--- name: "Ray" section: "1" platform: "linux" package: "ray" version: "2.3.1-9" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/Ray" --- # Ray(1) assemble genomes in parallel using the message-passing interface ## 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\.RaySeeds.fasta **-write-extensions** - Writes extension DNA sequences to RayOutput/Rank\.RayExtensions.fasta **-write-contig-paths** - Writes contig paths with coverage values to RayOutput/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\.OptimalReadMarkers.txt - Read markers. - RayOutput/Rank\.RaySeeds.fasta - Seed DNA sequences, required option: **-write-seeds** - RayOutput/Rank\.RayExtensions.fasta - Extension DNA sequences, required option: **-write-extensions** - RayOutput/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\.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\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: \ 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