GCATemplates available: no
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