Biowulf High Performance Computing at the NIH
QIIME2 on Biowulf

QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. QIIME 2 enables researchers to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical results.

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
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 QIIME
[user@cn3144 ~]$ cp -R $QIIME_EXAMPLES/qiime2-moving-pictures-tutorial .
[user@cn3144 ~]$ cd qiime2-moving-pictures-tutorial .
[user@cn3144 ~]$ qiime tools import --type EMPSingleEndSequences \
  --input-path emp-single-end-sequences \
  --output-path emp-single-end-sequences.qza
[user@cn3144 ~]$ qiime demux emp-single \
  --i-seqs emp-single-end-sequences.qza \
  --m-barcodes-file sample-metadata.tsv \
  --m-barcodes-category BarcodeSequence \
  --o-per-sample-sequences demux.qza
[user@cn3144 ~]$ qiime demux summarize \
  --i-data demux.qza \
  --o-visualization demux.qzv
[user@cn3144 ~]$ qiime dada2 denoise-single \
  --i-demultiplexed-seqs demux.qza \
  --p-trim-left 0 \
  --p-trunc-len 120 \
  --o-representative-sequences rep-seqs-dada2.qza \
  --o-table table-dada2.qza

[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. QIIME.sh). For example:

#!/bin/bash
module load QIIME
cp -R $QIIME_EXAMPLES/qiime2-atacama-tutorial .
cd qiime2-atacama-tutorial

qiime tools import \
  --type EMPPairedEndSequences \
  --input-path emp-paired-end-sequences \
  --output-path emp-paired-end-sequences.qza

qiime demux emp-paired \
  --verbose \
  --m-barcodes-file sample-metadata.tsv \
  --m-barcodes-category BarcodeSequence \
  --i-seqs emp-paired-end-sequences.qza \
  --o-per-sample-sequences demux \
 --p-rev-comp-mapping-barcodes

qiime demux summarize \
  --verbose \
  --i-data demux.qza \
  --o-visualization demux.qzv

qiime dada2 denoise-paired \
  --verbose \
  --p-n-threads $SLURM_CPUS_PER_TASK \
  --i-demultiplexed-seqs demux.qza \
  --o-table table \
  --o-representative-sequences rep-seqs \
  --p-trim-left-f 13 \
  --p-trim-left-r 13 \
  --p-trunc-len-f 150 \
  --p-trunc-len-r 150

qiime feature-table summarize \
  --verbose \
  --i-table table.qza \
  --o-visualization table.qzv \
  --m-sample-metadata-file sample-metadata.tsv

qiime feature-table tabulate-seqs \
  --verbose \
  --i-data rep-seqs.qza \
  --o-visualization rep-seqs.qzv

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=8 --mem=20g --gres:lscratch:20 --time=4:00:00 QIIME.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit set of independent commands requiring identical resources.

Create a swarmfile (e.g. QIIME.swarm). For example:

qiime dada2 denoise-single \
  --p-n-threads $SLURM_CPUS_PER_TASK \
  --p-trim-left 13 \
  --p-trunc-len 150 \
  --i-demultiplexed-seqs fmt-tutorial-demux-1.qza \
  --o-representative-sequences rep-seqs-1.qza \
  --o-table table-1.qza
qiime dada2 denoise-single \
  --p-n-threads $SLURM_CPUS_PER_TASK \
  --p-trim-left 13 \
  --p-trunc-len 150 \
  --i-demultiplexed-seqs fmt-tutorial-demux-2.qza \
  --o-representative-sequences rep-seqs-2.qza \
  --o-table table-2.qza
qiime dada2 denoise-single \
  --p-n-threads $SLURM_CPUS_PER_TASK \
  --p-trim-left 13 \
  --p-trunc-len 150 \
  --i-demultiplexed-seqs fmt-tutorial-demux-3.qza \
  --o-representative-sequences rep-seqs-3.qza \
  --o-table table-3.qza
qiime dada2 denoise-single \
  --p-n-threads $SLURM_CPUS_PER_TASK \
  --p-trim-left 13 \
  --p-trunc-len 150 \
  --i-demultiplexed-seqs fmt-tutorial-demux-4.qza \
  --o-representative-sequences rep-seqs-4.qza \
  --o-table table-4.qza

Submit this job using the swarm command.

swarm -f QIIME.swarm -g 10 -t 8 --module QIIME
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 QIIME Loads the QIIME module for each subjob in the swarm