SimWalk2 is a statistical genetics computer application for haplotype, parametric linkage, non-parametric linkage (NPL), identity by descent (IBD) and mistyping analyses on any size of pedigree. SimWalk2 uses Markov chain Monte Carlo (MCMC) and simulated annealing algorithms to perform these multipoint analyses.
Simwalk2 was developed by Eric Sobel, Kenneth Lange, Daniel Weeks, Jeff O'Connell, and Goncalo Abecasis at UCLA. SimWalk2 documentation at UCLA
Simwalk is also available on Helix . Users who need relatively few Simwalk runs should use it on Helix. It is advantageous to run Simwalk on Biowulf only if you need large numbers of Simwalk runs.
For each Simwalk job, you can set up a batch command file and submit via qsub to the Biowulf batch system. Each job will then be allotted a node. Since Simwalk is not parallelized, the job will use only 1 processor of the node, which is inefficient use of the system. A preferable way to submit large numbers of Simwalk jobs is via the swarm command.
- Set up the Simwalk jobs, each in a directory with the appropriate input files.
- Create a swarm command file as below, with one line for each simwalk job.
------------------ file cmdfile ----------------------- cd /data/user/simwalk/run1; simwalk2 cd /data/user/simwalk/run2; simwalk2 cd /data/user/simwalk/run3; simwalk2 [...etc...] -------------------------------------------------------
- Submit as a swarm job with the command:
swarm -f cmdfile
Typically, Simwalk runs should be done via non-interactive batch or the swarm command. It may sometimes be useful to run interactively for debugging purposes.
This test run uses the files MAP.DAT, LOCUS.DAT, PEDIGREE.DAT and PEN.DAT from the Simwalk Example set, and the example sampling analysis (file BATCH-01.DAT) is being performed. These files can be copied from /usr/local/src/simwalk/SimWalk289/Examples.
[user@biowulf ~]$ qsub -I -l nodes=1
qsub: waiting for job 521768.biobos to start
qsub: job 521768.biobos ready
[user@p554 ~]$ cd mydir
[user@p554 ~/mydir]$ simwalk2
SimWalk2 version 2.89
Type of data analysis: Pedigree Sampling
Locus data INPUT file: LOCUS.DAT
Pedigree data INPUT file: PEDIGREE.DAT
Map data INPUT file: MAP.DAT
Individual OUTPUT files: MODEL-01.mmm
Copy of all screen output: VIDEO-01.TXT
Here 'mmm' is from the order within the input pedigree file,
e.g., '001' for the first pedigree, etc.
Working on data initialization ...
WARNING. In the locus file: LOCUS.DAT
for the following loci, minor adjustments had to be made
to the allele frequencies to force them to sum to 1.0:
CACNL1A1 pY2/1 KCNA5 S93
Map data file 'MAP.DAT' completed initialization;
Locus data file 'LOCUS.DAT' completed initialization;
Pedigree #001 completed initialization;
All data completed initialization.
Working on pedigree analysis ...
Pedigree #001 ('20') working on simulated annealing ...
(Found an initial consistent state.)
25% done ...
50% done ...
75% done ...
Pedigree #001 ('20') completed simulated annealing.
Pedigree #001 ('20') working on Markov chain Monte Carlo process ...
25% done ...
50% done ...
75% done ...
Pedigree #001 ('20') completed Markov chain Monte Carlo process.
Pedigree #001 ('20') completed all analyses.
All individual pedigrees completed analysis.
Please see the following output files.
Individual OUTPUT files: MODEL-01.mmm
Copy of all screen output: VIDEO-01.TXT
Here 'mmm' is from the order within the input pedigree file,
e.g., '001' for the first pedigree, etc.
Program run completed!
[user@p554 mydir]$exit
[user@biowulf ~]
Simwalk documentation at UCLA.
