Biowulf High Performance Computing at the NIH
kallisto on Biowulf

kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.

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
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 ~]$ cp -r /fdb/kallisto/* . 
[user@cn3144 ~]$ kallisto index -i transcripts.kidx transcripts.fasta.gz

[build] loading fasta file transcripts.fasta.gz
[build] k-mer length: 31
[build] counting k-mers ... done.
[build] building target de Bruijn graph ...  done 
[build] creating equivalence classes ...  done
[build] target de Bruijn graph has 27 contigs and contains 22118 k-mers 

[user@cn3144 ~]$ kallisto quant \
 -i transcripts.kidx \
 -b 30 \
 -o kallisto_out \
 --genomebam \
 --gtf transcripts.gtf.gz \
 --chromosomes chrom.txt \
 reads_1.fastq.gz reads_2.fastq.gz

[quant] fragment length distribution will be estimated from the data
[index] k-mer length: 31
[index] number of targets: 14
[index] number of k-mers: 22,118
[index] number of equivalence classes: 20
Warning: 13 transcripts were defined in GTF file, but not in the index
[quant] running in paired-end mode
[quant] will process pair 1: reads_1.fastq.gz
                             reads_2.fastq.gz
[quant] finding pseudoalignments for the reads ... done
[quant] processed 10,000 reads, 9,413 reads pseudoaligned
[quant] estimated average fragment length: 178.02
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 52 rounds
[bstrp] running EM for the bootstrap: 30
[  bam] writing pseudoalignments to BAM format .. done
[  bam] sorting BAM files .. done
[  bam] indexing BAM file .. done

[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. kallisto.sh). For example:

#!/bin/sh
set -e
module load kallisto

kallisto index -i transcripts.kidx transcripts.fasta.gz

kallisto quant \
 -i transcripts.kidx \
 -b 30 \
 -o kallisto_out \
 --genomebam \
 --gtf transcripts.gtf.gz \
 --chromosomes chrom.txt \
 reads_1.fastq.gz reads_2.fastq.gz

Submit this job using the Slurm sbatch command.

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

kallisto quant -i transcripts.kidx -b 30 -o kallisto/sample-01 --genomebam --gtf transcripts.gtf.gz --chromosomes chrom.txt sample01/reads_{1,2}.fastq.gz
kallisto quant -i transcripts.kidx -b 30 -o kallisto/sample-02 --genomebam --gtf transcripts.gtf.gz --chromosomes chrom.txt sample02/reads_{1,2}.fastq.gz
kallisto quant -i transcripts.kidx -b 30 -o kallisto/sample-03 --genomebam --gtf transcripts.gtf.gz --chromosomes chrom.txt sample03/reads_{1,2}.fastq.gz
kallisto quant -i transcripts.kidx -b 30 -o kallisto/sample-04 --genomebam --gtf transcripts.gtf.gz --chromosomes chrom.txt sample04/reads_{1,2}.fastq.gz

Submit this job using the swarm command.

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