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

• TMAP: The Novel, by Nils Homer
• Type tmap --help at the prompt.

• Module Name: TMAP (see the modules page for more information)
• Multithreaded
• Environment variables set
  • PATH

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.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --cpus-per-task=8 --mem=20g
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 TMAP
[user@cn3144 ~]$ tmap mapall -n $SLURM_CPUS_PER_TASK -f /path/to/reference/file.fasta -r input.bam -v -Y -u --prefix-exclude 5 -o 2 stage1 map4 > output.bam 2>logfile.out

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

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

#!/bin/bash
module load TMAP
tmap mapall -n $SLURM_CPUS_PER_TASK -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=16 --mem=20g TMAP.sh

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

tmap mapall -n $SLURM_CPUS_PER_TASK -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 $SLURM_CPUS_PER_TASK -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 $SLURM_CPUS_PER_TASK -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 $SLURM_CPUS_PER_TASK -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 -g 20 -t 12 --module TMAP