phasebook on Biowulf

phasebook is a novel approach for reconstructing the haplotypes of diploid genomes from long reads de novo, that is without the need for a reference genome.


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 -c8 --mem=4g --gres=lscratch:10
salloc: Pending job allocation 33141417
salloc: job 33141417 queued and waiting for resources
salloc: job 33141417 has been allocated resources
salloc: Granted job allocation 33141417
salloc: Waiting for resource configuration
salloc: Nodes cn0881 are ready for job
srun: error: x11: no local DISPLAY defined, skipping
error: unable to open file /tmp/slurm-spank-x11.33141417.0
slurmstepd: error: x11: unable to read DISPLAY value

[user@cn0881 ~]$ module load phasebook
[+] Loading phasebook  1.0.0  on cn0881
[+] Loading singularity  3.8.5-1  on cn0881

[user@cn0881 ~]$ cd /lscratch/$SLURM_JOB_ID

[user@cn0881 33141417]$ cp -r $PHASEBOOK_TESTDATA .

[user@cn0881 33141417]$ cd TESTDATA

[user@cn0881 TESTDATA]$ -i reads.fa -t $SLURM_CPUS_PER_TASK -p hifi -g small -x
use preset parameters...
2022-02-25 13:20:59,226 - /opt/phasebook/scripts/[line:262] - INFO: splitting input fastx file into 1 subfiles...
2022-02-25 13:20:59,361 - /opt/phasebook/scripts/[line:270] - INFO: splitting finished.
start polishing...
2022-02-25 13:22:26,529 - /opt/phasebook/scripts/[line:374] - INFO: All has been finished successfully.

2022-02-25 13:22:26,529 - /opt/phasebook/scripts/[line:375] - INFO: The final output haplotype aware contigs are here: ./contigs.fa

2022-02-25 13:22:26,529 - /opt/phasebook/scripts/[line:376] - INFO: Thank you for using phasebook!

[user@cn0881 TESTDATA]$ ls
1.split_fastx  3.cluster        5.polish          clustered_reads.list  phasebook.log  reference.fa
2.overlap      4.asm_supereads  all.supereads.fa  contigs.fa            reads.fa

[user@cn0881 TESTDATA]$ exit
salloc: Relinquishing job allocation 33141417

[user@biowulf ~]$

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. For example:

set -e
mkdir -p /data/${USER}/phasebook/${SLURM_JOB_ID}
cd /data/${USER}/phasebook/${SLURM_JOB_ID}
module load phasebook -i /path/to/reads.fa -t $SLURM_CPUS_PER_TASK -p hifi -g small -x

Submit this job using the Slurm sbatch command.

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

mkdir -p /data/${USER}/phasebook/${SLURM_JOB_ID}; cd !$; -i /path/to/reads1.fa -t $SLURM_CPUS_PER_TASK -p hifi -g small -x
mkdir -p /data/${USER}/phasebook/${SLURM_JOB_ID}; cd !$; -i /path/to/reads2.fa -t $SLURM_CPUS_PER_TASK -p hifi -g small -x
mkdir -p /data/${USER}/phasebook/${SLURM_JOB_ID}; cd !$; -i /path/to/reads3.fa -t $SLURM_CPUS_PER_TASK -p hifi -g small -x
mkdir -p /data/${USER}/phasebook/${SLURM_JOB_ID}; cd !$; -i /path/to/reads4.fa -t $SLURM_CPUS_PER_TASK -p hifi -g small -x

Submit this job using the swarm command.

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