maharank-workflow

Snakemake workflow to generate the reference files for MahaRank

This workflow consists of nine workflows as follows:

• workflow/identifier.smk: ID retreival

• workflow/download.smk: Data download

• workflow/divide_plasmid_host.smk: Dividing plasmid/host amino acids sequences

• workflow/stats.smk: Some statistics such as length and GC contents of amino acids sequences

• workflow/rho.smk: k-mer

• workflow/reference.smk: Reference files (reference.tar.gz, reference_slim.tar.gz)

• workflow/distance.smk: Distance calculation

• workflow/roc.smk: ROC/AUC analysis

• workflow/plot.smk: Plot of ROC/AUC analysis

Requirements

• Bash: GNU bash, version 4.2.46(1)-release (x86_64-redhat-linux-gnu)
• Snakemake: 7.20.0
• Singularity: 3.9.2

Summary

How to reproduce this workflow

In local machine:

snakemake -s workflow/identifier.smk -j 4 --use-singularity
snakemake -s workflow/download.smk -j 4 --use-singularity
snakemake -s workflow/divide_plasmid_host.smk -j 4 --use-singularity
snakemake -s workflow/stats.smk -j 4 --use-singularity
snakemake -s workflow/rho.smk -j 4 --use-singularity
snakemake -s workflow/reference.smk -j 4 --use-singularity
snakemake -s workflow/distance.smk -j 4 --use-singularity
snakemake -s workflow/roc.smk -j 1 --use-singularity
snakemake -s workflow/plot.smk -j 1 --use-singularity

In parallel environment (GridEngine):

snakemake -s workflow/identifier.smk -j 32 --cluster "qsub -l nc=4 -p -50 -r yes -q node.q" --cluster-cancel qdel --latency-wait 2000 --use-singularity
snakemake -s workflow/download.smk -j 32 --cluster "qsub -l nc=4 -p -50 -r yes -q node.q" --cluster-cancel qdel --latency-wait 2000 --use-singularity
snakemake -s workflow/divide_plasmid_host.smk -j 32 --cluster "qsub -l nc=4 -p -50 -r yes -q node.q" --cluster-cancel qdel --latency-wait 2000 --use-singularity
snakemake -s workflow/stats.smk -j 32 --cluster "qsub -l nc=4 -p -50 -r yes -q node.q" --cluster-cancel qdel --latency-wait 2000 --use-singularity
snakemake -s workflow/rho.smk -j 32 --cluster "qsub -l nc=4 -p -50 -r yes -q node.q" --cluster-cancel qdel --latency-wait 2000 --use-singularity
snakemake -s workflow/reference.smk -j 32 --cluster "qsub -l nc=4 -p -50 -r yes -q node.q" --cluster-cancel qdel --latency-wait 2000 --use-singularity
snakemake -s workflow/distance.smk -j 32 --cluster "qsub -l nc=4 -p -50 -r yes -q node.q" --cluster-cancel qdel --latency-wait 2000 --use-singularity
snakemake -s workflow/roc.smk -j 1 --cluster "qsub -l nc=4 -p -50 -r yes -q large.q" --latency-wait 2000 --use-singularity
snakemake -s workflow/plot.smk -j 1 --cluster "qsub -l nc=4 -p -50 -r yes -q node.q" --cluster-cancel qdel --latency-wait 2000 --use-singularity

In parallel environment (Slurm):

snakemake -s workflow/identifier.smk -j 32 --cluster sbatch --cluster-cancel scancel --latency-wait 2000 --use-singularity
snakemake -s workflow/download.smk -j 32 --cluster sbatch --cluster-cancel scancel --latency-wait 2000 --use-singularity
snakemake -s workflow/divide_plasmid_host.smk -j 32 --cluster sbatch --cluster-cancel scancel --latency-wait 2000 --use-singularity
snakemake -s workflow/stats.smk -j 32 --cluster sbatch --cluster-cancel scancel --latency-wait 2000 --use-singularity
snakemake -s workflow/rho.smk -j 32 --cluster sbatch --cluster-cancel scancel --latency-wait 2000 --use-singularity
snakemake -s workflow/reference.smk -j 32 --cluster sbatch --cluster-cancel scancel --latency-wait 2000 --use-singularity
snakemake -s workflow/distance.smk -j 32 --cluster sbatch --cluster-cancel scancel --latency-wait 2000 --use-singularity
snakemake -s workflow/roc.smk -j 1 --cluster sbatch --cluster-cancel scancel --latency-wait 2000 --use-singularity
snakemake -s workflow/plot.smk -j 1 --cluster sbatch --cluster-cancel scancel --latency-wait 2000 --use-singularity

License

Copyright (c) 2023 Koki Tsuyuzaki Artistic License 2.0.

Authors

• Koki Tsuyuzaki