Sepp¶
Introduction¶
Sepp
stands for SATé-Enabled Phylogenetic Placement and addresses the problem of phylogenetic placement for meta-genomic short reads.
For more information, please check its website: https://biocontainers.pro/tools/sepp and its home page on Github.
Versions¶
4.5.1
Commands¶
run_sepp.py
run_upp.py
split_sequences.py
sumlabels.py
sumtrees.py
Module¶
You can load the modules by:
module load biocontainers
module load sepp
Example job¶
Warning
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 Sepp on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=sepp
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers sepp
run_sepp.py -t mock/rpsS/sate.tre \
-r mock/rpsS/sate.tre.RAxML_info \
-a mock/rpsS/sate.fasta \
-f mock/rpsS/rpsS.even.fas \
-o rpsS.out.default