TreeTime provides routines for ancestral sequence reconstruction and inference of molecular-clock phylogenies, i.e., a tree where all branches are scaled such that the positions of terminal nodes correspond to their sampling times and internal nodes are placed at the most likely time of divergence.
Allocate an interactive session and run the program.
Sample session (user input in bold):
[user@biowulf]$ sinteractive --gres=lscratch:10
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job
[user@cn3144 ~]$ module load treetime
[+] Loading singularity 3.8.5-1 on cn0847
[+] Loading treetime 0.9.0 ...
[user@cn3144 ~]$ cd /lscratch/$SLURM_JOB_ID
[user@cn3144 ~]$ cp -r $TREETIME_TEST_DATA/data/ebola/*
[user@cn3144 ~]$ treetime --aln ebola.fasta \
--tree ebola.nwk \
--dates ebola.metadata.csv
Attempting to parse dates...
Using column 'name' as name. This needs match the taxon names in the tree!!
Using column 'date' as date.
0.00 -TreeAnc: set-up
5.01 -WARNING: character U is unknown. Treating it as missing information
5.04 WARNING: Previous versions of TreeTime (<0.7.0) RECONSTRUCTED sequences of
tips at positions with AMBIGUOUS bases. This resulted in unexpected
behavior is some cases and is no longer done by default. If you want to
replace those ambiguous sites with their most likely state, rerun with
`reconstruct_tip_states=True` or `--reconstruct-tip-states`.
18.95 TreeTime.reroot: with method or node: least-squares
18.95 TreeTime.reroot: rerooting will ignore covariance and shared ancestry.
19.59 TreeTime.reroot: with method or node: least-squares
19.59 TreeTime.reroot: rerooting will ignore covariance and shared ancestry.
28.47 ###TreeTime.run: INITIAL ROUND
42.43 TreeTime.reroot: with method or node: least-squares
42.44 TreeTime.reroot: rerooting will ignore covariance and shared ancestry.
43.00 ###TreeTime.run: rerunning timetree after rerooting
60.59 ###TreeTime.run: ITERATION 1 out of 2 iterations
88.84 ###TreeTime.run: ITERATION 2 out of 2 iterations
117.79 TreeTime: the following tips have been marked as outliers. Their date
constraints were not used. Please remove them from the tree. Their dates
have been reset:
117.79 EM_NG_2016_029366, input date: 2016.21, apparent date: 2015.17
117.79 EM_NG_2016_029364, input date: 2016.21, apparent date: 2015.17
117.79 EM_NG_2016_029417, input date: 2016.22, apparent date: 2015.17
117.79 NZG_0381, input date: 2016.23, apparent date: 2015.17
117.79 NZG_0393, input date: 2016.24, apparent date: 2015.24
117.79 NZG_0422, input date: 2016.25, apparent date: 2015.24
117.79 NZG_0358, input date: 2016.22, apparent date: 2015.24
117.79 J0169, input date: 2014.85, apparent date: 2015.42
117.79 2607_C2_12916_EMLH, input date: 2015.32, apparent date: 2016.02
117.79 2607_C2_12855_EMLH, input date: 2015.28, apparent date: 2016.02
117.79 1708_C1_13031_EMLH, input date: 2015.38, apparent date: 2016.15
117.79 1507_C1_18660_EMLH, input date: 2015.52, apparent date: 2016.56
117.79 1507_C1_18650_EMLH, input date: 2015.52, apparent date: 2016.49
117.79 1507_C1_13268_EMLH, input date: 2015.47, apparent date: 2016.56
117.79 1507_C1_18647_EMLH, input date: 2015.52, apparent date: 2016.42
117.79 0208_C1_MK10173, input date: 2015.58, apparent date: 2016.49
117.79 1507_C1_18706_EMLH, input date: 2015.53, apparent date: 2016.49
117.79 2208_C2_18659R_EMLH, input date: 2015.52, apparent date: 2016.62
117.79 2208_C2_18642R_EMLH, input date: 2015.51, apparent date: 2016.56
117.79 1507_C1_18636_EMLH, input date: 2015.51, apparent date: 2016.62
117.79 2208_C2_18687R_EMLH, input date: 2015.53, apparent date: 2016.62
Inferred sequence evolution model (saved as sequence_evolution_model.txt):
Substitution rate (mu): 1.0
Equilibrium frequencies (pi_i):
A: 0.3139
C: 0.2144
G: 0.1979
T: 0.2638
-: 0.01
Symmetrized rates from j->i (W_ij):
A C G T -
A 0 0.3826 2.5275 0.2294 6.7955
C 0.3826 0 0.1691 3.5602 12.1805
G 2.5275 0.1691 0 0.3724 5.295
T 0.2294 3.5602 0.3724 0 27.7433
- 6.7955 12.1805 5.295 27.7433 0
Actual rates from j->i (Q_ij):
A C G T -
A 0 0.1201 0.7933 0.072 2.133
C 0.0821 0 0.0363 0.7634 2.612
G 0.5002 0.0335 0 0.0737 1.0478
T 0.0605 0.9393 0.0982 0 7.3198
- 0.0676 0.1212 0.0527 0.2761 0
Inferred sequence evolution model (saved as molecular_clock.txt):
Root-Tip-Regression:
--rate: 7.895e-04
--r^2: 0.81
--- saved tree as
timetree.pdf
--- root-to-tip plot saved to
root_to_tip_regression.pdf
--- alignment including ancestral nodes saved as
ancestral_sequences.fasta
--- saved divergence times in
dates.tsv
--- tree saved in nexus format as
timetree.nexus
--- divergence tree saved in nexus format as
divergence_tree.nexus
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$
Create a batch input file (e.g. treetime.sh). For example:
#!/bin/bash
set -e
module load treetime
treetime --aln aln.fasta \
--tree tree.nwk \
--dates dates.csv
Submit this job using the Slurm sbatch command.
sbatch [--mem=#] treetime.sh
Create a swarmfile (e.g. treetime.swarm). For example:
treetime --aln aln.fasta --tree tree1.nwk --dates dates.csv treetime --aln aln.fasta --tree tree2.nwk --dates dates.csv treetime --aln aln.fasta --tree tree3.nwk --dates dates.csv treetime --aln aln.fasta --tree tree4.nwk --dates dates.csv
Submit this job using the swarm command.
swarm -f treetime.swarm [-g #] --module treetimewhere
| -g # | Number of Gigabytes of memory required for each process (1 line in the swarm command file) |
| --module treetime | Loads the treetime module for each subjob in the swarm |