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titleML_analysis.o148122

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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
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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.

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