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This job is allocated 1 CPU cores on
n025nfs
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PBS: Submitted to normal@n029.default.domain
PBS: Working directory is /home/jcxxxxx/paup
PBS: Job identifier is 148122.jobmgr.hpc.jcu.edu.au
PBS: Job name is ML_analysis_example
------------------------------------------------------
P A U P *
Portable version 4.0b10 for Unix
Tue Mar 11 13:36:52 2014
-----------------------------NOTICE-----------------------------
This is a beta-test version. Please report any crashes,
apparent calculation errors, or other anomalous results.
There are no restrictions on publication of results obtained
with this version, but you should check the WWW site
frequently for bug announcements and/or updated versions.
See the README file on the distribution media for details.
----------------------------------------------------------------
Processing of file "~/ML_analysis.nex" begins...
Data read in DNA format
Data matrix has 8 taxa, 200 characters
Valid character-state symbols: ACGT
Missing data identified by '?'
"Equate" macros in effect:
R,r ==> {AG}
Y,y ==> {CT}
M,m ==> {AC}
K,k ==> {GT}
S,s ==> {CG}
W,w ==> {AT}
H,h ==> {ACT}
B,b ==> {CGT}
V,v ==> {ACG}
D,d ==> {AGT}
N,n ==> {ACGT}
Neighbor-joining search settings:
Ties (if encountered) will be broken systematically
Distance measure = uncorrected ("p")
(Tree is unrooted)
Tree found by neighbor-joining method stored in tree buffer
Time used = <1 sec (CPU time = 0.00 sec)
Neighbor-joining tree:
/--------------------------------------------- A
|
+-------------------------------------------- B
|
| /----------------------------------------------- C
| |
| | /------------------------------------------------- D
| | |
\---------------+ /--+ /--------------------------------------------- G
| | \----+
| | \------------------------------------------ H
\------+
| /------------------------------------------ E
\-------+
\----------------------------------------- F
Likelihood scores of tree(s) in memory:
Likelihood settings:
Number of substitution types = 2 (HKY85 variant)
Transition/transversion ratio estimated via ML
Assumed nucleotide frequencies (empirical frequencies):
A=0.35000 C=0.28813 G=0.20563 T=0.15625
Among-site rate variation:
Assumed proportion of invariable sites = none
Distribution of rates at variable sites = gamma (discrete approximation)
Shape parameter (alpha) = estimated
Number of rate categories = 4
Representation of average rate for each category = mean
These settings correspond to the HKY85+G model
Number of distinct data patterns under this model = 152
Molecular clock not enforced
Starting branch lengths obtained using Rogers-Swofford approximation method
Branch-length optimization = one-dimensional Newton-Raphson with pass
limit=20, delta=1e-06
-ln L (unconstrained) = 936.27218
Tree 1
------------------------
-ln L 1646.41982
Ti/tv:
exp. ratio 4.167819
kappa 8.796257
Shape 0.429541
Time used to compute likelihoods = 1 sec (CPU time = 0.79 sec)
Optimality criterion set to likelihood.
Heuristic search settings:
Optimality criterion = likelihood
Likelihood settings:
Number of substitution types = 2 (HKY85 variant)
Transition/transversion ratio = 4.16782 (kappa = 8.7962568)
Assumed nucleotide frequencies (empirical frequencies):
A=0.35000 C=0.28813 G=0.20563 T=0.15625
Among-site rate variation:
Assumed proportion of invariable sites = none
Distribution of rates at variable sites = gamma (discrete
approximation)
Shape parameter (alpha) = 0.429541
Number of rate categories = 4
Representation of average rate for each category = mean
These settings correspond to the HKY85+G model
Number of distinct data patterns under this model = 152
Molecular clock not enforced
Starting branch lengths obtained using Rogers-Swofford approximation
method
Trees with approximate likelihoods 5% or further from the target score
are rejected without additional iteration
Branch-length optimization = one-dimensional Newton-Raphson with pass
limit=20, delta=1e-06
-ln L (unconstrained) = 936.27218
Starting tree(s) obtained via stepwise addition
Addition sequence: random
Number of replicates = 5
Starting seed = 1412047148
Number of trees held at each step during stepwise addition = 1
Branch-swapping algorithm: tree-bisection-reconnection (TBR)
Steepest descent option not in effect
Initial 'MaxTrees' setting = 100
Branches collapsed (creating polytomies) if branch length is less than or
equal to 1e-08
'MulTrees' option in effect
Topological constraints not enforced
Trees are unrooted
Heuristic search completed
Total number of rearrangements tried = 128
Score of best tree(s) found = 1645.76314
Number of trees retained = 1
Time used = 4 sec (CPU time = 3.49 sec)
Tree-island profile:
First Last First Times
Island Size tree tree Score replicate hit
----------------------------------------------------------------------
1 1 1 1 1645.76314 1 5
Processing of file "~/ML_analysis.nex" completed.
|