Biowulf High Performance Computing at the NIH
Misopy on HPC

MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples. By modeling the generative process by which reads are produced from isoforms in RNA-Seq, the MISO model uses Bayesian inference to compute the probability that a read originated from a particular isoform.


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  --mem=20g --cpus-per-task=8
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 misopy
[user@cn3144 ~]$ miso --run ./indexed ./accepted_hits.bam --output-dir miso_out --read-len 76
[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. For example:

set -e
module load misopy
cd dir
miso --run ./indexed ./accepted_hits.bam --output-dir miso_out --read-len 76

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=8 --mem=20g
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. job.swarm). For example:

cd dir1; miso --run ./indexed ./accepted_hits.bam --output-dir miso_out --read-len 76
cd dir2; miso --run ./indexed ./accepted_hits.bam --output-dir miso_out --read-len 76
cd dir3; miso --run ./indexed ./accepted_hits.bam --output-dir miso_out --read-len 76

Submit this job using the swarm command.

swarm -f job.swarm -g 20 -t 8 --module misopy
-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 Loads the module for each subjob in the swarm

Submit a Parallel Job

Refer to Notes section regarding miso setting file.

1. Create a script file similar to the lines below.

module load misopy
cd /data/$USER/dir
miso --run \
./indexed \
./accepted_hits.bam \
--output-dir miso_out_cluster \
--read-len 76 \
--use-cluster \

2. Submit the script on biowulf:

$ sbatch jobscript

In this example, events will be split into multiple chunks, each chunk contains 1000 events, and each chunk will be submitted as a single job to the cluster. By default each job will run on 1 core and 20gb or memory. The default walltime is 99 hours.

For more memory or walltime, copy and modify the miso_setting.txt file and add '--settings-filename=/data/$USER/..../miso_settings_cluster.txt' to the miso command.