This repository contains singularity definition file and Nextflow script for ORPER.
Please first install singularity, follow: https://stackoverflow.com/questions/63865962/singularity-3-6-2-installation
Please build the singularity container using ORPER.def.
git clone https://github.com/Lcornet/ORPER
sudo singularity build ORPER.sif ORPER.def
Classical command line to work on a phylum, here Cyanobacteria.
nextflow ORPER.nf --reftaxolevel=phylum --refgroup=Cyanobacteria --outtaxolevel=phylum --outgroup=Melainabacteria --outgenbank=yes --cpu=30 --SSU=SequencesULC4Luc.fasta -with-singularity ORPER.sif
This command should give a nextflow report like this:
executor > local (23)
[3f/8bd288] process > RiboDBSetUp (1) [100%] 1 of 1 ✔
[1b/d33ae5] process > Taxonomy (1) [100%] 1 of 1 ✔
[0b/e20645] process > RefSeq (1) [100%] 1 of 1 ✔
[ff/04aef1] process > GenBank (1) [100%] 1 of 1 ✔
[b8/c9dc0a] process > GetRefGenomesRefseq (1) [100%] 1 of 1 ✔
[71/94add5] process > GetRefGenomesGenbank (1) [100%] 1 of 1 ✔
[40/965983] process > RefGenomesCheckm (1) [100%] 1 of 1 ✔
[aa/5f3aa2] process > RefGenomesBarnap (1) [100%] 1 of 1 ✔
[23/4dcb16] process > RefGenomesFilter (1) [100%] 1 of 1 ✔
[1a/059ff6] process > RefGenomesDereplication (1) [100%] 1 of 1 ✔
[65/b930c7] process > GetRefRelProteomes (1) [100%] 1 of 1 ✔
[d9/2f9308] process > GetOutGenomesRefSeq (1) [100%] 1 of 1 ✔
[2b/666443] process > GetOutGenomesGenbank (1) [100%] 1 of 1 ✔
[40/269a15] process > OutGenomesCheckm (1) [100%] 1 of 1 ✔
[4d/cb7dbd] process > OutGenomesBarnap (1) [100%] 1 of 1 ✔
[c9/1792af] process > OutGenomesFilter (1) [100%] 1 of 1 ✔
[f5/a63730] process > GetOutRelProteomes (1) [100%] 1 of 1 ✔
[01/69d4d9] process > RiboDBFortytwo (1) [100%] 1 of 1 ✔
[91/8f3231] process > AlignmentMUSCLE (1) [100%] 1 of 1 ✔
[79/153441] process > ConcatScafos (1) [100%] 1 of 1 ✔
[d5/6d85e1] process > ReferenceTreeRaxml (1) [100%] 1 of 1 ✔
[84/6240bd] process > SSUDereplication (1) [100%] 1 of 1 ✔
[2a/23433b] process > ConstrainTreeRaxml (1) [100%] 1 of 1 ✔
[1e/1edc61] process > PublicationResults (1) [100%] 1 of 1 ✔
Completed at: 07-Sep-2021 09:22:27
Duration : 20h 47m 27s
CPU hours : 25.6
Succeeded : 24
Please follow the help of ORPER:
Mandatory arguments:
--refgroup Group of interest
--outgroup Outgroup
--reftaxolevel Taxonomic level of reference group - Choice between four taxa levels: phylum, class, order, family
--outtaxolevel Taxonomic level of outgroup - Choice between four taxa levels: phylum, class, order, family
--SSU Path to fasta file containing SSU sequences
Optional arguments:
--ribodb Path to directory containing ribodb fasta files - automatic setup by default
--companion Path to ORPER-companion.py
--taxdump Path to taxdump directory - automatic setup by default
--cpu Number of cpus, default = 1
--genbank Download GenBank metadata, activated by default - yes or no. Needed if refgenbank or outgenbank is activated
--refgenbank add GenBank for reference group, Deactivated by default - yes or no
--outgenbank add GenBank for outgroup, Deactivated by default - yes or no
--dRep dRep dereplication for group of interest, activated by default - yes or no
--cdhit cdhit dereplication of provided SSU sequences, activated by default - yes or no
--shrink TreeShrink cutoff value, 0.1 by default
For HPC usage, we recommend to use Nextflow configuration file: nextflow.config.
This file, which as to be in the folder where you ORPER should look like this:
process.container = '/scratch/ulg/bioec/lcornet/ORPER/ORPER.sif'
singularity.enabled = true
singularity.cacheDir = "$PWD"
singularity.autoMounts = false
singularity.runOptions = '-B <Path-to-ORPER-working-dir> -B <Path-to-symlink-dir>'
Please note that if your HPC system use symbolic link to mount partition, both links (hard link and symlink) has to be added in the bind (-B) linl of the config file.
This software is copyright (c) 2017 by University of Liege / Unit of Eukaryotic Phylogenomics / Luc CORNET and Denis BAURAIN.
This is free software; you can redistribute it and/or modify.