Flappie on Biowulf
Basecall Fast5 reads using flip-flop basecalling (Oxford Nanopore).
Documentation
Important Notes
- Module Name: flappie (see the modules page for more information)
- Multithreaded using parallel
- Example files in /usr/local/apps/flappie/TEST_DATA/
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. flappie.sh). For example:
#!/bin/bash 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 flappie.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. 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 flappiewhere
| -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 |