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Mach2qtl on Biowulf

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.

Setting up a swarm of Mach2qtl jobs

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

[...]
If each Mach2qtl process requires less than 1 GB of memory, submit this to the batch system with the command:
swarm -f cmdfile --module mach2qtl

If each Mach2qtl process requires more than 1 GB of memory, use

swarm -g # -f cmdfile --module mach2qtl
where '#' 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.

Documentation

See the Helix Mach2qtl webpage or read the file /usr/local/mach2qtl/README