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pMLST.md

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Executing pMLST

Use the below code to execute pMLST in Abel.

pMLST enables investigators to determine the ST based on WGS data.

Contact Jeevan in slack if you have any issues or further assistance (F. ex. run the tool for multiple isolates).

User Manual

https://bitbucket.org/genomicepidemiology/pmlst/src

Here is the EXAMPLE SLURM script for Abel to excute the tool.

Important rules to follow

  • Refer the user manual for all the parameters in the tool
  • Keep your data in /project/nn9305k/
  • Store your resutls also in /project/nn9305k/
  • Execute the script from your home directory
#!/bin/bash
#SBATCH --job-name=DontKillMe
#SBATCH --account=nn9305k
#SBATCH --time=01:00:00
#SBATCH --mem-per-cpu=32G

## Set up job environment:
source /cluster/bin/jobsetup

conda activate pMLST

# Location of pMLST DB
pMLST_DB="/work/projects/nn9305k/src/pMLST/pMLST_DB/pmlst_db/"

python3 /work/projects/nn9305k/src/pMLST/src/pmlst.py -i <Input File> -p $pMLST_DB -o Output

conda deactivate