Provided by: ray_2.3.1-7build1_amd64 bug

NAME

       Ray - assemble genomes in parallel using the message-passing interface

SYNOPSIS

       mpiexec  -n  NUMBER_OF_RANKS  Ray  -k  KMERLENGTH  -p  l1_1.fastq l1_2.fastq -p l2_1.fastq
       l2_2.fastq -o test

       mpiexec -n NUMBER_OF_RANKS Ray Ray.conf # with commands in a file

DESCRIPTION:

       The Ray genome assembler is built on  top  of  the  RayPlatform,  a  generic  plugin-based
       distributed  and  parallel  compute  engine  that  uses  the message-passing interface for
       passing messages.

       Ray targets several applications:

              - de novo genome assembly (with Ray vanilla) - de novo meta-genome  assembly  (with
              Ray  Meta)  -  de  novo  transcriptome  assembly  (works,  but  not tested a lot) -
              quantification of  contig  abundances  -  quantification  of  microbiome  consortia
              members (with Ray Communities) - quantification of transcript expression - taxonomy
              profiling of samples (with Ray Communities) - gene ontology  profiling  of  samples
              (with Ray Ontologies)

       -help

              Displays this help page.

       -version

              Displays Ray version and compilation options.

              Using a configuration file

              Ray  can  be  launched  with  mpiexec -n 16 Ray Ray.conf The configuration file can
              include comments (starting with #).

              K-mer length

       -k kmerLength

              Selects the length of k-mers. The default value is 21.   It  must  be  odd  because
              reverse-complement  vertices are stored together.  The maximum length is defined at
              compilation by MAXKMERLENGTH Larger k-mers utilise more memory.

              Inputs

       -p leftSequenceFile rightSequenceFile [averageOuterDistance standardDeviation]

              Provides  two  files  containing  paired-end   reads.    averageOuterDistance   and
              standardDeviation are automatically computed if not provided.

       -i interleavedSequenceFile [averageOuterDistance standardDeviation]

              Provides  one  file  containing interleaved paired-end reads.  averageOuterDistance
              and standardDeviation are automatically computed if not provided.

       -s sequenceFile

              Provides a file containing single-end reads.

              Outputs

       -o outputDirectory

              Specifies the directory for outputted files. Default is RayOutput

              Assembly options (defaults work well)

       -disable-recycling

              Disables read recycling during the assembly reads will be set free in 3  cases:  1.
              the  distance  did  not  match  for  a pair 2. the read has not met its mate 3. the
              library population indicates a wrong placement see Constrained traversal of repeats
              with  paired sequences.  Sebastien Boisvert, Elenie Godzaridis, Francois Laviolette
              & Jacques Corbeil.  First Annual RECOMB Satellite Workshop  on  Massively  Parallel
              Sequencing, March 26-27 2011, Vancouver, BC, Canada.

       -disable-scaffolder

              Disables the scaffolder.

       -minimum-contig-length minimumContigLength

              Changes the minimum contig length, default is 100 nucleotides

       -color-space

              Runs  in  color-space Needs csfasta files. Activated automatically if csfasta files
              are provided.

       -use-maximum-seed-coverage maximumSeedCoverageDepth

              Ignores any seed with a coverage  depth  above  this  threshold.   The  default  is
              4294967295.

       -use-minimum-seed-coverage minimumSeedCoverageDepth

              Sets  the  minimum  seed coverage depth.  Any path with a coverage depth lower than
              this will be discarded. The default is 0.

              Distributed storage engine (all these values are for each MPI rank)

       -bloom-filter-bits bits

              Sets the number of bits for the Bloom filter Default  is  268435456  bits,  0  bits
              disables the Bloom filter.

       -hash-table-buckets buckets

              Sets  the  initial  number  of  buckets.  Must  be  a  power of 2 !  Default value:
              268435456

       -hash-table-buckets-per-group buckets

              Sets the number of buckets per group for sparse storage Default value: 64, Must  be
              between >=1 and <= 64

       -hash-table-load-factor-threshold threshold

              Sets  the load factor threshold for real-time resizing Default value: 0.75, must be
              >= 0.5 and < 1

       -hash-table-verbosity

              Activates verbosity for the distributed storage engine

              Biological abundances

       -search searchDirectory

              Provides a directory containing fasta files to be searched in the de Bruijn  graph.
              Biological   abundances  will  be  written  to  RayOutput/BiologicalAbundances  See
              Documentation/BiologicalAbundances.txt

       -one-color-per-file

              Sets one color per file instead of one per sequence.  By default, each sequence  in
              each  file has a different color.  For files with large numbers of sequences, using
              one single color per file may be more efficient.

              Taxonomic profiling with colored de Bruijn graphs

       -with-taxonomy Genome-to-Taxon.tsv TreeOfLife-Edges.tsv Taxon-Names.tsv

              Provides a  taxonomy.   Computes  and  writes  detailed  taxonomic  profiles.   See
              Documentation/Taxonomy.txt for details.

       -gene-ontology OntologyTerms.txt
              Annotations.txt

              Provides   an   ontology   and  annotations.   OntologyTerms.txt  is  fetched  from
              http://geneontology.org Annotations.txt is a 2-column file (EMBL_CDS handle       &
              gene ontology identifier) See Documentation/GeneOntology.txt

              Other outputs

       -enable-neighbourhoods

              Computes   contig   neighborhoods   in   the   de   Bruijn   graph   Output   file:
              RayOutput/NeighbourhoodRelations.txt

       -amos

              Writes the AMOS file called RayOutput/AMOS.afg An AMOS file contains read positions
              on contigs.  Can be opened with software with graphical user interface.

       -write-kmers

              Writes  k-mer  graph  to  RayOutput/kmers.txt The resulting file is not utilised by
              Ray.  The resulting file is very large.

       -write-read-markers

              Writes read markers to disk.

       -write-seeds

              Writes seed DNA sequences to RayOutput/Rank<rank>.RaySeeds.fasta

       -write-extensions

              Writes extension DNA sequences to RayOutput/Rank<rank>.RayExtensions.fasta

       -write-contig-paths

              Writes contig paths with coverage values to RayOutput/Rank<rank>.RayContigPaths.txt

       -write-marker-summary

              Writes marker statistics.

              Memory usage

       -show-memory-usage

              Shows memory usage. Data is fetched from /proc on GNU/Linux Needs __linux__

       -show-memory-allocations

              Shows memory allocation events

              Algorithm verbosity

       -show-extension-choice

              Shows the choice made (with other choices) during the extension.

       -show-ending-context

              Shows the ending context of each extension.  Shows the children of the vertex where
              extension was too difficult.

       -show-distance-summary

              Shows summary of outer distances used for an extension path.

       -show-consensus

              Shows the consensus when a choice is done.

              Checkpointing

       -write-checkpoints checkpointDirectory

              Write checkpoint files

       -read-checkpoints checkpointDirectory

              Read checkpoint files

       -read-write-checkpoints checkpointDirectory

              Read and write checkpoint files

              Message routing for large number of cores

       -route-messages

              Enables  the  Ray  message  router.  Disabled  by default.  Messages will be routed
              accordingly so that any rank can communicate  directly  with  only  a  few  others.
              Without  -route-messages,  any  rank  can communicate directly with any other rank.
              Files     generated:      Routing/Connections.txt,      Routing/Routes.txt      and
              Routing/RelayEvents.txt and Routing/Summary.txt

       -connection-type type

              Sets  the  connection  type  for  routes.  Accepted values are debruijn, hypercube,
              polytope, group, random, kautz and complete. Default is debruijn.

              debruijn: a full de Bruijn  graph  a  given  alphabet  and  diameter  hypercube:  a
              hypercube,  alphabet  is  {0,1} and the vertices is a power of 2 polytope: a convex
              regular polytope, alphabet is {0,1,...,B-1} and the vertices is a power of B group:
              silly  model  where  one  representative  per  group can communicate with outsiders
              random: Erdos-Renyi model kautz: a full de Kautz graph, which is a subgraph of a de
              Bruijn graph complete: a full graph with all the possible connections

              With  the  type  debruijn,  the  number  of  ranks  must  be  a power of something.
              Examples: 256 = 16*16, 512=8*8*8, 49=7*7, and so on.  Otherwise, don't use debruijn
              routing  but  use  another  one  With the type kautz, the number of ranks n must be
              n=(k+1)*k^(d-1) for some k and d

       -routing-graph-degree degree

              Specifies the outgoing degree for the routing graph.  See Documentation/Routing.txt

              Hardware testing

       -test-network-only

              Tests the network and returns.

       -write-network-test-raw-data

              Writes one additional file per rank detailing the network test.

       -exchanges NumberOfExchanges

              Sets the number of exchanges

       -disable-network-test

              Skips the network test.

              Debugging

       -verify-message-integrity

              Checks message data reliability for any non-empty message.  add '-D CONFIG_SSE_4_2'
              in the Makefile to use hardware instruction (SSE 4.2)

       -run-profiler

              Runs  the  profiler  as  the code runs. By default, only show granularity warnings.
              Running the profiler increases running times.

       -with-profiler-details

              Shows number of messages sent and received in each  methods  during  in  each  time
              slices (epochs). Needs -run-profiler.

       -show-communication-events

              Shows all messages sent and received.

       -show-read-placement

              Shows read placement in the graph during the extension.

       -debug-bubbles

              Debugs  bubble code.  Bubbles can be due to heterozygous sites or sequencing errors
              or other (unknown) events

       -debug-seeds

              Debugs seed code.  Seeds are paths in the graph that are likely unique.

       -debug-fusions

              Debugs fusion code.

       -debug-scaffolder

              Debug the scaffolder.

       FILES

              Input files

              Note: file format is determined with file extension.

              .fasta .fasta.gz (needs HAVE_LIBZ=y at compilation) .fasta.bz2 (needs HAVE_LIBBZ2=y
              at  compilation)  .fastq  .fastq.gz  (needs  HAVE_LIBZ=y at compilation) .fastq.bz2
              (needs HAVE_LIBBZ2=y at compilation) .sff (paired reads must be extracted manually)
              .csfasta (color-space reads)

              Outputted files

              Scaffolds

              RayOutput/Scaffolds.fasta

              The scaffold sequences in FASTA format

              RayOutput/ScaffoldComponents.txt

              The components of each scaffold

              RayOutput/ScaffoldLengths.txt

              The length of each scaffold

              RayOutput/ScaffoldLinks.txt

              Scaffold links

              Contigs

              RayOutput/Contigs.fasta

              Contiguous sequences in FASTA format

              RayOutput/ContigLengths.txt

              The lengths of contiguous sequences

              Summary

              RayOutput/OutputNumbers.txt

              Overall numbers for the assembly

              de Bruijn graph

              RayOutput/CoverageDistribution.txt

              The distribution of coverage values

              RayOutput/CoverageDistributionAnalysis.txt

              Analysis of the coverage distribution

              RayOutput/degreeDistribution.txt

              Distribution of ingoing and outgoing degrees

              RayOutput/kmers.txt

              k-mer graph, required option: -write-kmers

              The resulting file is not utilised by Ray.  The resulting file is very large.

              Assembly steps

              RayOutput/SeedLengthDistribution.txt

              Distribution of seed length

              RayOutput/Rank<rank>.OptimalReadMarkers.txt

              Read markers.

              RayOutput/Rank<rank>.RaySeeds.fasta

              Seed DNA sequences, required option: -write-seeds

              RayOutput/Rank<rank>.RayExtensions.fasta

              Extension DNA sequences, required option: -write-extensions

              RayOutput/Rank<rank>.RayContigPaths.txt

              Contig paths with coverage values, required option: -write-contig-paths

              Paired reads

              RayOutput/LibraryStatistics.txt

              Estimation of outer distances for paired reads

              RayOutput/Library<LibraryNumber>.txt

              Frequencies for observed outer distances (insert size + read lengths)

              Partition

              RayOutput/NumberOfSequences.txt

              Number of reads in each file

              RayOutput/SequencePartition.txt

              Sequence partition

              Ray software

              RayOutput/RayVersion.txt

              The version of Ray

              RayOutput/RayCommand.txt

              The exact same command provided

              AMOS

              RayOutput/AMOS.afg

              Assembly representation in AMOS format, required option: -amos

              Communication

              RayOutput/MessagePassingInterface.txt

              Number of messages sent

              RayOutput/NetworkTest.txt

              Latencies in microseconds

              RayOutput/Rank<rank>NetworkTestData.txt

              Network test raw data

       DOCUMENTATION

              -  mpiexec  -n  1  Ray  -help|less  (always  up-to-date)  -  This help page (always
              up-to-date) - The directory Documentation/ -  Manual  (Portable  Document  Format):
              InstructionManual.tex    (in    Documentation)    -    Mailing    list    archives:
              http://sourceforge.net/mailarchive/forum.php?forum_name=denovoassembler-users

       AUTHOR

              Written by Sebastien Boisvert.

       REPORTING BUGS

              Report   bugs    to    denovoassembler-users@lists.sourceforge.net    Home    page:
              <http://denovoassembler.sourceforge.net/>

       COPYRIGHT

              This  program  is free software: you can redistribute it and/or modify it under the
              terms of the  GNU  General  Public  License  as  published  by  the  Free  Software
              Foundation, version 3 of the License.

              This  program  is  distributed  in the hope that it will be useful, but WITHOUT ANY
              WARRANTY; without even the implied warranty of MERCHANTABILITY  or  FITNESS  FOR  A
              PARTICULAR PURPOSE.  See the GNU General Public License for more details.

              You  have received a copy of the GNU General Public License along with this program
              (see LICENSE).

       Ray 2.1.0

       License for Ray: GNU General Public License version 3 RayPlatform version:  1.1.0  License
       for RayPlatform: GNU Lesser General Public License version 3

       MAXKMERLENGTH:  32  KMER_U64_ARRAY_SIZE: 1 Maximum coverage depth stored by CoverageDepth:
       4294967295  MAXIMUM_MESSAGE_SIZE_IN_BYTES:  4000  bytes  FORCE_PACKING  =  n  ASSERT  =  n
       HAVE_LIBZ  =  y  HAVE_LIBBZ2  =  y  CONFIG_PROFILER_COLLECT  =  n CONFIG_CLOCK_GETTIME = n
       __linux__ = y _MSC_VER = n __GNUC__ = y RAY_32_BITS =  n  RAY_64_BITS  =  y  MPI  standard
       version: MPI 2.1 MPI library: Open-MPI 1.4.2 Compiler: GNU gcc/g++ 4.4.5