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SW:POTION

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POTION

GCATemplates available: no

POTION homepage


POTION BUG

A user has identified that the columns for the final_results.out file do not match the columns in the positive.out file.

The POTION developer has been notified and the developer has acknowledged that the columns in the final_results.out file are out of order.

For Example:
   In the file final_results.out there may be 3 P's (in column 2) for model m78
   and 76 P's for m12 (in column 3). However, in the positive.out file it is reversed, there
   are 76 sequences listed for model 8 (m78) and only 3 for model 2 (m12)

POTION (POsitive selecTION) is an open source, modular and end-to-end software for genomic scale detection of positive Darwinian selection in groups of homologous coding sequences through estimation of dN/dS ratios.

module spider POTION

POTION requires multiple steps to be run on the command line prior to running a job script:

module load POTION/1.1.2-intel-2015B-Perl-5.20.0

rsync -r $EBROOTPOTION/bin ./
rsync -r $EBROOTPOTION/config_files ./

ln -s $EBROOTPAML/bin/codeml bin/
ln -s $EBROOTPHYLIP/bin/consense bin/
ln -s $EBROOTMUSCLE/bin/muscle bin/
ln -s $EBROOTPHIPACK/bin/Phi bin/
ln -s $EBROOTPRANK/bin/prank bin/
ln -s $EBROOTPHYLIP/bin/proml bin/
ln -s $EBROOTPHYLIP/bin/dnaml bin/
ln -s $EBROOTPHYLIP/bin/seqboot bin/
ln -s $EBROOTTRIMAL/bin/trimal bin/
ln -s $EBROOTMAFFT/bin/mafft bin/
ln -s $EBROOTPAGAN/bin/pagan bin/
ln -s $EBROOTPHYML/bin/phyml bin/

cp ./config_files/dummy_potion_user_config_file_site_standard my_config_file

Edit the following variables in your my_config_file:

CDS_dir_path = /path/to/CDS                         # path to folder containing CDS data; you create the CDS directory and put your data there
homology_file_path = /path/to/all_orthomcl.out      # path to the ORTHOMCL 1.4 main output file
project_dir_path = /path/to/potion_results_out      # path to the main directory where results will be created.Parent directory must exist.
max_processors
multiple_alignment
phylogenetic_tree

Then edit only the potion_dir variable in the ./config_files/potion_config file and set it to the full path of your current working directory

potion_dir = $EBROOTPOTION/           # change this to the full path of your working directory

OrthoMCL version 1.4 is required if generating the all_orthomcl.out input file for POTION.

Sample job script run from your working directory:

#!/bin/bash
#SBATCH --export=NONE               # do not export current env to the job
#SBATCH --job-name=my_job           # job name
#SBATCH --time=7-00:00:00           # max job run time dd-hh:mm:ss
#SBATCH --ntasks-per-node=1         # tasks (commands) per compute node
#SBATCH --cpus-per-task=48          # CPUs (threads) per command
#SBATCH --mem=360G                  # total memory per node
#SBATCH --output=stdout.%j          # save stdout to file
#SBATCH --error=stderr.%j           # save stderr to file

module load POTION/1.1.2

./bin/potion.pl --conf_file_path /absolute/pato/to/working/directory/my_config_file