Quick Links Documentation Notes Interactive job Batch job Swarm of jobs

DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3  to ther formats such as MaCH or PLINK.

• http://genome.sph.umich.edu/wiki/DosageConvertor

• Module Name: dosageconvertor (see the modules page for more information)

Allocate an interactive session and run the program. Sample session:

[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 dosageconvertor
[user@cn3144 ~]$ dosageconvertor command
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. batch.sh). For example:

#!/bin/bash
set -e
module load dosageconvertor
dosageconvertor command

Submit this job using the Slurm sbatch command.

sbatch [--mem=#] batch.sh

Create a swarmfile (e.g. job.swarm). For example:

cd dir1;dosageconvertor command
cd dir2;dosageconvertor command
cd dir3;dosageconvertor command

Submit this job using the swarm command.

swarm -f job.swarm [-g #] --module dosageconvertor

where

-g #	Number of Gigabytes of memory required for each process (1 line in the swarm command file)
--module	Loads the module for each subjob in the swarm