Running GARLI Version 2.01.1067 (18 May 2012)
->Single processor version for 64-bit OS<-
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 This is GARLI 2.0, the first "official" release including 
          partitioned models.  It is a merging of
   official release 1.0 and beta version GARLI-PART 0.97
  Briefly, it includes models for nucleotides, amino acids,
 codons, and morphology-like characters, any of which can be 
  mixed together and applied to different subsets of data.

    General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
      see this page for details on partitioned usage:
  http://www.nescent.org/wg/garli/Partition_testing_version
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg/garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
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Compiled Jul  2 2012 15:52:18 using GNU gcc compiler version 4.2.1
Using NCL version 2.1.17

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Reading config file garli.conf
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READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	dnaPlusGapCoding.nex ...
Reading TAXA block... successful
Reading CHARACTERS block... found dna data... successful
Reading CHARACTERS block... found standard data... successful
Reading SETS block... successful

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PARTITIONING OF DATA AND MODELS

CHECK: DIFFERENT MODEL TYPES AND MODEL PARAMETERS APPLY
	TO EACH DATA SUBSET (no linkage)

GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1GapsAsMissing")
	CHARPARTITION subset #1 ("1")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Summary of data:
	  64 sequences.
	  687 constant characters.
	  338 parsimony-informative characters.
	  44 uninformative variable characters.
	  2 characters were completely missing or ambiguous (removed).
	  1069 total characters (1071 before removing empty columns).
	  787 unique patterns in compressed data matrix.
	Pattern processing required < 1 second

GARLI data subset 2
	CHARACTERS block #1 ("Untitled DATA Block 1GapsAsMissing")
	CHARPARTITION subset #2 ("2")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Summary of data:
	  64 sequences.
	  687 constant characters.
	  341 parsimony-informative characters.
	  39 uninformative variable characters.
	  3 characters were completely missing or ambiguous (removed).
	  1067 total characters (1070 before removing empty columns).
	  800 unique patterns in compressed data matrix.
	Pattern processing required < 1 second

GARLI data subset 3
	CHARACTERS block #1 ("Untitled DATA Block 1GapsAsMissing")
	CHARPARTITION subset #3 ("3")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Summary of data:
	  64 sequences.
	  666 constant characters.
	  346 parsimony-informative characters.
	  54 uninformative variable characters.
	  4 characters were completely missing or ambiguous (removed).
	  1066 total characters (1070 before removing empty columns).
	  799 unique patterns in compressed data matrix.
	Pattern processing required < 1 second

GARLI data subset 4
	CHARACTERS block #2 ("Untitled DATA Block 1GapsAsBinary")
	Data read as Standard k-state data, variable only,
	modeled as Standard k-state data, variable only
	NOTE: entirely missing characters removed from matrix:  736 792 1244 1644 1645 1993-1995 2195
	Subset of data with 2 states:
	  chars 1-735 737-791 793-1243 1245-1643 1646-1992 1996-2194 2196-2723
	Summary of data:
	  64 sequences.
	  0 constant characters.
	  1530 parsimony-informative characters.
	  1184 uninformative variable characters.
	  2714 total characters.
	  768 unique patterns in compressed data matrix.
	Pattern processing required < 1 second


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NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 196 MB
  good			approx 195 MB to 126 MB
  low			approx 125 MB to 52 MB
  very low		approx 52 MB to 40 MB
the minimum required availablememory is 40 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 293.0 MB of memory
**Your memory level is: great (you don't need to change anything)**

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Found outgroup specification:  1

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STARTING RUN

>>>Search rep 1 (of 2)<<<
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.3211 0.2053 0.1693 0.3043 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.5000
    with an invariant (invariable) site category, proportion estimated
      0.1607
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.1607
      0.0334	0.2098
      0.2519	0.2098
      0.8203	0.2098
      2.8944	0.2098

Model 2
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.3490 0.2203 0.1345 0.2962 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.5000
    with an invariant (invariable) site category, proportion estimated
      0.1610
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.1610
      0.0334	0.2098
      0.2519	0.2098
      0.8203	0.2098
      2.8944	0.2098

Model 3
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.3516 0.2003 0.1525 0.2956 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.5000
    with an invariant (invariable) site category, proportion estimated
      0.1562
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.1562
      0.0334	0.2110
      0.2519	0.2110
      0.8203	0.2110
      2.8944	0.2110

Model 4
  Number of states = 2 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    1.00  1.00  1.00  1.00
Starting with seed=558821

creating random starting tree...
Initial ln Likelihood: -130238.3436
optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs, subset rates...
pass 1:+23019.697 (branch=20315.82 scale=171.66 alpha=920.61 freqs=166.50 rel rates=112.55 pinv=545.55 subset rates=787.00)
pass 2:+ 3142.907 (branch=2540.85 scale=  1.40 alpha=173.03 freqs= 16.15 rel rates= 15.76 pinv=257.52 subset rates=138.20)
pass 3:+  835.620 (branch= 380.39 scale=  8.60 alpha=272.65 freqs=  5.15 rel rates= 18.80 pinv= 82.85 subset rates= 67.19)
pass 4:+  340.762 (branch= 189.10 scale= 12.96 alpha= 33.80 freqs=  6.94 rel rates= 10.24 pinv=  0.00 subset rates= 87.73)
