ricopili on Biowulf

Quick Links

RICOPILI stands for Rapid Imputation and COmputational PIpeLIne for GWAS.

The software consists of four independent modules: Preimputation (QC), PCA, Imputation, and Meta-Analysis. These modules are not meant to be used linearly. For example, it may be necessary to repeat QC after discovering your data contains multiple populations from PCA.

References:

Lam M, Awasthi S, Watson HJ, Goldstein J, Panagiotaropoulou G, Trubetskoy V, Karlsson R, Frei O, Fan CC, De Witte W, Mota NR, Mullins N, Brügger K, Lee SH, Wray NR, Skarabis N, Huang H, Neale B, Daly MJ, Mattheisen M, Walters R, Ripke S. RICOPILI: Rapid Imputation for COnsortias PIpeLIne. Bioinformatics. 2020 Feb 1;36(3):930-933. doi: 10.1093/bioinformatics/btz633.Pubmed

Documentation

Important Notes

Module Name: ricopili (see the modules page for more information)
Multithreaded
Environment variables set: copy config and log to home folder, and edit config file before running the program.
- config file in $RICOPILI_TEST_DATA/ricopili.conf
- log file in $RICOPILI_TEST_DATA/log
Example files in $RICOPILI_TEST_DATA

Interactive job

Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --mem=12g --cpus-per-task=24
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144]$ module load ricopili
[user@cn3144]$ cp $RICOPILI_TEST_DATA/ricopili.conf ~/
[user@cn3144]$ mkdir -p ~/ricopili; cp -r $RICOPILI_TEST_DATA/log ~/ricopili/
[user@cn3144]$ mkdir -p /data/$USER/ricopili
[user@cn3144]$ cd /data/$USER/ricopili/; tar -zxvf $RICOPILI_TEST_DATA/test_sample.tar.gz 
[user@cn3144]$ cd test_samle
[user@cn3144]$ preimp_dir --disease sim --outname hapgen_5cohorts
switched on SERIAL mode because of configuration file

       _                 _ _ _
  _ __(_) ___ ___  _ __ (_) (_)
 | '__| |/ __/ _ \| '_ \| | | |
 | |  | | (_| (_) | |_) | | | |
 |_|  |_|\___\___/| .__/|_|_|_|
                  |_|

#######################################################################
#######################################################################
##                                                                  ###
##   preimp_dir    - module of ricopili pipeline                    ###
##                      version: 2019_Jun_25.001                     ###
##                                                                  ###
## https://sites.google.com/a/broadinstitute.org/ricopili/home      ###
## Stephan Ripke: sripke@broadinstitute.org                         ###
##                                                                  ###
#######################################################################
#######################################################################


Running job: plague
switched on SERIAL mode because of configuration file

       _                 _ _ _
  _ __(_) ___ ___  _ __ (_) (_)
 | '__| |/ __/ _ \| '_ \| | | |
 | |  | | (_| (_) | |_) | | | |
 |_|  |_|\___\___/| .__/|_|_|_|
                  |_|

#######################################################################
#######################################################################
##                                                                  ###
##   preimp_dir    - module of ricopili pipeline                    ###
##                      version: 2019_Jun_25.001                     ###
##                                                                  ###
## https://sites.google.com/a/broadinstitute.org/ricopili/home      ###
## Stephan Ripke: sripke@broadinstitute.org                         ###
##                                                                  ###
#######################################################################
#######################################################################



Running job: qc
-----------------------------------------------------
switched on SERIAL mode because of configuration file

       _                 _ _ _
  _ __(_) ___ ___  _ __ (_) (_)
 | '__| |/ __/ _ \| '_ \| | | |
 | |  | | (_| (_) | |_) | | | |
 |_|  |_|\___\___/| .__/|_|_|_|
                  |_|

#######################################################################
#######################################################################
##                                                                  ###
##   preimp_dir    - module of ricopili pipeline                    ###
##                      version: 2019_Jun_25.001                     ###
##                                                                  ###
## https://sites.google.com/a/broadinstitute.org/ricopili/home      ###
## Stephan Ripke: sripke@broadinstitute.org                         ###
##                                                                  ###
#######################################################################
#######################################################################


Running job: finished


##################################################################
##### CONGRATULATIONS:
##### preimp_pipeline finished successfully:
##### preimp_dir --disease sim --outname hapgen_5cohorts
##### now start with imputation pipeline (see README in subdir qc/)
##### have a look at the wiki page
##### https://sites.google.com/a/broadinstitute.org/ricopili/
##################################################################


[user@cn3144]$ cd qc 
[user@cn3144]$ pcaer --prefercase --preferfam --out pca_hap1a sim_sim5_eur_yourini-qc1.bim
----------------------------------------------------
witched on SERIAL mode because of configuration file

       _                 _ _ _
  _ __(_) ___ ___  _ __ (_) (_)
 | '__| |/ __/ _ \| '_ \| | | |
 | |  | | (_| (_) | |_) | | | |
 |_|  |_|\___\___/| .__/|_|_|_|
                  |_|

#######################################################################
#######################################################################
##                                                                  ###
##   pcaer         - module of ricopili pipeline                    ###
##                      version: 2019_Jun_25.001                     ###
##                                                                  ###
## https://sites.google.com/a/broadinstitute.org/ricopili/home      ###
## Stephan Ripke: sripke@broadinstitute.org                         ###
##                                                                  ###
#######################################################################
#######################################################################


Running job: me300
-----------------------------------------------------

Running job: finished

[user@cn3144]$ exit 

salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Batch job

Most jobs should be run as batch jobs.

Create a batch input file (e.g. ricopili_run.sh). Remember you still need to set up the config files first. For example:

#!/bin/bash
set -e
module load ricopili
cd /data/$USER/ricopili/test_sample
preimp_dir --disease sim --outname hapgen_5cohorts

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=24 --mem=12g ricopili_run.sh