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TMAP

TMAP is a fast and accurate alignment software for short and long nucleotide sequences produced by Ion Torrent sequencing technologies.

There are multiple versions of TMAP available. An easy way of selecting the version is to use modules. To see the modules available, type

module avail TMAP

To select a module, type

module load TMAP/[ver]

where [ver] is the version of choice.

Environment variables set:

On Helix

Sample session:

$ module load TMAP
$ tmap mapall -n 8 -f /path/to/reference/file.fasta -r input.bam -v -Y -u --prefix-exclude 5 -o 2 stage1 map4 > output.bam 2> logfile.out

NOTE: By default, tmap will attempt to use ALL CPUS ON THE HOST. Please indicate the number of threads with the -n or --num-threads option.

Batch job on Biowulf

Create a batch input file (e.g. tmap.sh), which uses the input file 'input.bam'. For example:

#!/bin/bash
module load TMAP
# Aligning to reference genome
tmap mapall -n 8 -f /path/to/reference/file.fasta -r input.bam -v -Y -u --prefix-exclude 5 -o 2 stage1 map4 > output.bam 2>logfile.out

Submit this job using the Slurm sbatch command.

$ sbatch --cpus-per-task=8 --mem=20g tmap.sh
Swarm of Jobs on Biowulf

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

tmap mapall -n 12 -f /path/to/reference/file.fasta -r input.bam -v -Y -u --prefix-exclude 5 -o 2 stage1 map4 > output1.bam 2>logfile1.out
tmap mapall -n 12 -f /path/to/reference/file.fasta -r input.bam -v -Y -u --prefix-exclude 5 -o 2 stage1 map4 > output2.bam 2>logfile2.out
tmap mapall -n 12 -f /path/to/reference/file.fasta -r input.bam -v -Y -u --prefix-exclude 5 -o 2 stage1 map4 > output3.bam 2>logfile3.out
tmap mapall -n 12 -f /path/to/reference/file.fasta -r input.bam -v -Y -u --prefix-exclude 5 -o 2 stage1 map4 > output4.bam 2>logfile4.out

Submit this job using the swarm command.

$ swarm -f tmap.swarm -t 12 -g 20
Interactive job on Biowulf

Once an interactive job has been started,

sinteractive --cpus-per-task=8 --mem=20g

load the module and run the command.

module load TMAP
tmap mapall -n 8 -f /path/to/reference/file.fasta -r input.bam -v -Y -u --prefix-exclude 5 -o 2 stage1 map4 > output.bam 2>logfile.out
Documentation