Mach2qtl performs QTL analysis based on imputed dosages/posterior_probabilities. Mach2qtl was developed by Goncalo Abecasis at the University of Michigan. Mach2qtl website.
Small numbers of simultaneous Mach2qtl jobs (< 3 simultaneous) are most easily run on Helix. Mach2qtl on Biowulf is intended for large numbers of simultaneous jobs, or Mach2qtl jobs that will run for a long time.
It is easiest to run a large number of simultaneous Mach2qtl jobs via swarm.
The mach2qtl executable can be added to your path by using the 'module load mach2qtl' command as below.
[user@helix]$ module load mach2qtl [user@helix]$ module list Currently Loaded Modulefiles: 1) mach2qtl
Set up a swarm command file along the following lines:
#------- this file is swarmcmd ------------------ mach2qtl -d sample1.dat -p sample1.ped -i sample1.mlinf --probfile sample1.mlp > sample1.out mach2qtl -d sample2.dat -p sample2.ped -i sample2.mlinf --probfile sample2.mlp > sample2.out mach2qtl -d sample1.dat -p sample3.ped -i sample3.mlinf --probfile sample3.mlp > sample3.out mach2qtl -d sample4.dat -p sample4.ped -i sample4.mlinf --probfile sample4.mlp > sample4.out [...]
swarm -f cmdfile --module mach2qtl
If each Mach2qtl process requires more than 1 GB of memory, use
swarm -g # -f cmdfile --module mach2qtlwhere '#' is the number of Gigabytes of memory required by each Mach2qtl process.
The swarm program will package the commands for best efficiency and send them to the batch system.
See the Helix Mach2qtl webpage or read the file /usr/local/mach2qtl/README