Purdue University

Commands

• add_descriptions.py
• convert_table.py
• hsp.py
• metagenome_pipeline.py
• pathway_pipeline.py
• picrust2_pipeline.py
• place_seqs.py
• print_picrust2_config.py
• run_abundance.py
• run_sepp.py
• run_tipp.py
• run_tipp_tool.py
• run_upp.py
• shuffle_predictions.py
• split_sequences.py
• sumlabels.py
• sumtrees.py

Module

You can load the modules by:

module load biocontainers
module load picrust2

Example job

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Picrust2 on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 10
#SBATCH --job-name=picrust2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers picrust2


place_seqs.py -s ../seqs.fna -o out.tre -p 10 \
          --intermediate intermediate/place_seqs

hsp.py -i 16S -t out.tre -o marker_predicted_and_nsti.tsv.gz -p 10 -n

hsp.py -i EC -t out.tre -o EC_predicted.tsv.gz -p 10

metagenome_pipeline.py -i ../table.biom -m marker_predicted_and_nsti.tsv.gz -f EC_predicted.tsv.gz -o EC_metagenome_out --strat_out 

convert_table.py EC_metagenome_out/pred_metagenome_contrib.tsv.gz \
             -c contrib_to_legacy \
             -o EC_metagenome_out/pred_metagenome_contrib.legacy.tsv.gz

pathway_pipeline.py -i EC_metagenome_out/pred_metagenome_contrib.tsv.gz \
                -o pathways_out -p 10

add_descriptions.py -i EC_metagenome_out/pred_metagenome_unstrat.tsv.gz -m EC \
                -o EC_metagenome_out/pred_metagenome_unstrat_descrip.tsv.gz


add_descriptions.py -i pathways_out/path_abun_unstrat.tsv.gz -m METACYC \
                -o pathways_out/path_abun_unstrat_descrip.tsv.gz

picrust2_pipeline.py -s chemerin_16S/seqs.fna -i chemerin_16S/table.biom \
    -o picrust2_out_pipeline -p 10