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

RAY(1) User Commands RAY(1)

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
November 2012 Ray version 2.1.0