Biowulf High Performance Computing at the NIH
sailfish on Biowulf

Sailfish quantifies the expression of a given set of transcripts using NGS reads. It is run in two stages: (1) The indexing step is run once per set of transcripts (2) The quantification step is run once for each sample.

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 --mem=8g --cpus-per-task=4 --gres=lscratch:20
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 sailfish
[user@cn3144]$ zcat $SAILFISH_TEST_DATA/gencode.vM9.transcripts.fa.gz > M9.fa
[user@cn3144]$ sailfish index -t M9.fa -o M9.idx -p $SLURM_CPUS_PER_TASK
[user@cn3144]$ cp $SAILFISH_TEST_DATA/ENCFF138LJO.fastq.gz .
[user@cn3144]$ sailfish quant -i M9.idx -r <(zcat ENCFF138LJO.fastq.gz) --libType U \
                      -o quant -p $SLURM_CPUS_PER_TASK

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

#! /bin/bash

module load sailfish/0.10.0 || exit 1
wd=$PWD
cd /lscratch/$SLURM_JOB_ID || exit 1

# get transcriptome from the example directory
# This is usually done once - not for each job. Only included
# here to show all steps involved in sailfish quantitation.
zcat $SAILFISH_TEST_DATA/gencode.vM9.transcripts.fa.gz \
    > gencode.vM9.transcripts.fa

# index the transcripts
sailfish index -t gencode.vM9.transcripts.fa -o gencode.vM9.idx \
    -p $SLURM_CPUS_PER_TASK

# quantify the transcripts
cp $SAILFISH_TEST_DATA/ENCFF138LJO.fastq.gz .
sailfish quant -i gencode.vM9.idx -l U \
    -r <(zcat ENCFF138LJO.fastq.gz) \
    -o quant -p $SLURM_CPUS_PER_TASK
cp -r quant $wd

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=8 --mem=8g --gres=lscratch:16 sailfish.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. sailfish.swarm). For example:

sailfish quant -i gencode.vM9.idx -l U -r <(zcat sample1.fq.gz) \
    -o quant_sample1 -p $SLURM_CPUS_PER_TASK
sailfish quant -i gencode.vM9.idx -l U -r <(zcat sample2.fq.gz) \
    -o quant_sample2 -p $SLURM_CPUS_PER_TASK
sailfish quant -i gencode.vM9.idx -l U -r <(zcat sample3.fq.gz) \
    -o quant_sample3 -p $SLURM_CPUS_PER_TASK

Submit this job using the swarm command.

swarm -f sailfish.swarm -g 8 -t 8 --module sailfish/0.10.0
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 sailfish Loads the sailfish module for each subjob in the swarm