HPC_DiamondX

Pipeline for parrallel submission of BLASTX diamond jobs (SLURM scheduler)

Installation and prerequisites

Installation of Diamond v2.0.14 is required. On CSC Puhti, the tool is pre-installed in the module biokit).

If the system doesn't have Diamond install, a conda environment can be created as followed:

conda create -n diamond_env
conda activate diamond_env
conda install -c bioconda diamond
conda deactivate

Next, clone this repository on your working folder:

git clone https://github.com/aponsero/HPC_DiamondX.git

Creating a custom Diamond database

Diamond provides an easy and fast way to create a custom protein database of reference.

1. Upload to the working directory a protein fasta file.

Beware, make sure to remove any extra spaces or trailing spaces from the file. Extra spaces or incorrectly formated fasta file will stop the database building job

2. Request an interactive node to run the command. In Puhti CSC:

sinteractive

3. Run the database building command:

module load biokit

diamond makedb --in [my_references.faa] -d [NAME_DATABASE] -p 4

If the command worked, you should now have a NAME_DATABASE.dmnd file created.

CSC has some database pre-indexed, see https://docs.csc.fi/apps/diamond/ for more informations

Running Diamond

1. Edit the config.sh file as followed:

Inputs and output files:

[IN_DIR]= Input directory with the fasta samples to process
[OUT_DIR]= Output directory where to save the diamond output

Diamond configurations:

[DB]= custom or non-custom diamond database to use
[MAX_TAR]= max targets match per query

2. Modify the list_to_process.txt file.

This imput file needs to contain the list of files you want to process. Each file on one line.

3. Submit job

Open the 1_Diamond.sh file and add the correct project ID for billing. Submit the jobs as:

./Submit_Diamond.sh

To do

filtering step to calculate relative abundance of protein hits

aponsero / HPC_DiamondX