Biowulf High Performance Computing at the NIH
mosdepth on Biowulf

Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.

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 follow the example in the following example session.

[user@biowulf]$ sinteractive --mem=10g --cpus-per-task=4 --gres=lscratch:50
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 mosdepth
[user@cn3144 ~]$ cd /lscratch/$SLURM_JOB_ID
[user@cn3144 ~]$ cp -rL ${MOSDEPTH_TEST_DATA} . # ~20 GB of data
[user@cn3144 ~]$ # whole exome data analyzed by capture probes
[user@cn3144 ~]$ mosdepth --by data/Agilent_SureSelect_Human_AllExon_V4_Covered.bed \
                      HG00096_WES data/HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam

[user@cn3144 ~]$ ls -lh
-rw-r--r-- 1 user group 336K May  8 18:41 HG00096_WES.mosdepth.global.dist.txt
-rw-r--r-- 1 user group 149K May  8 18:41 HG00096_WES.mosdepth.region.dist.txt
-rw-r--r-- 1 user group 570M May  8 18:41 HG00096_WES.per-base.bed.gz
-rw-r--r-- 1 user group  87K May  8 18:41 HG00096_WES.per-base.bed.gz.csi
-rw-r--r-- 1 user group 2.2M May  8 18:41 HG00096_WES.regions.bed.gz
-rw-r--r-- 1 user group 350K May  8 18:41 HG00096_WES.regions.bed.gz.csi

Note that version 0.2.0 produced only a single distribution file ( HG00096_WES.mosdepth.dist.txt.

[user@cn3144 ~]$ # create some graphs. Output file is dist.html [user@cn3144 ~]$ plot-dist.py HG00096_WES.mosdepth.region.dist.txt [user@cn3144 ~]$ # WGS data in 500 nt windows. No per-base data is written (-n) [user@cn3144 ~]$ mosdepth -t3 -n --by 500 HG00096_WGS \ data/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam [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. mosdepth.sh), which uses the input file 'mosdepth.in'. For example:

#! /bin/bash

module load mosdepth/0.2.3 || exit 1

cd /lscratch/$SLURM_JOB_ID || exit 1
mkdir data
cp ${MOSDEPTH_TEST_DATA}/Agilent_SureSelect_Human_AllExon_V4_Covered.bed data
cp ${MOSDEPTH_TEST_DATA}/HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam data

mosdepth -n -t2 --by data/Agilent_SureSelect_Human_AllExon_V4_Covered.bed \ 
    HG00096_WES data/HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam
plot-dist.py HG00096_WES.mosdepth.region.dist.txt

Submit this job using the Slurm sbatch command.

sbatch --mem=5g mosdepth.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. mosdepth.swarm). For example:

mosdepth -t2 -n --by 500 sample1 sample1.bam
mosdepth -t2 -n --by 500 sample2 sample2.bam
mosdepth -t2 -n --by 500 sample3 sample3.bam

Submit this job using the swarm command.

swarm -f mosdepth.swarm -g 5 --module mosdepth
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 mosdepth Loads the mosdepth module for each subjob in the swarm