Pipeline to extract proteins and pathway analysis

Ensure:

• Assembled Genomes (complete) are in the genomes/ directory and are in the format: {sample}.fna.gz
• Singularity image files in the bin directory: sepathway.sif prokka.sif and R_environment.sif - (see notes on how to obtain these)
• Ensure you have a working version of python/snakemake and singularity (type: source dependencies for UEA cluster)

Then launch the pipeline: ./1_launch_snake.sh

Pathway output will be generated in the interproscan/ directory

Collating Pathway Results:

You can then collate all results for each pathway using an R container with:

cd bin/ && singularity exec R_environment.sif Rscript collate_pathways.R; cd ../

You may receive the message Fatal: Kernel too old - copy and run the above code on another machine

Downloading Genomes

Kai Blin's NCBI-genome-downloader is also installed in the prokka.sif container making downloading genomes easy.

Example:

• Launch the singularity singularity shell bin/prokka.sif
• Download the all complete bacterial genomes for the genus Fusobacterium to the genomes/ folder ncbi-genome-download --format fasta --assembly-level complete --genus Fusobacterium -o genomes/
• Move all genomes to the genomes folder mv genomes/refseq/*/*/*.gz genomes/; rm -rf genomes/refseq/

More options can be observed with ncbi-genome-download --help

you can exit the singularity any time with exit

If something goes wrong and you need to cancel the pipeline. Before re-launching, ensure the directory is unlocked: snakemake --snakefile run_ipsn.snake --unlock

Notes:

Obtaining singularity image files:

All def files used to create singularity images are in dmp/

Downloading from sylabs (ensure singularity is installed):

• navigate to bin: cd bin/
• download prokka singularity: singularity pull -UF library://a_gihawi/prokka/prokka.sif:latest
• download R singularity: singularity pull -UF library://a_gihawi/default/tidyverse_environment:latest
• download interproscan singularity: visit https://ueamobilecho.uea.ac.uk/node_share_links/10?token=1dcb5159-dbe6-4511-bc42-160881caf6b8 (link active until 16th Dec 2020)