Dosageconvertor on HPC
DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3 to ther formats such as MaCH or PLINK.
Documentation
- Module Name: dosageconvertor (see the modules page for more information)
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.
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 ~]$
Batch job
Most jobs should be run as batch jobs.
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
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.
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 dosageconvertorwhere
-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 |