Ubuntu Manpage: Ray - 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<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/>

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