A clade project is run using closely related genomes, e.g., genomes of the same species. For this example we use 10 Dehalococoides genomes downloaded from NCBI.
#!/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 MiGA_clade # you can give your job a name for easier identification (same as -J)
########## Command Lines to Run ##########
rm -rf ~/miga_clade
mkdir ~/miga_clade
cd ~/miga_clade
singularity shell ~/MiGA << EOF
miga new -P ~/miga_clade -t clade
miga add -P . -t genome -i assembly ~/dehalo_genomes/*.fna -m run_mytaxa_scan=false,run_distances=true
time miga daemon start -t -P . --shutdown-when-done
exit
EOF
Entering
less ~/miga_clade/data/10.clades/02.ani/miga-project.class.tsv
presents a table with the genomes in the first column and their clade assignment in the second column:
GCF_000011905_1_ASM1190v1_genomic 1
GCF_000341655_1_ASM34165v1_genomic 2
GCF_000341695_1_ASM34169v1_genomic 2
GCF_000830925_1_ASM83092v1_genomic 3
GCF_001010485_1_ASM101048v1_genomic 3
GCF_001547795_1_ASM154779v1_genomic 2
GCF_001610775_1_ASM161077v1_genomic 2
GCF_001889305_1_ASM188930v1_genomic 3
GCF_002007845_1_ASM200784v1_genomic 2
GCF_004684285_1_ASM468428v1_genomic 2
A tree of the genomes in Newick format can be obtained from ~/miga_clade/data/10.clades/02.ani/miga-project.class.nwk
Times reported for this project were (real = wall time):
| _ | Time |
|---|---|
| real | 20m45.196s |
| user | 95m26.944s |
| sys | 1m03.999s |