Loki on Biowulf

Loki is a linkage analysis package, primarily for large and complex pedigrees, which uses Markov chain Monte Carlo (MCMC) techniques to avoid many of the computational problems that prevent exact computational methods being used for large pedigrees. Loki was originally designed for linkage analysis of quantitative traits, though there is some limited support for qualitative trait linkage analysis. The other supported analysis performed by Loki is the estimation of IBD relationship matrices for use with variance component programs such as SOLAR, which is also installed on Biowulf.

Version 2.4.7_4 is currently installed on Biowulf.

The swarm utility should be used for multiple jobs in order to efficiently use the cluster since swarm will make use of both processors on each node while submit the job to batch system using 'qsub' only makes use of one processor and waste the other one. Below are sample sessions for swarm submission and for initiate Loki interactively. Please see User Documentation of Loki for information about setting up a Loki parameter file.

Swarm Sample Session:

1. First create different directories for each loki run. Put all the required input files under each of the directories.

2. Create a swarm command file containing a single job on each line, e.g.

-------------------- /data/user/loki/cmdfile -------------------------
cd /data/user/loki/run1;/usr/local/bin/loki parameter.file > logfile
cd /data/user/loki/run2;/usr/local/bin/loki parameter.file > logfile
cd /data/user/loki/run3;/usr/local/bin/loki parameter.file > logfile
............
.........
cd /data/user/loki/runX;/usr/local/bin/loki parameter.file > logfile
------------------------------------------------------------------------

% > swarm -f cmdfile

Interactive Sample Session:

<biowulf>% qsub -I -l nodes=1
qsub: waiting for job 593807.biobos to start
qsub: job 593807.biobos ready

<p3>% cd /data/user/loki/run1
<p3>% loki parameterfile > logfile

This document is available as http://biowulf.nih.gov/apps/loki.html
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