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
- Bash: GNU bash, version 4.2.46(1)-release (x86_64-redhat-linux-gnu)
- Snakemake: 7.20.0
- Singularity: 3.9.2
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
Copyright (c) 2023 Koki Tsuyuzaki Artistic License 2.0.
- Koki Tsuyuzaki
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