Biowulf High Performance Computing at the NIH
MToolBox on Biowulf

MToolBox is a highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from high throughput sequencing data. It includes an updated computational strategy to assemble mitochondrial genomes from whole exome and/or genome sequencing and an improved fragment-classify tool for haplogroup assignment, functional and prioritization analysis of mitochondrial variants. It also provides pathogenicity scores, profiles of genome variability and disease-associations for mitochondrial variants and a Variant Call Format file featuring allele-specific heteroplasmy.


Important Notes

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 input in bold):

[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 mtoolbox
[user@cn3144 ~]$ cd /path/to/mtoolbox/input/dir
[user@cn3144 ~]$ -i input file 
[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. For example:

set -e
module load mtoolbox
cd MToolbox/input/files/dir -i fastq -I -M -r RCRS

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#]
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. mtoolbox.swarm). For example:

cd /MToolbox/input/dir1 && -i <input_format> -r <reference_sequence> -m "<mapExome_options>" -a "<assembleMTgenome_options>" -c "<mt-classifier_options>"
cd /MToolbox/input/dir2 && -i <input_format> -r <reference_sequence> -m "<mapExome_options>" -a "<assembleMTgenome_options>" -c "<mt-classifier_options>"
cd /MToolbox/input/dir3 && -i <input_format> -r <reference_sequence> -m "<mapExome_options>" -a "<assembleMTgenome_options>" -c "<mt-classifier_options>"
cd /MToolbox/input/dir4 && -i <input_format> -r <reference_sequence> -m "<mapExome_options>" -a "<assembleMTgenome_options>" -c "<mt-classifier_options>"

Submit this job using the swarm command.

swarm -f mtoolbox.swarm [-g #] [-t #] --module mtoolbox
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t # Number of threads/CPUs required for each process (1 line in the swarm command file).
--module mtoolbox Loads the MToolBox module for each subjob in the swarm