Introduction
You can run OMA as a standalone program. Included are the algorithms for OMA itself plus its addition ESPRIT. The software can be installed on Linux (x86, both 64bit and 32bit) and MacOSX (x86, both 32bit and 64bit).
For a short summary and pointers to detailed algorithmic publications of OMA, please refer to the OMA browser page:
http://omabrowser.org/oma/about/
For background info on ESPRIT, please refer to this article:
http://dx.doi.org/10.1093/bib/bbr038
If you have specific questions about the installation or the usage of OMA, please contact adrian.altenhoff at inf.ethz.ch or christophe.dessimoz at unil.ch.
Downloads
The current version of OMA standalone can be found here:
See the release notes to get an overview of recent function improvements and bug fixes.
Previous releases of OMA standalone are still available for download.
Installation
You do not need to install OMA standalone on your system; the script will also run if you just call it by using the complete path to bin/oma in the installer folder. But we still encourage you to run the installer script, since it makes working with OMA considerably more convenient.
To install OMA standalone on your system, download the installer, untar the package and run the included installer script:
curl http://omabrowser.org/standalone/OMA.2.2.0.tgz -o oma.tgz tar xvzf oma.tgz cd OMA.2.2.0 ./install.sh /your/install/prefix
If you do not choose an install prefix, OMA will be installed in /usr/local/OMA (for this, you might need to install it using the root account or sudo ).
After installation, make sure the bin folder of OMA is in your PATH variable, e.g., if you are using bash and used /your/install/prefix as installer prefix, add a line in ~/.profile such as:
export PATH=$PATH:/your/install/prefix/OMA/bin
For other shells, choose the appropriate syntax.
Homebrew/Linuxbrew
Alternatively, OMA standalone is also available on Homebrew and Linuxbrew . To install OMA standalone with Homebrew or Linuxbrew make sure you have installed the respective package and then run
brew tap brewsci/bio brew install oma
Usage
First, set up a working directory. Copy the file parameters.drw into this folder (if you installed OmaStandalone, you can alternatively run OMA -p to get the parameter file with default values) and change it to your needs. Create a directory DB in your working directory that holds the genome data in FASTA format (see "File formats") and copy your data into this directory. If you want to use ESPRIT, the FASTA file containing the contigs should be called {YourGenome}.contig.fa . Then, simply call OMA from your working directory to run OMA and/or ESPRIT
If you have not installed OMA yet, use the complete path to bin/oma in the installer folder to start the script.
As an example, assume you installed OMA in /your/install/prefix and want to use ESPRIT on two genome files and one file with contigs (all in /home/you/fasta , do something like this:
# create working directory mkdir myWorkingDir cd myWorkingDir # create DB directory in working directory mkdir DB # copy FASTA files into DB directory cp /home/you/fasta/yourFirstGenomeFile.fa DB/ cp /home/you/fasta/yourSecondGenomeFile.fa DB/ cp /home/you/fasta/yourContigFile.contig.fa DB/ cp /your/install/prefix/OMA/OMA.2.2.0/parameters.drw ./ # adjust parameters vim parameters.drw # run OMA OMA
To get a first impression of OMA you could cd into the ToyExample directory, have a look at parameters.drw and run OMA to process our example files.
Command-line options
OMA standalone has a few commandline options you can set. The available options together with a brief description is available using the "-h" option, i.e. OMA -h
OMA -h
bin/oma - runs OMA standalone
bin/oma [options] [paramfile]
Runs the standalone version of the Orthologous MAtrix (OMA) pipeline
to infer orthologs among complete genomes. A highlevel description
of its algorithm is available here: http://omabrowser.org/oma/about
The all-against-all Smith-Waterman alignment step of OMA requires
a lot of CPU time. OMA standalone can therefore be run in parallel.
If you intend to use OMA standalone on a HPC cluster with a scheduler
such as LSF, PBS Pro, Slurm or SunGridEngine, you should use the
jobarray option of those systems,
e.g. bsub -J "oma[1-500]" bin/oma (on LSF).
qsub -t 1-500 bin/oma (on SunGridEngine)
In case you run OMA on a single computer with several cores, use
the -n option.
Options:
-n <number> number of parallel jobs to be started on this computer
-v version
-d <level> increase debug info to <level>. By default level is set to 1.
-i interactive session, do not quit in case of error and at the end
of the run.
-s stop after the AllAll phase. This is the part which is parallelized.
The option can be useful on big datasets that require lot of
memory for the later phases of OMA. It allows to stop after the
parallelized step and restart again a single process with more
memory.
-c stop after database conversion. This option is useful if you
work with a large dataset and/or the filesystem you use is
slow.
-W <secs> maximum amount of Wall-clock time (in secs) that the job should
run before terminating in a clean way. This option has only an
effect in the all-against-all phase. If the job terminates
because it reaches the time limit, it quits with the exit
code 3.
-p copy the default parameter file to the current directory. This
is useful if want to analyse a new dataset and previously
installed OmaStandalone.
-h/? this help
paramfile path to the parameter file. it defaults to ./parameters.drw
EXIT
0 normal exit
1 a general error (i.e. configuration problem) occured
3 reached timelimit (provided with -W flag)
Parallelization
The all-against-all phase of OMA is the most time-consuming one, but it can be parallelized (unlike all other steps, which cannot run in parallel). The way it works is that the parameter "AlignBatchSize" and the total number of genomes (n) will determine into how many chunks the all-against-all phase is divided. AlignBatchSize will split the n*(n-1)/2 genome pairs further into chunks of at most "AlignBatchSize" alignments. The larger AlignBatchSize is, the more and smaller jobs will be executed.
Scheduling is straightforward: all compute processes need to start from the same directory, and each one will try to do an equal amount of chunks sequentially. However, before starting a new chunk, each process ensures that it has not yet already been processed by another process (i.e. no result file yet exists).
On a single computer with multiple processors and/or cores, it is recomended to start "N" parallel processes with the "-n" option, i.e.
OMA -n 5will start 5 parallel jobs. Note that on HPC with schedulers there is a better way described below
Therefore, there is not need to specify which parts are to be done by which process. One should only ensure that all processes start from a shared directory, such that each chunk gets computed by a single process only.
Parallelization with LSF, PBS Pro, Slurm, or SunGridEngine
With a scheduler such as LSF or SGE, running parallel jobs is particularly easy, as the parallel jobs can be start using as a job array. OMA will automatically spread the work for the all-against-all among all processes. For a brief discussion on the required resources refer to the section below Do not start OMA with the -n option for that. Instead, use a job array with one of the supported schedulers below (the example is to start 100 jobs in parallel).
New in 2.0: The user should now explicitly set the number of total processes that should run in the job array. This is done by setting the environment variable 'NR_PROCESSES'. E.g. in bash/tcsh use
export NR_PROCESSES=100 # bash setenv NR_PROCESSES 100 # tcshprior to submitting the job. The main advantage of this new form is that single jobs can be more easily resubmitted, and very large job arrays that do not all run simultaneously will work more reliably.
LSF
export NR_PROCESSES=100 bsub -J "OMA[1-$NR_PROCESSES]" -o "out.%I" "OMA"
Sun Grid Engine (aka Oracle Grid Engine)
export NR_PROCESSES=100 qsub -t 1-$NR_PROCESSES "OMA"
PBS Pro
Prepare a job script called e.g. job.sh:
#!/bin/bash # set the number of nodes and processes per node #PBS -l select=1:ncpus=1:mem=1000mb # set max wallclock time #PBS -l walltime=01:00:00 #PBS -J 1-100 export NR_PROCESSES=100 OMAThe script can then be submitted as follows:
qsub job.sh
Slurm
sbatch --array=1-100 -N1 <<EOF #!/bin/sh export NR_PROCESSES=100 /absolute/path/to/bin/OMA EOF
Required Resources
Depending on the dataset to be analysed, OMA can require quite a significant amount of computational resources, i.e. RAM and cpu time. Most computing time is spent to compute the all-against-all sequence alignments, which is why this part has been parallelized. Although cpu intensive this phase does not require too much memory. As a rule of thumb you can assume it requires roughly 10 times the size of your DB folder, but at minimum 650MB. The second part of OMA runs sequential on a single core, but it requires a lot more memory: Asymptotically it grows quadratic in the number of genomes. From a few real data runs we estimated that as a rule of thumb, you should count with 400MB * pow(nr_genomes, 1.4) . Obviously this depends also a lot on the size of your genomes. 60 metazoas have been successfully computed using 120GB, and for the same number of bacterial genomes, 50GB were reported to be enough.
Because of this imbalance regarding the required memory the OMA starter script has command line option -s to run only the first part of the OMA pipeline. Using this option, the computation can be split into a parallel phase with little memory requirement , and a single process requiring a lot more RAM. Running the OMA thus becomes a two stage process like this:
# first stage, little memory: OMA -s # once first stage terminated, run second stage OMANote that this staging is mostly useful on computing clusters where often memory and cpu time has to be reserved at job submission.
Adding/Updating new genomes
It is possible to add new genomes without recomputing the all-against-all phase for pre-existing genomes. To do so, simply add the new fasta databases in the DB/ directory and re-run OMA. Likewise, it is possible to update a genome by deleting the old genome from the DB/ directory, and adding a new file. Important: to avoid clashes with previously computed results, the updated genome must use a different filename than any previously computed result.
Advanced usages of OMA standalone
In this section we collect a few ideas to push the limits of OMA standalone.
Specifying the maximum amount of computing time
Often it is desirable to have many short jobs than a few long running ones, especially in a HPC environment. There, usually each job is limited to a certain amount of time, where short jobs usually get a higher priority assigned. With the -W command line option, one can inform OMA of the maximum amount of time (in seconds) it should use before exiting in a clean way. Once this time limit is reached, OMA terminates with an exit value of 3, which can be used on many schedulers to re-queue the job automatically. On LSF, you can use for example -Q "3". Sensible values for -W are usually between 3600 (1 hour) or higher. Note that this flag does not replace any resource allocation option from the scheduler.
File Formats
Input Files
OMA uses two different input formats: FASTA files for genome input and a Darwin file for parameter input.
The Fasta format is explained in detail on wikipedia.
As almost everywhere else, OMA uses the greater-than symbol ">" to distinguish labels from sequences. Each sequence in a genome is supposed to have its own label. Have a look at the FASTA files included in ToyExample/DB in our installer package for some example files.
In case your genomes contain multiple alternative splicing variants, you can add a text-based file per genome calledDB/{YourGenome}.splice that put together the different splicing variants, e.g. to indicate that the three splicing variants ENSP00000384207, ENSP00000263741 and ENSP00000353094 are encoded by the same gene, add the following line to the splice file:
ENSP00000384207; ENSP00000263741; ENSP00000353094OMA requires that the individual IDs are unique prefixes of your FASTA headers.
If you want to use ESPRIT, make sure that FASTA files containing contigs are called {YourGenome}.contig.fa . So if you want to experiment with some mouse genome, call the FASTA file mouse.contig.fa or mymouse.contig.fa or something similar.
Parameter files use Darwin syntax. Key-value-pairs are written as
key := value;
Note the colon in := and the semicolon at the end of the line. If your parameter file does not use valid Darwin syntax, OMA will print out a short message and stop its execution.
Output Files
OMA Output
The output of OMA gets written to files stored in a directory Output in your working directory. This can be changed by changing the OutputFolder parameter, There are text files and directories organized as described in Table 1. If not all output files are needed, note that the production of some of them can be disabled (see Table 4 below).
| Filename or Directory | Contents |
|---|---|
| Map-SeqNum-ID.txt | Lists all genes of all datasets with their unique sequence number and the labels read from the FASTA files. |
| OrthologousGroups.txt | The groups of orthologs are given as one per row, starting with a unique group identifier, followed by all group members, all separated by tabs. |
| OrthologousMatrix.txt | More compact version of OrthologousGroups.txt . The groups of orthologs are given as matrix with group per row and one genome per tab-separated column. Numbers refer to entry number as listed in the file Map-SeqNum-ID.txt . |
| OrthologousGroups.orthoxml | The OMA groups of orthologs stored in orthoxml format. |
| OrthologousGroupsFasta/ | Each OMA group is provided as a separate Fasta file, with the species name as identifer. This format is particularly suitable as starting point for a phylogenetic reconstruction. |
| PairwiseOrthologs/ | The textfiles in Output/PairwiseOrthologs are named according to {genome a}-{genome b}.txt and consist of a list of pairwise orthologs for the two given genomes. Every pair is listed only once, and in no particular order. Each line in the file contains one pair; all fields are separated by tabs. In the first two field, the unique IDs of the proteins are given. The next two fields contain the labels of the proteins, and in the last two fields, the type of orthology and (if any) the OMA group is given. |
| OrthologousPairs.orthoxml | The pairwise orthologs stored in orthoxml format. Each group in the file will have orthologs between genes from only two genomes. |
| HierarchicalGroups.orthoxml | The hierarchical groups of orthologs in OrthoXML format. A detailed description of how these groups are computed is forthcoming. |
| EstimatedSpeciesTree.nwk | The inferred species tree on which the hierarchical groups inference procedure is based, in Newick format. |
| HOGFasta/ | For each top-level HOG group we provide a separate Fasta file with all protein sequences clustered to it. This format is particularly suitable as starting point for a phylogenetic reconstruction of a gene tree. |
| used_splicing_variants.txt | If UseOnlyOneSplicingVariant is activated and splicing information is available, the variant which has been used for calling the orthologous relations is stored in this file. The format is a tab-delimited text file with the species in the first column and the id of the used splicing variant in the second column. |
| gene_function.gaf | The predicted Gene Ontology function assignments as a gaf formatted file. The file is only created if DoGroupFunctionPrediction is set to true in the parameter file and at least some exported genomes with GO annotations are included in the analysis. |
ESPRIT Output
ESPRIT stores its output files in a directory calledEspritOutput in your working directory. The output consists of three text files and one tarball. In the tarball, FASTA files with the MSAs of the hits ESPRIT found are stored. The other three files are explained in detail in Table 2.
| Filename | Contents |
|---|---|
| params.txt | This file is kept as a reference and contains all parameters used in the current run. |
| hits.txt | All hits found by ESPRIT are listed in this file. It is a list of contigs, ordered according to their position relative to the putative ortholog. Each line describes one contig, the fields are separated by tabs. In the first field, the fragment pair ID is printed; the next two fields contain the labels of the first and second fragments found in this hit. The forth and fifth fields contain the label of the corresponding full gene and its genome name. Then follows the distance difference between the two fragments and the number of positions between them (i.e. the gap); at last, an array is listed containing the IDs of all s3 genes corresponding to this hit. |
| dubious.txt | ESPRIT often detects more candidate pairs than it will list in the hits.txt file, but not all of them survive the quality check. Still, if you want to see which triplets have been filtered out, have a look at dubious.txt where they are still listed. The file format is the same as for hits.txt . |
Parameters
All parameters for OMA and/or ESPRIT are set in a parameters file. There is an example file in the OMA installer package; we encourage you to copy this file into your working directory and change it to your needs.
The parameter file consists of three main parts: First, general parameters for OMA are set. Table 3 describes these parameters in detail.
Next, there are a few optional parameters, listed in Table 4, to avoid producing particular output files. Indeed, in large analyses, disabling the generation of unused output might save a substantial amount of computing time and might drastically reduce the number of produced files.
And third, more specific parameters that only affect the ESPRIT algorithm can be changed. These parameters are explained in Table 5. Note that changing the ESPRIT parameters will not have an effect unless you set the boolean variable UseEsprit to true .
| Parameter | Meaning | Default |
|---|---|---|
| InputDataType | Type of input sequences. This can be set either to 'AA' for amino acid sequences or 'DNA' for nucleotide sequences | AA |
| OutputFolder | Folder to which the output is written. At each run, the content of this folder will be overwritten. Don't store any important files in it. The OutputFolder must not contain any spaces. | Output |
| ReuseCachedResults | If you want to recompute everything from scratch everytime the script is run, set this to false . | true |
| AlignBatchSize | In the all-against-all phase, each genome pair is split in smaller chunks of AlignBatchSize protein comparisons. The larger this number, the longer each unit runs, and the fewer files get produced. This allows to adjust the frequency of milestone steps (e.g. in case of computer crash) or to process few but large genomes with many CPUs efficiently. | 1000000 |
| MinScore | Alignments which have a score lower than MinScore will not be considered. The scores are in Gonnet PAM matrices units. | 181 |
| LengthTol | Length tolerance ratio. If the length of the effective alignment is less than LengthTol * min( length(s1), length(s2) ), then the alignment is not considered. | 0.61 |
| StablePairTol | During the stable pair formation, if a pair has a distance provable higher than another pair (i.e. StablePairTol standard deviations away) then it is discarded. | 1.81 |
| VerifiedPairTol | Tolerance parameter for the detection of differential gene losses using a third genome. The larger the tolerance, the liberaler the algorithm assigns orthologous relations. A detailed description is provided here. | 1.53 |
| MinSeqLen | Any sequence which is less than MinSeqLen amino acids long in regular genomes is not considered. | 50 |
| UseOnlyOneSplicingVariant | Enables/disables the filtering on a single represetative splicing variant. If enabled, OMA selects the variant that has the most homologous matches with all other genomes. Orthology inference is then only based on this variant. If disabled, alternative splicing variants will usually be infered as paralogs. | true |
| StableIdsForGroups | Enables/disables the generation of stable identifiers for OMA groups (and Hierarchical Groups if the top-down algorithm is selected). The identifier consists of a prefix to determine the type of the group ('OMA' or 'HOG'), and a subsequence of the amino acid sequence uniquely present in this group. The computation of these ids might require a substantial amount of time. The ids are stored in the OrthoXML files only. | false |
| GuessIdType | Enable/disable guessing of the id types while generating the orthoxml file. In this context we refer to ID type guessing as the task to gussing whether an ID should be stored in the geneId, protId or transcriptId tag. If the flag is set to false, the whole fasta header is used and stored as is in the protId tag. | false |
| DoHierarchicalGroups | Enables/disables and selects the algorithm to compute the hierarchical orthologous groups (HOGs). Valid parameters are false , 'top-down' and 'bottom-up' . The top-down approach was the only algorithm until OMA standalone 2.0. The bottom-up approach is as of now still an experimental feature, but will become the default choice in the future. | 'top-down' |
| MaxTimePerLevel | Define maximum amount of time (in sec) spent by the program for breaking every connected component of the orthology graph at its weakest link on a given taxonomic level. If set to a negative value, no timelimit is enforced. | 1200 |
| SpeciesTree | The hierarchical groups require a (partially) resolved species phylogeny. With the parameter SpeciesTree the user can specify a phylogeny in Newick-format, or, by setting the variable to "estimate", compute a species tree based on the OMA Groups and use this one. | estimate |
| ReachabilityCutoff | The cutoff of "average reachability within two steps" defines up to what point a cluster is split into sub-clusters. This paramter applies only to the top-down HOG inference approach. See parameter DoHierarchicalGroups for additional information. | 0.65 |
| MinEdgeCompletenessFraction | The cutoff in GETHOGs bottom-up algorithm to make an edge trusted in the orthology graph among HOGs. This parameter applies only to the bottom-up approach. See parameter DoHierarchicalGroups for additional information. | 0.80 |
| DoGroupFunctionPrediction | Compute Gene Ontology function predictions based on the OMA Groups assignments. The predictions are then stored in a gaf file. Computing these predictions can take a substantial amount of time. Note: Predictions are based on transfering existing annotations from genomes. Only genomes exported through the OMA Browser export interface have usable input annotations. | true |
| GroupFunctionCutoff | Parameter to specify the fraction of genes in a group that need to be annotated with a GO term in order to propagate the annotation to the unannotated group members. The parameter ensures that predictions are not propagated too liberally. Note that it requires at least the specified fraction of genomes to be exported from the OMA Browser. | 0.5 |
| CladeDefinition | Path to tab-seperated file that provides a mapping from the species names to the clade/group to which annotations should at most be propagated. If set to default , the algorithm infers a species tree an propages GO annotations to user genomes only within some predefined clades. These predifined clades are 'Amphibia', 'Archaea', 'Arthropoda', 'Bacteria', 'Clupeocephala', 'Dictyostelium', 'Fungi', 'Mammalia', 'Nematoda', 'Sauria' and 'Viridiplantae'. If the parameter is set to false or none , no limitations on the clades are used to propagate the function annotations. | default |
| Parameter | Meaning | Default |
|---|---|---|
| WriteOutput_PairwiseOrthologs | Switches to disable the generation of pairwise ortholog output files if set to false . | true |
| WriteOutput_OrthologousPairs_orthoxml | Switches to disable the generation of the pairwise ortholog output file in OrthoXML format if set to false . | true |
| WriteOutput_OrthologousGroupsFasta | Switches to disable the generation of orthologous group output files (Fasta format, one file per group) if set to false . | true |
| WriteOutput_HOGFasta | Switches to disable the generation of hierarchical orthologous group files (Fasta format, one file per group) if set to false . | true |
| Parameter | Meaning | Default |
|---|---|---|
| UseEsprit | You can either set this to true , which will enable ESPRIT and shut down the parts of OMA that are not directly needed for ESPRIT, or set it to false to make no use of ESPRIT at all. | false |
| DistConfLevel | Confidence level variable for contigs. This is the parameter tol described in the paper. | 2 |
| MinProbContig | Minimal proportion of genomes with which contigs form many:1 BestMatches to consider that we might be dealing with fragments of the same gene. This is the parameter MinRefGenomes described in the paper, normalized by the total number of reference genomes. | 0.4 |
| MaxContigOverlap | Maximum overlap between fragments of same gene from different contigs. | 5 |
| MinSeqLenContig | Any sequence which is less than MinSeqLenContig amino acids long in contigs is not considered. | 20 |
| MinBestScore | Minimum best score for BestMatch in scaffold recognition. | 250 |
Getting help
The preferred way to get help about OMA is via the Biostars community resource. Please consider asking your question there, including the tags "OMA" and "orthologs".
If your question requires privacy, we are also reachable by email at contact@omabrowser.org.
License
OMA standalone is licensed under the Mozilla Public License Version 2.0. For more info, please consult the following page:
http://www.mozilla.org/MPL/2.0/
In a nutshell, OMA standalone is open source and free for commercial and non-commercial use.
Software distributed under the License is distributed on an "AS IS" basis,WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License for the specific language governing rights and limitations under the License.