High-Performance Computing at the NIH
GitHub YouTube @nih_hpc RSS Feed
DosageConvertor on NIH HPC Systems

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

On Helix

Sample session:

[USER@helix ~]$ module load dosageconvertor
[USER@helix ~]$ DosageConvertor --help

Batch job on Biowulf

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


cd /data/$USER/dir
module load dosageconvertor
DosageConvertor command .........

Then submit the file on biowulf

sbatch dosageconvertor.sh

Please read user guide for more sbatch options

Useful utilities for job monitoring and debugging

Swarm of Jobs on Biowulf

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

# this file is called dosageconvertor.swarm
cd dir1; DosageConvertor command 
cd dir2; DosageConvertor command 
cd dir3; DosageConvertor command

Submit this job using the swarm command.

biowulf >$ swarm -f dosageconvertor.swarm --module dosageconvertor

More options for swarm job can be viewed here.

Interactive job on Biowulf
Allocate an interactive session. Sample session:
[USER@biowulf ~]$ sinteractive 
salloc.exe: Pending job allocation 15194042
salloc.exe: job 15194042 queued and waiting for resources
salloc.exe: job 15194042 has been allocated resources
salloc.exe: Granted job allocation 15194042
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn1719 are ready for job

[USER@cn1719 ~]$ module load dosageconvertor

[USER@cn1719 ~]$ DosageConvertor command ....