OrthoFinder-Sapelo2

Category

Bioinformatics

Program On

Sapelo2

Version

2.1.2, 2.2.7, 2.3.7

Author / Distributor

OrthoFinder

Description

"OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics. It finds orthologues and orthogroups infers rooted gene trees for all orthogroups and infers a rooted species tree for the species being analysed. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. OrthoFinder is simple to use and all you need to run it is a set of protein sequence files (one per species) in FASTA format." More details are at OrthoFinder

Running Program

Also refer to Running Jobs on Sapelo2 Also refer to Run X window Jobs and Run interactive Jobs

• Version 2.1.2, installed at /usr/local/apps/gb/orthofinder/2.1.2

All required dependencies are installed: dlcpar/1.0, MCL/14.137-foss-2016b, FastME/2.1.5-foss-2016b, BLAST+/2.6.0-foss-2016b-Python-2.7.14, MAFFT/7.313-foss-2016b-with-extensions, FastTree/2.1.10-foss-2016b, and DIAMOND/0.9.19-foss-2016b. Python 2.7.14 is loaded in this module.

To use this version of OrthoFinder, please first load the module with

module load orthofinder/2.1.2

• Version 2.2.7, installed at /usr/local/apps/eb/OrthoFinder/2.2.7-foss-2018a-Python-2.7.14

All required dependencies are installed: DLCpar/1.0-foss-2018a-Python-2.7.14, MCL/14.137-GCCcore-6.4.0-Perl-5.26.1, FastME/2.1.6.1-foss-2018a, BLAST+/2.7.1-foss-2018a, MAFFT/7.407-foss-2018a-with-extensions, FastTree/2.1.10-foss-2018a, DIAMOND/0.9.22-foss-2018a, and MMseqs2/5-9375b-foss-2018a. Python 2.7.14 is loaded in this module.

To use this version of OrthoFinder, please first load the module with

module load OrthoFinder/2.2.7-foss-2018a-Python-2.7.14

• Version 2.3.7, installed at /usr/local/apps/eb/OrthoFinder/2.3.7-foss-2018a-Python-2.7.14

OrthoFinder v2.3.7 includes all its dependencies now. No external modules will be loaded except for Python/2.7.14 module. More details at OrthoFinder.

To use this version of OrthoFinder, please first load the module with

module load OrthoFinder/2.3.7-foss-2018a-Python-2.7.14

Here is an example of a shell script sub.sh to run orthofinder.py of version 2.1.2 at the batch queue:

#!/bin/bash
#PBS -N j_OrthoFinder
#PBS -q batch
#PBS -l nodes=1:ppn=1:AMD
#PBS -l walltime=480:00:00
#PBS -l mem=10gb

cd $PBS_O_WORKDIR

module load orthofinder/2.1.2

orthofinder.py [options] 1>job.out 2>job.err   

Here is an example of a shell script sub.sh to run orthofinder.py of version 2.2.7 at the batch queue:

#!/bin/bash
#PBS -N j_OrthoFinder
#PBS -q batch
#PBS -l nodes=1:ppn=1
#PBS -l walltime=480:00:00
#PBS -l mem=10gb

cd $PBS_O_WORKDIR

module load OrthoFinder/2.2.7-foss-2018a-Python-2.7.14

orthofinder.py [options] 1>job.out 2>job.err   

Here is an example of a shell script sub.sh to run orthofinder.py of version 2.3.7 at the batch queue:

#!/bin/bash
#PBS -N j_OrthoFinder
#PBS -q batch
#PBS -l nodes=1:ppn=1
#PBS -l walltime=480:00:00
#PBS -l mem=10gb

cd $PBS_O_WORKDIR

module load OrthoFinder/2.3.7-foss-2018a-Python-2.7.14
module load BLAST+/2.7.1-foss-2018a
module load MAFFT/7.407-foss-2018a-with-extensions

orthofinder.py [options] 1>job.out 2>job.err

Here is an example of job submission

qsub  ./sub.sh 

Documentation

module load orthofinder/2.1.2
orthofinder.py -h

OrthoFinder version 2.1.2 Copyright (C) 2014 David Emms

SIMPLE USAGE:
Run full OrthoFinder analysis on FASTA format proteomes in <dir>
  orthofinder [options] -f <dir>

Add new species in <dir1> to previous run in <dir2> and run new analysis
  orthofinder [options] -f <dir1> -b <dir2>

OPTIONS:
 -t <int>          Number of parallel sequence search threads [Default = 16]
 -a <int>          Number of parallel analysis threads [Default = 1]
 -M <txt>          Method for gene tree inference. Options 'dendroblast' & 'msa'
                   [Default = dendroblast]
 -S <txt>          Sequence search program [Default = blast]
                   Options: blast, blast_gz, diamond
 -A <txt>          MSA program, requires '-M msa' [Default = mafft]
                   Options: mafft, muscle, mafft
 -T <txt>          Tree inference method, requires '-M msa' [Default = fasttree]
                   Options: mafft, iqtree, fasttree, raxml
 -R <txt>          Tree reconciliation method [Default = of_recon]
                   Options: of_recon, dlcpar, dlcpar_deepsearch
 -s <file>         User-specified rooted species tree
 -I <int>          MCL inflation parameter [Default = 1.5]
 -x <file>         Info for outputting results in OrthoXML format
 -p <dir>          Write the temporary pickle files to <dir>
 -1                Only perform one-way sequence search 
 -n <txt>          Name to append to the results directory
 -h                Print this help text

WORKFLOW STOPPING OPTIONS:
 -op               Stop after preparing input files for BLAST
 -og               Stop after inferring orthogroups
 -os               Stop after writing sequence files for orthogroups
                   (requires '-M msa')
 -oa               Stop after inferring alignments for orthogroups
                   (requires '-M msa')
 -ot               Stop after inferring gene trees for orthogroups 

WORKFLOW RESTART COMMANDS:
 -b  <dir>         Start OrthoFinder from pre-computed BLAST results in <dir>
 -fg <dir>         Start OrthoFinder from pre-computed orthogroups in <dir>
 -ft <dir>         Start OrthoFinder from pre-computed gene trees in <dir>

LICENSE:
 Distributed under the GNU General Public License (GPLv3). See License.md

CITATION:
 When publishing work that uses OrthoFinder please cite:
 Emms D.M. & Kelly S. (2015), Genome Biology 16:157

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Installation

source code from OrthoFinder

System

64-bit Linux