PICRUSt (pronounced “pie crust”) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.

References:

• Douglas, Gavin M., et al. "PICRUSt2 for prediction of metagenome functions." Nature Biotechnology 38.6 (2020): 685-688.

• PICRUSt Main Site
• PICRUSt on GitHub

• Module Name: picrust (see the modules page for more information)
• Remember to set the processes option/argument pair like so: -p $SLURM_CPUS_PER_TASK
• Environment variables set
  • PICRUST_HOME
• Example files in $PICRUST_HOME/tutorials
• Recent versions of PICRUSt on Biowulf are technically PICRUSt2

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf ~]$ sinteractive -c8 --mem=16g --gres=lscratch:10
salloc: Pending job allocation 30152043
salloc: job 30152043 queued and waiting for resources
salloc: job 30152043 has been allocated resources
salloc: Granted job allocation 30152043
salloc: Waiting for resource configuration
salloc: Nodes cn0890 are ready for job
srun: error: x11: no local DISPLAY defined, skipping
error: unable to open file /tmp/slurm-spank-x11.30152043.0
slurmstepd: error: x11: unable to read DISPLAY value

[user@cn0890 ~]$ cd /lscratch/$SLURM_JOB_ID

[user@cn0890 30152043]$ module load picrust/2.4.2
[+] Loading picrust  2.4.2  on cn0890
[+] Loading singularity  3.8.5-1  on cn0890

[user@cn0890 30152043]$ cp $PICRUST_HOME/tutorials/chemerin_16S.zip .

[user@cn0890 30152043]$ unzip chemerin_16S.zip
Archive:  chemerin_16S.zip
  inflating: chemerin_16S/metadata.tsv
  inflating: chemerin_16S/seqs.fna
  inflating: chemerin_16S/table.biom

[user@cn0890 30152043]$ picrust2_pipeline.py -s chemerin_16S/seqs.fna -i chemerin_16S/table.biom -o \
     picrust2_out_pipeline -p $SLURM_CPUS_PER_TASK




All ASVs were below the max NSTI cut-off of 2.0 and so all were retained for downstream analyses.

All ASVs were below the max NSTI cut-off of 2.0 and so all were retained for downstream analyses.



[user@cn0890 30152043]$ ls picrust2_out_pipeline/
EC_metagenome_out    intermediate       KO_predicted.tsv.gz               out.tre
EC_predicted.tsv.gz  KO_metagenome_out  marker_predicted_and_nsti.tsv.gz  pathways_out

[user@cn0890 30152043]$ exit
exit
salloc: Relinquishing job allocation 30152043

[user@biowulf ~]$

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

#!/bin/bash
set -e
module load picrust
picrust2_pipeline.py -s seqs.fna -i table.biom -o output -p $SLURM_CPUS_PER_TASK

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] picrust.sh

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

picrust2_pipeline.py -s seqs1.fna -i table1.biom -o output -p $SLURM_CPUS_PER_TASK
picrust2_pipeline.py -s seqs2.fna -i table2.biom -o output -p $SLURM_CPUS_PER_TASK
picrust2_pipeline.py -s seqs3.fna -i table3.biom -o output -p $SLURM_CPUS_PER_TASK
picrust2_pipeline.py -s seqs4.fna -i table4.biom -o output -p $SLURM_CPUS_PER_TASK

Submit this job using the swarm command.

swarm -f picrust.swarm [-g #] [-t #] --module picrust