Biowulf High Performance Computing at the NIH
Manta on Biowulf

Manta is a packaged used to discover structural variants and indels from next generation sequencing data. It is optimized for rapid clinical analysis, calling structural variants, medium-sized indels and large insertions. Manta makes use of split read and paired end information and includes scoring models optimized for germline analysis of diploid genomes and tumor-normal genome comparisons. Major use cases (as listed in the manta manual):

There is also experimental RNA-Seq support.


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 -c 10 --mem 10g
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 manta

[user@cn3144 ~]$ \
  --normalBam=${MANTA_TEST_DATA}/ \
  --tumorBam=${MANTA_TEST_DATA}/G15512.HCC1954.1.COST16011_region.bam \
  --referenceFasta=${MANTA_TEST_DATA}/Homo_sapiens_assembly19.COST16011_region.fa \
  --region=8:107652000-107655000 \
  --region=11:94974000-94989000 \
  --candidateBins=4 --exome --runDir=./test

[user@cn3144 ~]$ tree test
|-- [user   4.0K]  results
|   |-- [user   4.0K]  stats
|   `-- [user   4.0K]  variants
|-- [user   7.0K]
|-- [user   3.0K]
`-- [user   4.0K]  workspace

[user@cn3144 ~]$ test/ -m local -j 10 -g 10

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

The workflow is executed by running the generated script. In our case, this is wrapped into a slurm batch script

Batch job
Most jobs should be run as batch jobs.

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

module load manta || exit 1
test/ -m local -j $SLURM_CPUS_PER_TASK -g $((SLURM_MEM_PER_NODE / 1024))

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=4 --mem=10g
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. manta.swarm). For example:

normal1_vs_tumor1/ -m local -j $SLURM_CPUS_PER_TASK -g $((SLURM_MEM_PER_NODE / 1024))
normal2_vs_tumor2/ -m local -j $SLURM_CPUS_PER_TASK -g $((SLURM_MEM_PER_NODE / 1024))
normal3_vs_tumor3/ -m local -j $SLURM_CPUS_PER_TASK -g $((SLURM_MEM_PER_NODE / 1024))

Submit this job using the swarm command.

swarm -f manta.swarm -g 10 -t 10 --module manta
-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 manta Loads the manta module for each subjob in the swarm