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jellyfish on Biowulf

Jellyfish counts k-mers in fasta or fastq files (and sam/bam/cram starting at version 2.2.7). k-mer counts are saved in a binary format that can be queried or dumped to text based format.

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@biowulf]$ sinteractive --cpus-per-task=6 --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 jellyfish
[user@cn3144 ~]$ cp -L $JELLYFISH_TEST_DATA/* .
[user@cn3144 ~]$ ls -lh
total 445M
-rw-r--r-- 1 user group 387M Feb 24 13:59 ENCFF001NGB.bam
-rw-r--r-- 1 user group  56M Feb 24 13:59 ERR458495.fastq.gz

[user@cn3144 ~]$ # count 16-mers in fastq file (S. cerevisiae RNA-Seq data)
[user@cn3144 ~]$ # jellyfish does not natively read compressed data - uncompress on the fly
[user@cn3144 ~]$ jellyfish count -t $SLURM_CPUS_PER_TASK \
                        -m 16 -s 10M -C -o 16mer.jf <(zcat ERR458495.fastq.gz)
[user@cn3144 ~]$ ls -lh 16mer.jf
-rw-r--r-- 1 user group 51M Feb 26 07:54 16mer.jf
[user@cn3144 ~]$ jellyfish stats 16mer.jf
Unique:    3319471
Distinct:  6625582
Total:     38369851
Max_count: 2284

[user@cn3144 ~]$ jellyfish dump -L 2 -o 16mer.fa 16mer.jf
[user@cn3144 ~]$ head 16mer.fa
>259
AAAAAAAAAAAAAAAA
>3
CAATTTAGCCTTTCGC
>2
CTCATCCATGTGAAAA
>2
AAGTCAGGCACAAATC
>2
CTTCATTTTGCCACCA

[user@cn3144 ~]$ jellyfish query 16mer.jf AGCCAATTTGACTTCA
AGCCAATTTGACTTCA 45
[user@cn3144 ~]$ jellyfish histo -t $SLURM_CPUS_PER_TASK .jf > hist
[user@cn3144 ~]$ head -5 hist
1 3319471
2 1114139
3 594139
4 359875
5 238815

[user@cn3144 ~]$ # count 16mers in alinged mouse data in bam format
[user@cn3144 ~]$ jellyfish count -t $SLURM_CPUS_PER_TASK -m 16 -s 10M -C \
                        -o mouse_16mers.jf --sam ENCFF001NGB.bam

[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. jellyfish.sh), which uses the input file 'jellyfish.in'. For example:

#!/bin/bash
module load jellyfish/2.2.7 || exit 1
jellyfish count -t $SLURM_CPUS_PER_TASK -m 16 -s 10M -C \
    -o mouse_16mers.jf --sam ENCFF001NGB.bam

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=6 --mem=10g jellyfish.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. jellyfish.swarm). For example:

jellyfish count -t $SLURM_CPUS_PER_TASK -m 12 -s 10M -o sample1_12.jf --sam sample1.bam
jellyfish count -t $SLURM_CPUS_PER_TASK -m 12 -s 10M -o sample2_12.jf --sam sample2.bam
jellyfish count -t $SLURM_CPUS_PER_TASK -m 12 -s 10M -o sample3_12.jf --sam sample3.bam

Submit this job using the swarm command.

swarm -f jellyfish.swarm -g 10 -t 4 --module jellyfish/2.2.7
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 jellyfish Loads the jellyfish module for each subjob in the swarm