

This is RAxML version 8.2.12 released by Alexandros Stamatakis on May 2018.

Alignment has 8170 distinct alignment patterns

Proportion of gaps and completely undetermined characters in this alignment: 7.31%

RAxML Model Optimization up to an accuracy of 0.100000 log likelihood units

Using 1 distinct models/data partitions with joint branch length optimization


All free model parameters will be estimated by RAxML
GAMMA model of rate heterogeneity, ML estimate of alpha-parameter

GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units

Partition: 0
Alignment Patterns: 8170
Name: No Name Provided
DataType: AA
Substitution Matrix: WAG
Using fixed base frequencies


RAxML was called as follows:

/fast_data/manni/app/raxmlHPC-PTHREADS-SSE3 -f e -T 40 -m PROTGAMMAWAG -t ./tree_ARCHAEA_fastTree_constraint.nwk -n test_metadata -s ./superalignment_clean.faa 

Overall Time for Tree Evaluation 22.100948
Final GAMMA  likelihood: -1899976.972816

Number of free parameters for AIC-TEST(BR-LEN): 974
Number of free parameters for AIC-TEST(NO-BR-LEN): 1


Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA
alpha[0]: 0.906969 
Tree-Length: 69.288048
rate A <-> R: 0.705217
rate A <-> N: 0.651871
rate A <-> D: 0.944853
rate A <-> C: 1.313132
rate A <-> Q: 1.161697
rate A <-> E: 2.023768
rate A <-> G: 1.811361
rate A <-> H: 0.405245
rate A <-> I: 0.247190
rate A <-> L: 0.508758
rate A <-> K: 1.158714
rate A <-> M: 1.142388
rate A <-> F: 0.269129
rate A <-> P: 1.839272
rate A <-> S: 4.309757
rate A <-> T: 2.711966
rate A <-> W: 0.144647
rate A <-> Y: 0.307794
rate A <-> V: 2.564804
rate R <-> N: 0.812328
rate R <-> D: 0.188337
rate R <-> C: 0.675324
rate R <-> Q: 3.881068
rate R <-> E: 0.561488
rate R <-> G: 0.747529
rate R <-> H: 2.732474
rate R <-> I: 0.239064
rate R <-> L: 0.636302
rate R <-> K: 6.842111
rate R <-> M: 0.873463
rate R <-> F: 0.131322
rate R <-> P: 0.868767
rate R <-> S: 1.565200
rate R <-> T: 0.708850
rate R <-> W: 1.488141
rate R <-> Y: 0.487813
rate R <-> V: 0.322004
rate N <-> D: 6.941838
rate N <-> C: 0.339146
rate N <-> Q: 1.973636
rate N <-> E: 1.211049
rate N <-> G: 1.439096
rate N <-> H: 5.058353
rate N <-> I: 0.708624
rate N <-> L: 0.168166
rate N <-> K: 3.851035
rate N <-> M: 0.253437
rate N <-> F: 0.122949
rate N <-> P: 0.249423
rate N <-> S: 5.081291
rate N <-> T: 2.595553
rate N <-> W: 0.091950
rate N <-> Y: 1.388516
rate N <-> V: 0.250912
rate D <-> C: 0.038734
rate D <-> Q: 0.788594
rate D <-> E: 7.894033
rate D <-> G: 1.106701
rate D <-> H: 1.189925
rate D <-> I: 0.050423
rate D <-> L: 0.108428
rate D <-> K: 0.613523
rate D <-> M: 0.132656
rate D <-> F: 0.059748
rate D <-> P: 0.542089
rate D <-> S: 1.370309
rate D <-> T: 0.479289
rate D <-> W: 0.165915
rate D <-> Y: 0.416441
rate D <-> V: 0.194769
rate C <-> Q: 0.126345
rate C <-> E: 0.027300
rate C <-> G: 0.392101
rate C <-> H: 0.318326
rate C <-> I: 0.217528
rate C <-> L: 0.491334
rate C <-> K: 0.094657
rate C <-> M: 0.499255
rate C <-> F: 0.508892
rate C <-> P: 0.139880
rate C <-> S: 1.799778
rate C <-> T: 0.655881
rate C <-> W: 0.916817
rate C <-> Y: 0.695323
rate C <-> V: 1.281296
rate Q <-> E: 6.993045
rate Q <-> G: 0.421991
rate Q <-> H: 5.490277
rate Q <-> I: 0.145650
rate Q <-> L: 1.111694
rate Q <-> K: 4.979863
rate Q <-> M: 1.975707
rate Q <-> F: 0.127755
rate Q <-> P: 1.193372
rate Q <-> S: 1.315472
rate Q <-> T: 1.096912
rate Q <-> W: 0.275833
rate Q <-> Y: 0.291141
rate Q <-> V: 0.385206
rate E <-> G: 0.725860
rate E <-> H: 0.728811
rate E <-> I: 0.162882
rate E <-> L: 0.197234
rate E <-> K: 3.304348
rate E <-> M: 0.402905
rate E <-> F: 0.103735
rate E <-> P: 0.872432
rate E <-> S: 0.901307
rate E <-> T: 1.051954
rate E <-> W: 0.200167
rate E <-> Y: 0.250985
rate E <-> V: 0.752728
rate G <-> H: 0.318886
rate G <-> I: 0.038932
rate G <-> L: 0.078380
rate G <-> K: 0.477616
rate G <-> M: 0.222597
rate G <-> F: 0.063840
rate G <-> P: 0.311419
rate G <-> S: 1.715597
rate G <-> T: 0.288741
rate G <-> W: 0.430853
rate G <-> Y: 0.132464
rate G <-> V: 0.239406
rate H <-> I: 0.176684
rate H <-> L: 0.638592
rate H <-> K: 1.138471
rate H <-> M: 0.516718
rate H <-> F: 0.868616
rate H <-> P: 0.890131
rate H <-> S: 0.946350
rate H <-> T: 0.605151
rate H <-> W: 0.335710
rate H <-> Y: 4.952425
rate H <-> V: 0.151328
rate I <-> L: 4.054275
rate I <-> K: 0.414039
rate I <-> M: 5.443417
rate I <-> F: 1.354596
rate I <-> P: 0.127765
rate I <-> S: 0.408423
rate I <-> T: 1.864345
rate I <-> W: 0.271672
rate I <-> Y: 0.537212
rate I <-> V: 10.000000
rate L <-> K: 0.329299
rate L <-> M: 6.206155
rate L <-> F: 2.704371
rate L <-> P: 0.531681
rate L <-> S: 0.440769
rate L <-> T: 0.417606
rate L <-> W: 0.850637
rate L <-> Y: 0.509657
rate L <-> V: 2.301842
rate K <-> M: 1.194528
rate K <-> F: 0.113582
rate K <-> P: 0.712025
rate K <-> S: 1.236534
rate K <-> T: 1.773337
rate K <-> W: 0.175808
rate K <-> Y: 0.170386
rate K <-> V: 0.390516
rate M <-> F: 1.522292
rate M <-> P: 0.219054
rate M <-> S: 0.631487
rate M <-> T: 1.938450
rate M <-> W: 0.659361
rate M <-> Y: 0.547782
rate M <-> V: 2.631851
rate F <-> P: 0.206416
rate F <-> S: 0.698005
rate F <-> T: 0.219788
rate F <-> W: 1.955736
rate F <-> Y: 8.252183
rate F <-> V: 0.830926
rate P <-> S: 2.062675
rate P <-> T: 1.016946
rate P <-> W: 0.178238
rate P <-> Y: 0.276228
rate P <-> V: 0.402602
rate S <-> T: 5.597561
rate S <-> W: 0.669635
rate S <-> Y: 1.006218
rate S <-> V: 0.297571
rate T <-> W: 0.141746
rate T <-> Y: 0.372250
rate T <-> V: 1.774935
rate W <-> Y: 3.177720
rate W <-> V: 0.467146
rate Y <-> V: 0.402401

freq pi(A): 0.086628
freq pi(R): 0.043972
freq pi(N): 0.039089
freq pi(D): 0.057045
freq pi(C): 0.019308
freq pi(Q): 0.036728
freq pi(E): 0.058059
freq pi(G): 0.083252
freq pi(H): 0.024431
freq pi(I): 0.048466
freq pi(L): 0.086209
freq pi(K): 0.062029
freq pi(M): 0.019503
freq pi(F): 0.038432
freq pi(P): 0.045763
freq pi(S): 0.069518
freq pi(T): 0.061013
freq pi(W): 0.014386
freq pi(Y): 0.035274
freq pi(V): 0.070896

Final tree written to:                 /fast_data/manni/busco-odb12-tree-autolineage/archaea/make_tree/RAxML_result.test_metadata
Execution Log File written to:         /fast_data/manni/busco-odb12-tree-autolineage/archaea/make_tree/RAxML_log.test_metadata
