Purdue University

Commands

• rsd_search
• rsd_blast
• rsd_format

Module

You can load the modules by:

module load biocontainers
module load reciprocal_smallest_distance

Example job

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Reciprocal Smallest Distance on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=reciprocal_smallest_distance
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers reciprocal_smallest_distance

rsd_search 
    -q Mycoplasma_genitalium.aa \
    --subject-genome=Mycobacterium_leprae.aa \
    -o Mycoplasma_genitalium.aa_Mycobacterium_leprae.aa_0.8_1e-5.orthologs.txt

rsd_format -g Mycoplasma_genitalium.aa

rsd_blast -v -q Mycoplasma_genitalium.aa \
    --subject-genome=Mycobacterium_leprae.aa \
    --forward-hits q_s.hits --reverse-hits s_q.hits \
    --no-format --evalue 0.1