TVC on Biowulf

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TVC is the standalone Torrent Variant Caller, part of the Ion Torrent Suite.

Documentation

TVC Main Site: Ion Community, at ThermoFisher Scientific
Type variant_caller_pipeline.py without any arguments.

Important Notes

Module Name: TVC (see the modules page for more information)
Multithreaded/singlethreaded/MPI...
Environment variables set
- PATH
- TVC_ROOT_DIR
Example files in $TVC_ROOT_DIR/share

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 --mem=20g --cpus-per-task=16
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 TVC
[user@cn3144 ~]$ variant_caller_pipeline.py -i /path/to/input.bam -r /path/to/reference/file.fasta -N $SLURM_CPUS_PER_TASK

[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. TVC.sh). For example:

#!/bin/bash
module load TVC
variant_caller_pipeline.py -i /path/to/input.bam -r /path/to/reference/file.fasta -N $SLURM_CPUS_PER_TASK

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=16 --mem=20g TVC.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. TVC.swarm). For example:

mkdir outdir1 ; variant_caller_pipeline.py -i /path/to/input1.bam -r /path/to/reference/file.fasta -N $SLURM_CPUS_PER_TASK -o outdir1
mkdir outdir2 ; variant_caller_pipeline.py -i /path/to/input2.bam -r /path/to/reference/file.fasta -N $SLURM_CPUS_PER_TASK -o outdir2
mkdir outdir3 ; variant_caller_pipeline.py -i /path/to/input3.bam -r /path/to/reference/file.fasta -N $SLURM_CPUS_PER_TASK -o outdir3
mkdir outdir4 ; variant_caller_pipeline.py -i /path/to/input4.bam -r /path/to/reference/file.fasta -N $SLURM_CPUS_PER_TASK -o outdir4

NOTE: By default, all output is written in the current working directory. When run in a swarm, it is ideal to create a directory for the output and redirect that output using the -o option. This will prevent overwriting the same file by indendent swarm subjobs.

Submit this job using the swarm command.

swarm -f TVC.swarm -g 10 -t 8 --module TVC

where

`-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 TVC`	Loads the TVC module for each subjob in the swarm