AdmixTools on Biowulf
ADMIXTOOLS (Patterson et al. 2012) is a software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates.
The package contains 6 programs:- convertf: See README.CONVERTF for documentation of programs for converting file formats.
- qp3Pop: See README.3PopTest for details of running f_3 test. This test can be used as a format test of admixture with 3 populations.
- qpBound: See README.3PopTest for details of running qpBound. This test can be used for estimating bounds on the admixture proportions, given 3 populations (2 reference and one target).
- qpDstat: See README.Dstatistics for details of running D-statistics. This is a formal test of admixture with 4 populations.
- qpF4Ratio: See README.F4RatioTest for details of running F4 ratio estimation. This program computes the admixture proportion by taking the ratio of two f4 tests.
- rolloff: See README.ROLLOFF/ README.ROLLOFF_OUTPUT for details for running rolloff. This program can be used for dating admixture events.
References:
- Paper
Documentation
- AdmixTools website at Harvard.
- AdmixTools on Github.
Important Notes
- Module Name: AdmixTools (see the modules page for more information)
- Example files in /usr/local/apps/AdmixTools/examples/
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 AdmixTools [+] Loading AdmixTools 4.1 ... [user@cn3144 examples]$ cp -r $AMT_DATA/* . [user@cn3144 examples]$ expfit.sh rolloff-test-parfile.par Running rexpfit.r Input file: ASW_CEU_YRI Output file: expfit_ASW_CEU_YRI Expfit logfile: expfit_ASW_CEU_YRI.flog Output plot: expfit_ASW_CEU_YRI.pdf expfit.sh rolloff-test-parfile.par Jackknife logfile: expfit_ASW_CEU_YRI.log Jackknife summary: ASW_CEU_YRI.jin Jackknife mean: 5.468 Jackknife std. err: 0.253 [user@cn3145 test]$ expfit.sh rolloff-test-parfile.par Running rexpfit.r Input file: ASW_CEU_YRI Output file: expfit_ASW_CEU_YRI Expfit logfile: expfit_ASW_CEU_YRI.flog Output plot: expfit_ASW_CEU_YRI.pdf Jackknife logfile: expfit_ASW_CEU_YRI.log Jackknife summary: ASW_CEU_YRI.jin Jackknife mean: 5.468 Jackknife std. err: 0.253 [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. AdmixTools.sh). For example:
#!/bin/bash # this file is called admix.sh module load AdmixTools convertf -p par.EIGENSTRAT.PED
Submit this job using the Slurm sbatch command.
sbatch [--mem=#] AdmixTools.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.
Create a swarmfile (e.g. AdmixTools.swarm). For example:
rolloff -p rolloff1.par > rolloff1.log 2>&1 rolloff -p rolloff2.par > rolloff2.log 2>&1 rolloff -p rolloff3.par > rolloff3.log 2>&1
Submit this job using the swarm command.
swarm -f AdmixTools.swarm [-g #] --module AdmixToolswhere
| -g # | Number of Gigabytes of memory required for each process (1 line in the swarm command file) |
| --module AdmixTools | Loads the AdmixTools module for each subjob in the swarm |