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Bioapplications puhti

This tutorial page provides step-by-step instructions on how to run Singularity containers of selected bio-applications in Puhti supercomputer. The selected examples shown below would serve as recipe for building your own customised singularity jobs.

DeepVariant pipeline

DeepVariant pipeline (Poplin et al., Nature biotechnology, 2018) is used to perform variant calling on WGS and WES data sets. More information about the deepvariant programmes can be found here

One needs to get DeepVariant docker image, models and test data in order to run the pipeline. Additionally, other prerequisites for running deepvariant method includes 1) obtaining a reference genome in FASTA format and its corresponding index file (.fai). 2) An aligned reads file in BAM format and its corresponding index file (.bai).

Convert docker image into Singularity image on your local machine

One way to build a Singularity image is to download the deepvariant docker image to local registry and then convert it to singularity one to avoid any possible erros with docker images pulled directly with singularity build command from google registry. Please note that one has to do these image conversions in your local machine or virtual machine in cPouta as Puhti does not grant root access to users.

Pull DeepVariant image and push it into local registry as below:

sudo docker pull gcr.io/deepvariant-docker/deepvariant:0.8.0
sudo docker tag gcr.io/deepvariant-docker/deepvariant:0.8.0 localhost:5000/deepvariant:latest
sudo docker run -d -p 5000:5000 --restart=always --name registry registry:2
sudo docker push localhost:5000/deepvariant:latest

then create a definition file (deffile) as follows:

Bootstrap: docker
Registry: http://localhost:5000
Namespace:
From:deepvariant:latest
and finally create a Singularity image as below:

sudo SINGULARITY_NOHTTPS=1 singularity build deepvariant.simg  deffile
Alternatively, one can download pre-converted singularity images (both cpu and gpu versions) along with test data from CSC's Allas object storage as below:

wget https://a3s.fi/pilot_projects/Deepvariant_singularity.zip

Prepare a batch script to run deepvariant pipeline on Puhti (file: deepvariant_puhti.sh)

#!/bin/bash
#SBATCH --time=00:05:00
#SBATCH --partition=test
#SBATCH --account=project_xxx

export TMPDIR=$PWD 

singularity -s exec -B $PWD:/data  \
deepvariant.simg \
/opt/deepvariant/bin/run_deepvariant \
--model_type=WGS \
--ref=/data/testdata/ucsc.hg19.chr20.unittest.fasta \
--reads=/data/testdata/NA12878_S1.chr20.10_10p1mb.bam \
--regions "chr20:10,000,000-10,010,000" \
--output_vcf=output.vcf.gz  \
--output_gvcf=output.g.vcf.gz

Submit job using sbatch command

sbatch  deepvariant_puhti.sh

Please note that one can use gpu version of deepvariant with the following sbatch script

#!/bin/bash
#SBATCH --time=00:05:00
#SBATCH --partition=gputest
#SBATCH --gres=gpu:v100:1
#SBATCH --account=project_xxx

export TMPDIR=$PWD

singularity -s exec --nv -B $PWD:/data \
deepvariant_gpu.simg \
/opt/deepvariant/bin/run_deepvariant \
--model_type=WGS \
--ref=/data/testdata/ucsc.hg19.chr20.unittest.fasta \
--reads=/data/testdata/NA12878_S1.chr20.10_10p1mb.bam  \
--regions "chr20:10,000,000-10,010,000" \
--output_vcf=output.vcf.gz  \
--output_gvcf=output.g.vcf.gz

Deepvariant as an interactive job in Puhti

One can run singularity containers also in the interactive mode. For example, deepvariant can be run as follows:

Download and unzip the deepvariant folder with data and singularity images in the login node

 wget https://a3s.fi/pilot_projects/Deepvariant_singularity.zip   
 unzip Deepvariant_singularity.zip
Then start interactive shell and provide requested parameters as prompted in terminal
sinteractive -i
Start interactive singularity session
cd Deepvariant_singularity
export TMPDIR=$PWD
singularity shell -B $PWD:/data deepvariant.simg
Execute the actual workflow commands in the singularity session

export PATH=/opt/deepvariant/bin:$PATH
cd /data/testdata/
run_deepvariant --model_type=WGS --ref=ucsc.hg19.chr20.unittest.fasta --reads=NA12878_S1.chr20.10_10p1mb.bam --regions "chr20:10,000,000-10,010,000" --output_vcf=output.vcf.gz --output_gvcf=output.g.vcf.gz
Exit from the singularity session and interactive batch job

exit
exit

Last edited Tue Apr 28 2020