Add P. aereuginosa as a query genome to the previous Pseudomonas genomes project. It will be classified relative to the reference genomes in the project.
#!/bin/bash --login
########## SBATCH Lines for Resource Request ##########
#SBATCH --time=02:00:00 # limit of wall clock time - how long the job will run (same as -t)
#SBATCH --nodes=1 # number of different nodes - could be an exact number or a range of nodes (same as -N)
#SBATCH --ntasks=1 # number of tasks - how many tasks (nodes) that you require (same as -n)
#SBATCH --cpus-per-task=12 # number of CPUs (or cores) per task (same as -c)
#SBATCH --mem-per-cpu=2G # memory required per allocated CPU (or core) - amount of memory (in bytes)
#SBATCH --job-name pseudo # you can give your job a name for easier identification (same as -J)
########## Command Lines to Run ##########
mkdir ~/miga_batch
cd ~/miga_batch
singularity shell ~/MiGA << EOF
miga add -P . -D P_aeruginosa -t genome --query -i assembly ~/miga_genomes/pseudo/P_aeruginosa.fna
time miga daemon start -t -P . --shutdown-when-done
exit
EOF
After the job finishes, entering the following:
less ~/miga_batch/data/09.distances/P_aeruginosa.intax.txt
returns:
Closest relative: P_alcaligenes with AAI: 67.73878174613809.
Rank Taxonomy P-value Signif.
---- -------- ------- -------
root ? 0.0 ****
domain ? 0.0137151106833494 ***
phylum ? 0.0137151106833494 ***
class ? 0.0137151106833494 ***
order ? 0.0137151106833494 ***
family ? 0.0955245428296439 **
genus ? 0.202358036573628 *
species ? 0.53055822906641
subspecies ? 0.702598652550529
dataset ? 0.705726660250241
Significance at p-value below: *0.5, **0.1, ***0.05, ****0.01.
The interpretation is that the query genome P. aeruginosa's closeset match among the reference genomes already in the project is P. alcalegenes; the two belong to the same order and possibly to the same genus.
Times reported for this project were (real = wall time):