FastTree
Overview
FastTree is a program to infer approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory.
Version 2.1.11 is installed on the CSF.
Restrictions on use
There are no restrictions on accessing the software on the CSF. It is released under the GNU GPL v2 license and all usage must adhere to that license.
Set up procedure
We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. Load the module file like this:
module load apps/intel-18.0/fasttree/2.1.11 # Serial and multi-core versions
Running the application
Please do not run FastTree on the login node. Jobs should be submitted to the compute nodes via batch.
Serial batch job submission
Create a batch submission script (which will load the modulefile in the jobscript), for example:
#!/bin/bash --login #SBATCH -p serial # Partition is required. Runs on Intel hardware #SBATCH -t 1-0 # Wallclock limit (days-hours). Required! # Max permitted is 7 days (7-0). # Purge your environment and load the FastTree module module purge module load apps/intel-18.0/fasttree/2.1.11 # Serial version of the app (will use 1 CPU-core) # To infer a tree for a protein alignment with the JTT+CAT model, use FastTree alignment.file > tree_file # To infer a tree for a nucleotide alignment with the GTR+CAT model, use FastTree -gtr -nt alignment_file > tree_file
Submit the jobscript using:
sbatch scriptname
where scriptname is the name of your jobscript.
Parallel batch job submission
FastTree can use multiple CPU cores in a single-compute node. The executable program is called FastTreeMP. Note that the FastTree website contains the following information about the multi-core version:
- As of version 2.1,
FastTreeMPwill not give exactly the same results asFastTreebecause the top-hits heuristics become non-deterministic (depending on which seed is reached first) and because the star topology test is turned off. However, in practice, the results are of the same quality.
Create a batch submission script (which will load the modulefile in the jobscript), for example:
#!/bin/bash --login #SBATCH -p multicore # Partition is required. Runs on an AMD Genoa hardware #SBATCH -n 4 # Number of cores, can be 2-168 #SBATCH -t 1-0 # Wallclock limit (days-hours). Required! # Max permitted is 7 days (7-0). # Purge your environment and load the FastTree module module purge module load apps/intel-18.0/fasttree/2.1.11 # Inform FastTreeMP how many cores to use. $SLURM_NTASKS is set to the number of cores above. export OMP_NUM_THREADS=$SLURM_NTASKS # To infer a tree for a protein alignment with the JTT+CAT model, use FastTreeMP alignment.file > tree_file # To infer a tree for a nucleotide alignment with the GTR+CAT model, use FastTreeMP -gtr -nt alignment_file > tree_file
Submit the jobscript using:
sbatch scriptname
where scriptname is the name of your jobscript.