hifiasm on Biowulf

Hifiasm is a fast haplotype-resolved de novo assembler initially designed for PacBio HiFi reads. Its latest release supports telomere-to-telomere assembly by utilizing ultralong Oxford Nanopore reads. It can produce better haplotype-resolved assemblies when given parental short reads or Hi-C data.

References:

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 --cpus-per-task 32
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 hifiasm

[user@cn3144 ~]$ hifiasm -t $SLURM_CPUS_PER_TASK -o NA24385_180901_0113427.asm /fdb/app_testdata/fastq/Homo_sapiens/HG002_NA24385_son-PacBio_CCS_15kb/m54238_180901_011437.Q20.fastq.gz

[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. hifiasm.sh). For example:

#!/bin/bash
set -e
module load hifiasm
hifiasm -t $SLURM_CPUS_PER_TASK -o NA24385_180901_0113427.asm /fdb/app_testdata/fastq/Homo_sapiens/HG002_NA24385_son-PacBio_CCS_15kb/m54238_180901_011437.Q20.fastq.gz

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=# [--mem=#] hifiasm.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. hifiasm.swarm). For example:

hifiasm -t $SLURM_CPUS_PER_TASK -o sample1.asm sample1.fq.gz
hifiasm -t $SLURM_CPUS_PER_TASK -o sample2.asm sample2.fq.gz
hifiasm -t $SLURM_CPUS_PER_TASK -o sample3.asm sample3.fq.gz
hifiasm -t $SLURM_CPUS_PER_TASK -o sample4.asm sample4.fq.gz

Submit this job using the swarm command.

swarm -f hifiasm.swarm [-g #] -t # --module hifiasm
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 hifiasm Loads the hifiasm module for each subjob in the swarm