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 mach2qtl

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