Ohana on Biowulf

Ohana is a suite of software for analyzing population structure and admixture history using unsupervised learning methods. We construct statistical models to infer individual clustering from which we identify outliers for selection analyses.

Important Notes

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
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 ohana
[user@cn3144 ~]$ convert ped2dgm sample.ped g.dgm
[user@cn3144 ~]$ qpas g.dgm -k 4 -qo q.matrix -fo f.matrix -mi 5
[user@cn3144 ~]$ python $OHANA_HOME/tools/plot_q.py q.matrix q-bar-chart.pdf
[user@cn3144 ~]$ convert cov2nwk f.matrix tree.nwk
[user@cn3144 ~]$ convert nwk2svg tree.nwk tree.svg
[user@cn3144 ~]$ selscan g.dgm f.matrix c.matrix > lle-ratios.txt
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$