Biowulf High Performance Computing at the NIH
pirs on Biowulf

pIRS is a profile-based Illumina paired-end Reads Simulator. It can simulate reads from haploid or diploid genomes using precomputed profiles from real data. Alternatively users can generate their own profiles.

References:

Documentation
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@biowulf]$ sinteractive --cpus-per-task=4 --mem=6g
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 pirs
[user@cn3144]$ cp $PIRS_TEST_DATA/chr22.fa .

Haplotype data can be simulated directly using the built in profile.

[user@cn3144]$ pirs simulate -l 100 -x 10 -m 200 -z -S 139347 \
                   --threads=$SLURM_CPUS_PER_TASK -o haplo_reads chr22.fa
[pIRS] Program:        pirs (Profile-based Illumina pair-end Reads Simulator)
[pIRS] Version:        2.0.0
[pIRS] Author:         Jianying Yuan (BGI-Shenzhen)
[pIRS] Contact:        yuanjianying@genomics.org.cn
[pIRS] Compile Date:   Oct 25 2019 time: 14:47:51
[pIRS] Current time:   Fri Oct 25 17:56:04 2019
[pIRS] Command line:   pirs simulate -l 100 -x 10 -m 200 -z -S 139347 --threads=4 -o haplo_reads chr22.fa
[pIRS]
[pIRS] Loading base-calling profile /usr/local/apps/pirs/2.0.2/share/pirs/Base-Calling_Profiles/humNew.PE100.matrix.gz
...

To get reads for a simulated diploid genome, first generate a second haplotype then simulate reads for both of them together.

[user@cn3144]$ pirs diploid -s 0.001 -R 2 -d 0.00001 -v 0.000001 \
                  -o chr22 chr22.fa
[user@cn3144]$ ls -lh chr22*
-rw-r--r-- 1 user staff  50M Oct 25 18:01 chr22.snp.indel.inversion.fa
-rw-r--r-- 1 user staff  50M Oct 25 17:42 chr22.fa
-rw-r--r-- 1 user staff  24K Oct 25 18:01 chr22.indel.lst
-rw-r--r-- 1 user staff 1.4K Oct 25 18:01 chr22.inversion.lst
-rw-r--r-- 1 user staff  50M Oct 25 18:01 chr22.snp.indel.inversion.fa
-rw-r--r-- 1 user staff 951K Oct 25 18:01 chr22.snp.lst

[user@cn3144]$ pirs simulate --diploid -l 100 -x 10 -m 800 -z -S 139347 \
                   --threads=$SLURM_CPUS_PER_TASK -o diplo_reads \
                  chr22.fa chr22.snp.indel.inversion.fa

[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. pirs.sh), which uses the input file 'pirs.in'. For example:

#!/bin/bash
module load pirs/2.0.2
pirs simulate -l 100 -x 10 -m 200 -z -S 139347 \
    --threads=$SLURM_CPUS_PER_TASK -o haplo_reads chr22.fa

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=6 --mem=8g pirs.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. pirs.swarm). For example:

pirs simulate -l 100 -x 10 -m 200 -z --threads=$SLURM_CPUS_PER_TASK -o haplo_reads_chr1 chr1.fa
pirs simulate -l 100 -x 10 -m 200 -z --threads=$SLURM_CPUS_PER_TASK -o haplo_reads_chr2 chr2.fa
pirs simulate -l 100 -x 10 -m 200 -z --threads=$SLURM_CPUS_PER_TASK -o haplo_reads_chr3 chr3.fa

Submit this job using the swarm command.

swarm -f pirs.swarm -g 8 -t 6 --module pirs
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 pirs Loads the pirs module for each subjob in the swarm