greedy conservative scaffolder
Name: Searcher
Description: Add colors in the graph and search things
Name: SeedExtender
Description: Computes long genome paths in the graph.
Name: SeedingData
Description: Computes unique paths in the graph
Name: SequencesIndexer
Description: Index the DNA readouts
Name: SequencesLoader
Description: Loads DNA
Name: SwitchMan
Description: Parallel coordinator (bundled with RayPlatform)
Name: VerticesExtractor
Description: Builds the distributed de Bruijn graph
Name: VirtualCommunicator
Description: Multiplexing and demultiplexing of worker messages
(bundled with RayPlatform)
Name: VirtualProcessor
Description: A thread pool running on 1 physical thread (bundled with
RayPlatform)
Sébastien
Le 2012-05-16 14:03, Louis Letourneau a écrit :
What did the plugin do/add?
Was it more for metahenomics/phylogeny?
Thanks I'll check that.
Louis
Sébastien Boisvert<sebastien.boisver...@ulaval.ca> wrote:
Hello,
You are using Ray v2.0-rc5.
I recently disabled the plugin GenomeNeighbourhood altogether.
There is v2.0-rc6 via git, but I am still working on some bugs.
But this problem has been solved.
Le 2012-05-16 04:41, Louis Letourneau a écrit :
Hello Ray users,
I'm trying to assemble a 300MB eukaryote genome that has a mix of pairs
and mates at about 100x.
I'm running on the mammouth cluster in canada if you know it.
I asked for 10nodes 24cores each. After 120hours it was still at 'fetching
contig path neighbours 50/567'
I hava assembled this genome with about half the reads on a small 48core server
in a few hours previously (not the same cluster) with Ray 1.x
Do you know what could be the culprit? I'm not an mpi expert but it's either
something in Ray2.0 (I doubt) or something with mpi.
I used module openmpi_gcc1.4.3_ofed.
Thanks
Louis
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