A set of tools to manipulate HDF5 files of the Oxford Nanopore .fast5 file format. This module only provides access to the command line tools, not the python API.

• Tools are documented on GitHub

• Module Name: ont-fast5-api (see the modules page for more information)
• Tools are multthreaded. Please match the number of threads to the number of allocated CPUs.
• Example files in $ONT_FAST5_API_TEST_DATA

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --gres=lscratch:100 --cpus-per-task=2 --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]$ cd /lscratch/${SLURM_JOB_ID}
[user@cn3144]$ module load ont-fast5-api
[user@cn3144]$ cp -rL ${ONT_FAST5_API_TEST_DATA:-none}/* .
[user@cn3144]$ ls
Zymo-GridION-EVEN-BB-SN
[user@cn3144]$ find Zymo-GridION-EVEN-BB-SN -name '*.fast5' -printf '.' | wc -c
160000
[user@cn3144]$ du -sh Zymo-GridION-EVEN-BB-SN
11G     Zymo-GridION-EVEN-BB-SN/
[user@cn3144]$ single_to_multi_fast5 -i Zymo-GridION-EVEN-BB-SN \
                    -s multi_fast5 -n 10000 -t $SLURM_CPUS_PER_TASK --recursive -c vbz
[user@cn3144]$ ls -lh multi_fast5
total 6.6G
-rw-r--r-- 1 user group 408M May 26 10:42 batch_0.fast5
-rw-r--r-- 1 user group 425M May 26 10:49 batch_10.fast5
-rw-r--r-- 1 user group 425M May 26 10:49 batch_11.fast5
...
[user@cn3144]$ du -sh multi_fast5
6.6G    multi_fast5

## copy results back to shared storage before exiting
[user@cn3144]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf]$

Create a batch input file (e.g. ont_fast5_api.sh) like so:

#!/bin/bash
wd=$PWD
module load ont-fast5-api
cd /lscratch/${SLURM_JOB_ID} || exit 1
module load ont-fast5-api/3.3.0
cp -rL ${ONT_FAST5_API_TEST_DATA:-none}/* .
single_to_multi_fast5 -i Zymo-GridION-EVEN-BB-SN \
    -s multi_fast5 -n 10000 -t $SLURM_CPUS_PER_TASK --recursive -c vbz
mv multi_fast5 $wd

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=4 --mem=10g --gres=lscratch:25 ont_fast5_api.sh

Create a swarmfile (e.g. ont_fast5_api.swarm). For example:

multi_to_single_fast5 -i batch_0.fast5 -s batch_0 -t $SLURM_CPUS_PER_TASK
multi_to_single_fast5 -i batch_1.fast5 -s batch_1 -t $SLURM_CPUS_PER_TASK
multi_to_single_fast5 -i batch_2.fast5 -s batch_2 -t $SLURM_CPUS_PER_TASK

Submit this job using the swarm command.

swarm -f ont_fast5_api.swarm -g 10 -t 4 --module ont-fast5-api/3.3.0