Biowulf High Performance Computing at the NIH
Flappie on Biowulf

Basecall Fast5 reads using flip-flop basecalling (Oxford Nanopore).

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 4 --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 flappie
[+] Loading flappie  1.0.0  on cn3214 
[+] Loading singularity  on cn3214 

[user@cn3144 ~]$ cp -r /usr/local/apps/flappie/TEST_DATA/reads .

[user@cn3144 ~]$ flappie --model help
r941_native : R9.4.1 model for MinION.  Trained from native DNA library  (default)
  r941_5mC : R9.4.1 model for PromethION; 5mC aware.  Trained from native NA12878 library  
  r10c_pcr : R10C model for MinION.  Trained from PCR'd DNA library  

[user@cn3144 ~]$ flappie reads/ > basecalls.fq

[user@cn3144 ~]$ flappie --model r941_5mC reads/ > basecalls.fq

[user@cn3144 ~]$ flappie --format sam reads/ > basecalls.sam

[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 flappie
flappie --format sam reads/ > basecalls.sam

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. flappie.swarm). For example:

flappie --format sam reads1/ > basecalls1.sam
flappie --format sam reads2/ > basecalls2.sam
flappie --format sam reads3/ > basecalls3.sam

Submit this job using the swarm command.

swarm -f flappie.swarm -g 10 -t 4 --module flappie
-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 flappie Loads the flappie module for each subjob in the swarm