
RAxML-NG v. 0.9.0git released on 26.11.2019 by The Exelixis Lab.
Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml

RAxML-NG was called at 04-Jul-2020 08:15:38 as follows:

/userhome/vinciane/bin/raxml-ng/bin/raxml-ng --all --msa ./alignments/OG0004509.msa.fa --model JTT+G4 --prefix ./raxmlng.tree/OG0004509 --threads 2 --seed 12345 --tree pars{25},rand{25} --bs-trees 100

Analysis options:
  run mode: ML tree search + bootstrapping (Felsenstein Bootstrap)
  start tree(s): random (25) + parsimony (25)
  bootstrap replicates: 100
  random seed: 12345
  tip-inner: OFF
  pattern compression: ON
  per-rate scalers: OFF
  site repeats: ON
  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
  SIMD kernels: AVX2
  parallelization: PTHREADS (2 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: ./alignments/OG0004509.msa.fa
[00:00:00] Loaded alignment with 90 taxa and 543 sites

WARNING: Sequences Angiopteris_fokiensis-m.48530_1 and scaffold-UGNK-2110053-Marattia_attenuata are exactly identical!
WARNING: Sequences scaffold-CJNT-2079899-Polypodium_glycyrrhiza and scaffold-IXLH-2107503-Polypodium_hesperium-B_type are exactly identical!
WARNING: Sequences scaffold-FQGQ-2009381-Polystichum_acrostichoides and scaffold-UFJN-2088801-Diplazium_wichurae are exactly identical!
WARNING: Sequences scaffold-FQGQ-2009381-Polystichum_acrostichoides and scaffold-WQML-2068772-Cryptogramma_acrostichoides are exactly identical!
WARNING: Sequences Plenasium_banksiaefolium-m.8156_1 and scaffold-RFMZ-2008459-Osmundastrum_cinnamomeum-B are exactly identical!
WARNING: Sequences Plenasium_banksiaefolium-m.8156_1 and scaffold-VIBO-2076433-Osmunda_javanica are exactly identical!
WARNING: Sequences scaffold-URCP-2066550-Athyrium_filix_femina and scaffold-WGTU-2075114-Leucostegia_immersa are exactly identical!
WARNING: Sequences scaffold-WCLG-2065397-Adiantum_aleuticum and scaffold-XDDT-2018917-Argyrochosma_nivea are exactly identical!
WARNING: Sequences scaffold-WCLG-2065397-Adiantum_aleuticum and scaffold-YCKE-2064940-Notholaena_montieliae are exactly identical!
WARNING: Duplicate sequences found: 9

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /data3/vinciane/transcriptome/phylogenomy/raxmlng.tree/OG0004509.raxml.reduced.phy

Alignment comprises 1 partitions and 422 patterns

Partition 0: noname
Model: JTT+G4m
Alignment sites / patterns: 543 / 422
Gaps: 25.36 %
Invariant sites: 55.80 %


NOTE: Binary MSA file created: ./raxmlng.tree/OG0004509.raxml.rba

[00:00:00] Generating 25 random starting tree(s) with 90 taxa
[00:00:00] Generating 25 parsimony starting tree(s) with 90 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 211 / 16880

Starting ML tree search with 50 distinct starting trees

[00:10:00] ML tree search #1, logLikelihood: -4333.743890
[00:12:51] ML tree search #2, logLikelihood: -4278.976921
[00:16:45] ML tree search #3, logLikelihood: -4290.195898
[00:19:23] ML tree search #4, logLikelihood: -4276.959657
[00:22:02] ML tree search #5, logLikelihood: -4277.471308
[00:24:52] ML tree search #6, logLikelihood: -4295.119517
[00:28:03] ML tree search #7, logLikelihood: -4279.961813
[00:31:30] ML tree search #8, logLikelihood: -4287.756625
[00:34:40] ML tree search #9, logLikelihood: -4288.992326
[00:37:14] ML tree search #10, logLikelihood: -4280.173614
[00:42:20] ML tree search #11, logLikelihood: -4279.635634
[00:45:09] ML tree search #12, logLikelihood: -4277.953069
[00:47:33] ML tree search #13, logLikelihood: -4285.519314
[00:52:41] ML tree search #14, logLikelihood: -4343.838479
[00:56:29] ML tree search #15, logLikelihood: -4278.067477
[00:59:10] ML tree search #16, logLikelihood: -4280.159514
[01:02:48] ML tree search #17, logLikelihood: -4283.208022
[01:08:54] ML tree search #18, logLikelihood: -4292.552199
[01:13:30] ML tree search #19, logLikelihood: -4286.757305
[01:17:20] ML tree search #20, logLikelihood: -4291.594903
[01:24:19] ML tree search #21, logLikelihood: -4295.761751
[01:28:16] ML tree search #22, logLikelihood: -4281.056681
[01:31:20] ML tree search #23, logLikelihood: -4296.191707
[01:34:04] ML tree search #24, logLikelihood: -4286.605088
[01:38:53] ML tree search #25, logLikelihood: -4279.857398
[01:44:16] ML tree search #26, logLikelihood: -4277.436636
[01:51:49] ML tree search #27, logLikelihood: -4276.895095
[01:54:11] ML tree search #28, logLikelihood: -4285.586200
[01:59:22] ML tree search #29, logLikelihood: -4281.235557
[02:03:47] ML tree search #30, logLikelihood: -4284.562132
[02:06:12] ML tree search #31, logLikelihood: -4279.488693
[02:13:34] ML tree search #32, logLikelihood: -4290.917537
[02:17:57] ML tree search #33, logLikelihood: -4286.909991
[02:29:56] ML tree search #34, logLikelihood: -4277.703201
[02:36:02] ML tree search #35, logLikelihood: -4276.912025
[02:40:41] ML tree search #36, logLikelihood: -4279.379583
[02:42:53] ML tree search #37, logLikelihood: -4277.433818
[02:45:30] ML tree search #38, logLikelihood: -4278.785203
[02:47:22] ML tree search #39, logLikelihood: -4296.261813
[02:51:12] ML tree search #40, logLikelihood: -4286.918076
[02:55:29] ML tree search #41, logLikelihood: -4276.957524
[02:57:28] ML tree search #42, logLikelihood: -4287.944841
[02:59:55] ML tree search #43, logLikelihood: -4278.618582
[03:02:35] ML tree search #44, logLikelihood: -4290.474929
[03:05:26] ML tree search #45, logLikelihood: -4277.710818
[03:09:22] ML tree search #46, logLikelihood: -4292.870786
[03:12:00] ML tree search #47, logLikelihood: -4287.398841
[03:15:27] ML tree search #48, logLikelihood: -4294.252246
[03:18:13] ML tree search #49, logLikelihood: -4290.870242
[03:20:18] ML tree search #50, logLikelihood: -4283.654289

[03:20:18] ML tree search completed, best tree logLH: -4276.895095

[03:20:18] Starting bootstrapping analysis with 100 replicates.

[03:22:34] Bootstrap tree #1, logLikelihood: -4209.154127
[03:25:46] Bootstrap tree #2, logLikelihood: -4005.810035
[03:29:19] Bootstrap tree #3, logLikelihood: -4246.251223
[03:31:30] Bootstrap tree #4, logLikelihood: -3995.806883
[03:46:02] Bootstrap tree #5, logLikelihood: -4008.223182
[03:49:06] Bootstrap tree #6, logLikelihood: -3936.312390
[03:52:42] Bootstrap tree #7, logLikelihood: -4129.259954
[03:57:55] Bootstrap tree #8, logLikelihood: -4455.042123
[04:00:33] Bootstrap tree #9, logLikelihood: -4465.471971
[04:03:45] Bootstrap tree #10, logLikelihood: -3953.524658
[04:05:22] Bootstrap tree #11, logLikelihood: -3894.306616
[04:08:01] Bootstrap tree #12, logLikelihood: -4249.147440
[04:10:29] Bootstrap tree #13, logLikelihood: -3860.539537
[04:12:40] Bootstrap tree #14, logLikelihood: -4038.788466
[04:14:57] Bootstrap tree #15, logLikelihood: -3979.535737
[04:18:13] Bootstrap tree #16, logLikelihood: -4266.779039
[04:21:46] Bootstrap tree #17, logLikelihood: -4254.842582
[04:24:18] Bootstrap tree #18, logLikelihood: -4162.843595
[04:26:05] Bootstrap tree #19, logLikelihood: -4303.363748
[04:28:10] Bootstrap tree #20, logLikelihood: -4229.586528
[04:31:44] Bootstrap tree #21, logLikelihood: -4131.566429
[04:35:31] Bootstrap tree #22, logLikelihood: -4232.776149
[04:38:36] Bootstrap tree #23, logLikelihood: -4163.028624
[04:42:25] Bootstrap tree #24, logLikelihood: -4339.567003
[04:44:17] Bootstrap tree #25, logLikelihood: -4430.874042
[04:47:10] Bootstrap tree #26, logLikelihood: -4541.538368
[04:51:10] Bootstrap tree #27, logLikelihood: -4622.810726
[04:54:48] Bootstrap tree #28, logLikelihood: -4074.394310
[05:01:34] Bootstrap tree #29, logLikelihood: -4334.109645
[05:03:36] Bootstrap tree #30, logLikelihood: -4594.091855
[05:06:34] Bootstrap tree #31, logLikelihood: -4077.328272
[05:09:15] Bootstrap tree #32, logLikelihood: -4002.221905
[05:15:11] Bootstrap tree #33, logLikelihood: -4401.137758
[05:17:02] Bootstrap tree #34, logLikelihood: -4193.862170
[05:20:28] Bootstrap tree #35, logLikelihood: -4223.952144
[05:22:19] Bootstrap tree #36, logLikelihood: -4104.063858
[05:25:43] Bootstrap tree #37, logLikelihood: -4048.692000
[05:28:40] Bootstrap tree #38, logLikelihood: -4301.109906
[05:31:13] Bootstrap tree #39, logLikelihood: -3678.452002
[05:33:22] Bootstrap tree #40, logLikelihood: -4030.286149
[05:36:26] Bootstrap tree #41, logLikelihood: -4342.497162
[05:40:27] Bootstrap tree #42, logLikelihood: -4300.796723
[05:43:15] Bootstrap tree #43, logLikelihood: -4335.716251
[05:46:55] Bootstrap tree #44, logLikelihood: -4378.444526
[05:51:44] Bootstrap tree #45, logLikelihood: -4267.635567
[05:54:13] Bootstrap tree #46, logLikelihood: -4170.421937
[05:57:32] Bootstrap tree #47, logLikelihood: -4044.351573
[06:00:14] Bootstrap tree #48, logLikelihood: -4355.576957
[06:03:37] Bootstrap tree #49, logLikelihood: -4088.824403
[06:08:40] Bootstrap tree #50, logLikelihood: -4057.513484
[06:10:43] Bootstrap tree #51, logLikelihood: -4300.287517
[06:13:31] Bootstrap tree #52, logLikelihood: -3739.261020
[06:15:57] Bootstrap tree #53, logLikelihood: -4064.878904
[06:18:51] Bootstrap tree #54, logLikelihood: -4522.030087
[06:21:59] Bootstrap tree #55, logLikelihood: -4327.627556
[06:24:14] Bootstrap tree #56, logLikelihood: -4412.787155
[06:27:27] Bootstrap tree #57, logLikelihood: -4097.731467
[06:31:49] Bootstrap tree #58, logLikelihood: -4816.897008
[06:33:58] Bootstrap tree #59, logLikelihood: -4356.028932
[06:36:41] Bootstrap tree #60, logLikelihood: -4510.416919
[06:41:56] Bootstrap tree #61, logLikelihood: -4393.215700
[06:45:49] Bootstrap tree #62, logLikelihood: -3967.371197
[06:47:35] Bootstrap tree #63, logLikelihood: -4366.874178
[06:51:29] Bootstrap tree #64, logLikelihood: -4179.121418
[06:53:21] Bootstrap tree #65, logLikelihood: -4424.278008
[06:57:05] Bootstrap tree #66, logLikelihood: -4232.277707
[07:01:25] Bootstrap tree #67, logLikelihood: -4255.875155
[07:06:03] Bootstrap tree #68, logLikelihood: -4437.022017
[07:10:09] Bootstrap tree #69, logLikelihood: -4232.347806
[07:13:32] Bootstrap tree #70, logLikelihood: -4202.299221
[07:18:53] Bootstrap tree #71, logLikelihood: -4268.359649
[07:20:55] Bootstrap tree #72, logLikelihood: -4274.202726
[07:25:45] Bootstrap tree #73, logLikelihood: -4221.484310
[07:28:42] Bootstrap tree #74, logLikelihood: -4280.301184
[07:32:31] Bootstrap tree #75, logLikelihood: -4079.185556
[07:35:43] Bootstrap tree #76, logLikelihood: -4255.119462
[07:38:37] Bootstrap tree #77, logLikelihood: -4229.110352
[07:41:20] Bootstrap tree #78, logLikelihood: -4508.340956
[07:43:10] Bootstrap tree #79, logLikelihood: -4687.386022
[07:47:28] Bootstrap tree #80, logLikelihood: -4549.396180
[07:50:24] Bootstrap tree #81, logLikelihood: -4102.368854
[07:53:41] Bootstrap tree #82, logLikelihood: -4180.181989
[07:55:51] Bootstrap tree #83, logLikelihood: -4296.739476
[07:57:32] Bootstrap tree #84, logLikelihood: -4611.165208
[08:01:32] Bootstrap tree #85, logLikelihood: -3996.071335
[08:03:40] Bootstrap tree #86, logLikelihood: -4280.499973
[08:08:05] Bootstrap tree #87, logLikelihood: -3872.421592
[08:13:14] Bootstrap tree #88, logLikelihood: -4287.887376
[08:15:59] Bootstrap tree #89, logLikelihood: -3916.508742
[08:17:52] Bootstrap tree #90, logLikelihood: -4109.662390
[08:21:03] Bootstrap tree #91, logLikelihood: -3963.470928
[08:23:06] Bootstrap tree #92, logLikelihood: -4671.181755
[08:28:00] Bootstrap tree #93, logLikelihood: -4307.960948
[08:29:46] Bootstrap tree #94, logLikelihood: -4376.418922
[08:31:51] Bootstrap tree #95, logLikelihood: -4076.942515
[08:37:06] Bootstrap tree #96, logLikelihood: -4045.363823
[08:39:48] Bootstrap tree #97, logLikelihood: -4144.371088
[08:44:32] Bootstrap tree #98, logLikelihood: -4203.338039
[08:46:56] Bootstrap tree #99, logLikelihood: -4558.406346
[08:48:43] Bootstrap tree #100, logLikelihood: -4092.003778

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: GAMMA (4 cats, mean),  alpha: 0.218266 (ML),  weights&rates: (0.250000,0.000947) (0.250000,0.044933) (0.250000,0.429632) (0.250000,3.524489) 
   Base frequencies (model): 0.076748 0.051691 0.042645 0.051544 0.019803 0.040752 0.061830 0.073152 0.022944 0.053761 0.091904 0.058676 0.023826 0.040126 0.050901 0.068765 0.058565 0.014261 0.032102 0.066005 
   Substitution rates (model): 58.000000 54.000000 81.000000 56.000000 57.000000 105.000000 179.000000 27.000000 36.000000 30.000000 35.000000 54.000000 15.000000 194.000000 378.000000 475.000000 9.000000 11.000000 298.000000 45.000000 16.000000 113.000000 310.000000 29.000000 137.000000 328.000000 22.000000 38.000000 646.000000 44.000000 5.000000 74.000000 101.000000 64.000000 126.000000 20.000000 17.000000 528.000000 34.000000 86.000000 58.000000 81.000000 391.000000 47.000000 12.000000 263.000000 30.000000 10.000000 15.000000 503.000000 232.000000 8.000000 70.000000 16.000000 10.000000 49.000000 767.000000 130.000000 112.000000 11.000000 7.000000 26.000000 15.000000 4.000000 15.000000 59.000000 38.000000 4.000000 46.000000 31.000000 9.000000 5.000000 59.000000 69.000000 17.000000 23.000000 7.000000 31.000000 78.000000 14.000000 223.000000 42.000000 115.000000 209.000000 62.000000 323.000000 26.000000 597.000000 9.000000 72.000000 292.000000 43.000000 4.000000 164.000000 53.000000 51.000000 18.000000 24.000000 20.000000 119.000000 26.000000 12.000000 9.000000 181.000000 18.000000 5.000000 18.000000 30.000000 32.000000 10.000000 7.000000 45.000000 23.000000 6.000000 6.000000 27.000000 14.000000 5.000000 24.000000 201.000000 33.000000 55.000000 8.000000 47.000000 16.000000 56.000000 45.000000 33.000000 40.000000 115.000000 73.000000 46.000000 8.000000 573.000000 11.000000 229.000000 21.000000 479.000000 89.000000 10.000000 40.000000 245.000000 9.000000 32.000000 961.000000 14.000000 388.000000 248.000000 102.000000 59.000000 25.000000 52.000000 24.000000 180.000000 65.000000 4.000000 21.000000 47.000000 103.000000 10.000000 8.000000 14.000000 43.000000 16.000000 29.000000 226.000000 24.000000 18.000000 323.000000 17.000000 92.000000 12.000000 53.000000 536.000000 62.000000 285.000000 118.000000 6.000000 10.000000 23.000000 477.000000 35.000000 63.000000 38.000000 12.000000 21.000000 112.000000 71.000000 25.000000 16.000000 


Final LogLikelihood: -4276.895095

AIC score: 8909.790190 / AICc score: 9084.856124 / BIC score: 9674.675649
Free parameters (model + branch lengths): 178

Best ML tree saved to: /data3/vinciane/transcriptome/phylogenomy/raxmlng.tree/OG0004509.raxml.bestTree
All ML trees saved to: /data3/vinciane/transcriptome/phylogenomy/raxmlng.tree/OG0004509.raxml.mlTrees
Best ML tree with Felsenstein bootstrap (FBP) support values saved to: /data3/vinciane/transcriptome/phylogenomy/raxmlng.tree/OG0004509.raxml.support
Optimized model saved to: /data3/vinciane/transcriptome/phylogenomy/raxmlng.tree/OG0004509.raxml.bestModel
Bootstrap trees saved to: /data3/vinciane/transcriptome/phylogenomy/raxmlng.tree/OG0004509.raxml.bootstraps

Execution log saved to: /data3/vinciane/transcriptome/phylogenomy/raxmlng.tree/OG0004509.raxml.log

Analysis started: 04-Jul-2020 08:15:38 / finished: 04-Jul-2020 17:04:22

Elapsed time: 31723.648 seconds

