Biowulf High Performance Computing at the NIH
nanopolish on Biowulf

nanopolish is a software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more

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 run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --mem 4g
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 nanopolish

[user@cn3144 ~]$ cp $NANOPOLISH_TESTDATA/* .

[user@cn3144 ~]$ tar -xf ecoli_2kb_region.tar.gz

[user@cn3144 ~]$ cd ecoli_2kb_region/

[user@cn3144 ~]$ nanopolish index -d fast5_files/ reads.fasta
[readdb] indexing fast5_files/
[readdb] num reads: 112, num reads with path to fast5: 112

[user@cn3144 ~]$ nanopolish
error: no command provided
usage: nanopolish [command] [options]
  valid commands: 
    --help
    --version
    call-methylation
    eventalign
    extract
    getmodel
    help
    index
    methyltrain
    phase-reads
    polya
    scorereads
    variants
    vcf2fasta
  for help on given command, type nanopolish command --help

[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. nanopolish.sh). For example:

#!/bin/bash
set -e
module load nanopolish
nanopolish index -d fast5_files/ reads.fasta

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=2 --mem=4g nanopolish.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. nanopolish.swarm). For example:

nanopolish index -d fast5_files1/ reads1.fasta
nanopolish index -d fast5_files2/ reads2.fasta
nanopolish index -d fast5_files3/ reads3.fasta

Submit this job using the swarm command.

swarm -f nanopolish.swarm -g 4 -t 2 --module nanopolish
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 nanopolish Loads the nanopolish module for each subjob in the swarm