RAxML-NG v. 1.0.2 released on 22.02.2021 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

System: Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM

RAxML-NG was called at 03-Jul-2021 06:01:57 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P22897/2_msa/P22897_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P22897/3_mltree/P22897 --seed 2 --threads 5 --tree rand{20} pars{20}

Analysis options:
  run mode: ML tree search
  start tree(s): random (20)
  random seed: 2
  tip-inner: OFF
  pattern compression: ON
  per-rate scalers: OFF
  site repeats: ON
  fast spr radius: AUTO
  spr subtree cutoff: 1.000000
  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
  SIMD kernels: AVX2
  parallelization: coarse-grained (auto), PTHREADS (5 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P22897/2_msa/P22897_trimmed_msa.fasta
[00:00:00] Loaded alignment with 998 taxa and 304 sites

WARNING: Sequences sp_Q90611_MMP2_CHICK_9031 and tr_G1MZ17_G1MZ17_MELGA_9103 are exactly identical!
WARNING: Sequences sp_Q90611_MMP2_CHICK_9031 and tr_A0A226N9V4_A0A226N9V4_CALSU_9009 are exactly identical!
WARNING: Sequences sp_Q90611_MMP2_CHICK_9031 and tr_A0A226P7U0_A0A226P7U0_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2I3HSS7_A0A2I3HSS7_NOMLE_61853 and tr_G3QHQ0_G3QHQ0_GORGO_9595 are exactly identical!
WARNING: Sequences tr_A0A2I3HSS7_A0A2I3HSS7_NOMLE_61853 and tr_H2NW01_H2NW01_PONAB_9601 are exactly identical!
WARNING: Sequences tr_A0A2I3HSS7_A0A2I3HSS7_NOMLE_61853 and sp_Q5KU26_COL12_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I3HSS7_A0A2I3HSS7_NOMLE_61853 and tr_A0A2R8MEH9_A0A2R8MEH9_CALJA_9483 are exactly identical!
WARNING: Sequences tr_G1SRJ7_G1SRJ7_RABIT_9986 and sp_P50757_MMP2_RABIT_9986 are exactly identical!
WARNING: Sequences tr_A0A2I3TEQ9_A0A2I3TEQ9_PANTR_9598 and sp_P08253_MMP2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I3TEQ9_A0A2I3TEQ9_PANTR_9598 and tr_A0A1D5QTJ7_A0A1D5QTJ7_MACMU_9544 are exactly identical!
WARNING: Sequences tr_A0A2I3TEQ9_A0A2I3TEQ9_PANTR_9598 and tr_A0A096NIF0_A0A096NIF0_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A2I3TEQ9_A0A2I3TEQ9_PANTR_9598 and tr_A0A0D9QZ11_A0A0D9QZ11_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A2I3TEQ9_A0A2I3TEQ9_PANTR_9598 and tr_A0A2K5KTG2_A0A2K5KTG2_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3TEQ9_A0A2I3TEQ9_PANTR_9598 and tr_A0A2K6BWB4_A0A2K6BWB4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I3TEQ9_A0A2I3TEQ9_PANTR_9598 and tr_A0A2K5ZKS9_A0A2K5ZKS9_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I3TEQ9_A0A2I3TEQ9_PANTR_9598 and tr_A0A2R9BYN6_A0A2R9BYN6_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QA14_H2QA14_PANTR_9598 and sp_P16112_PGCA_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2QA14_H2QA14_PANTR_9598 and tr_A0A2R9BUF1_A0A2R9BUF1_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QDM3_H2QDM3_PANTR_9598 and sp_Q9UBG0_MRC2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2QDM3_H2QDM3_PANTR_9598 and tr_A0A2R8ZZ20_A0A2R8ZZ20_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QFV0_H2QFV0_PANTR_9598 and sp_Q5IS41_NCAN_PANTR_9598 are exactly identical!
WARNING: Sequences sp_P14780_MMP9_HUMAN_9606 and tr_A0A2R9BNH8_A0A2R9BNH8_PANPA_9597 are exactly identical!
WARNING: Sequences sp_Q96GW7_PGCB_HUMAN_9606 and tr_A0A2R9BXM3_A0A2R9BXM3_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F6PK24_F6PK24_MACMU_9544 and tr_G7PEG9_G7PEG9_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F6PK24_F6PK24_MACMU_9544 and tr_A0A0D9RJK2_A0A0D9RJK2_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F6PK24_F6PK24_MACMU_9544 and tr_A0A2K6BGK4_A0A2K6BGK4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F6PK24_F6PK24_MACMU_9544 and tr_A0A2K5Y622_A0A2K5Y622_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F7C5R9_F7C5R9_MACMU_9544 and tr_A0A2K5LA53_A0A2K5LA53_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7C5R9_F7C5R9_MACMU_9544 and tr_A0A2K6C9F0_A0A2K6C9F0_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7C5R9_F7C5R9_MACMU_9544 and tr_A0A2K6AGV8_A0A2K6AGV8_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F7HJ53_F7HJ53_MACMU_9544 and tr_A0A2K6AVJ4_A0A2K6AVJ4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_H0ZAJ9_H0ZAJ9_TAEGU_59729 and tr_A0A218UXL2_A0A218UXL2_9PASE_299123 are exactly identical!
WARNING: Sequences tr_G1LW45_G1LW45_AILME_9646 and tr_A0A384C608_A0A384C608_URSMA_29073 are exactly identical!
WARNING: Sequences tr_G7PV37_G7PV37_MACFA_9541 and tr_A0A096P6B8_A0A096P6B8_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G7PV37_G7PV37_MACFA_9541 and tr_A0A0D9QV27_A0A0D9QV27_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G7PV37_G7PV37_MACFA_9541 and tr_A0A2K5LKL4_A0A2K5LKL4_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G7PV37_G7PV37_MACFA_9541 and tr_A0A2K6BY83_A0A2K6BY83_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7PV37_G7PV37_MACFA_9541 and tr_A0A2K5ZPI0_A0A2K5ZPI0_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F1MF56_F1MF56_BOVIN_9913 and sp_P52176_MMP9_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_F1MKH8_F1MKH8_BOVIN_9913 and sp_Q9GLE5_MMP2_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_A0A096NDK6_A0A096NDK6_PAPAN_9555 and tr_A0A0D9S4S5_A0A0D9S4S5_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A096NDK6_A0A096NDK6_PAPAN_9555 and tr_A0A2K5KQW7_A0A2K5KQW7_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A087QWV0_A0A087QWV0_APTFO_9233 and tr_A0A099ZYE4_A0A099ZYE4_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A087QX64_A0A087QX64_APTFO_9233 and tr_A0A091XNK8_A0A091XNK8_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_A0A087QX64_A0A087QX64_APTFO_9233 and tr_A0A091FU85_A0A091FU85_9AVES_55661 are exactly identical!
WARNING: Sequences tr_A0A087QX64_A0A087QX64_APTFO_9233 and tr_A0A099ZXQ1_A0A099ZXQ1_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A2I0M2G1_A0A2I0M2G1_COLLI_8932 and tr_A0A1V4K1L4_A0A1V4K1L4_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A2D0PWK8_A0A2D0PWK8_ICTPU_7998 and tr_W5UBM1_W5UBM1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RD47_A0A2D0RD47_ICTPU_7998 and tr_A0A2D0RE99_A0A2D0RE99_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RD47_A0A2D0RD47_ICTPU_7998 and tr_A0A2D0REZ6_A0A2D0REZ6_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RQM2_A0A2D0RQM2_ICTPU_7998 and tr_A0A2D0RQN8_A0A2D0RQN8_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2K5LVR0_A0A2K5LVR0_CERAT_9531 and tr_A0A2K5XWU9_A0A2K5XWU9_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2K5LZN3_A0A2K5LZN3_CERAT_9531 and tr_A0A2K6BGL1_A0A2K6BGL1_MACNE_9545 are exactly identical!
WARNING: Duplicate sequences found: 53

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P22897/3_mltree/P22897.raxml.reduced.phy

Alignment comprises 1 partitions and 304 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 304 / 304
Gaps: 24.59 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P22897/3_mltree/P22897.raxml.rba

Parallelization scheme autoconfig: 5 worker(s) x 1 thread(s)

Parallel reduction/worker buffer size: 1 KB  / 0 KB

[00:00:00] Generating 20 random starting tree(s) with 998 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 304 / 24320
[00:00:00] Data distribution: max. searches per worker: 4

Starting ML tree search with 20 distinct starting trees

[00:00:00 -503357.369993] Initial branch length optimization
[00:00:11 -419837.199863] Model parameter optimization (eps = 10.000000)
[00:01:32 -418456.073436] AUTODETECT spr round 1 (radius: 5)
[00:05:44 -285992.013216] AUTODETECT spr round 2 (radius: 10)
[00:10:05 -215096.839613] AUTODETECT spr round 3 (radius: 15)
[00:15:18 -174683.791509] AUTODETECT spr round 4 (radius: 20)
[00:21:04 -155254.463709] AUTODETECT spr round 5 (radius: 25)
[00:27:55 -152616.712609] SPR radius for FAST iterations: 25 (autodetect)
[00:27:55 -152616.712609] Model parameter optimization (eps = 3.000000)
[00:28:36 -152448.895689] FAST spr round 1 (radius: 25)
[00:34:21 -134636.070963] FAST spr round 2 (radius: 25)
[00:38:36 -133979.264468] FAST spr round 3 (radius: 25)
[00:42:04 -133888.270742] FAST spr round 4 (radius: 25)
[00:45:08 -133871.694712] FAST spr round 5 (radius: 25)
[00:48:00 -133863.855801] FAST spr round 6 (radius: 25)
[00:50:45 -133863.853629] Model parameter optimization (eps = 1.000000)
[00:51:18 -133860.331391] SLOW spr round 1 (radius: 5)
[00:55:02 -133834.438578] SLOW spr round 2 (radius: 5)
[00:58:47 -133832.796048] SLOW spr round 3 (radius: 5)
[01:02:24 -133832.795171] SLOW spr round 4 (radius: 10)
[01:06:12 -133832.794773] SLOW spr round 5 (radius: 15)
[01:14:22 -133830.419655] SLOW spr round 6 (radius: 5)
[01:19:15 -133829.650510] SLOW spr round 7 (radius: 5)
[01:23:26 -133829.650179] SLOW spr round 8 (radius: 10)
[01:27:31 -133829.650078] SLOW spr round 9 (radius: 15)
[01:35:11 -133829.187429] SLOW spr round 10 (radius: 5)
[01:40:00 -133829.154427] SLOW spr round 11 (radius: 10)
[01:44:46 -133829.153459] SLOW spr round 12 (radius: 15)
[01:52:03 -133829.152890] SLOW spr round 13 (radius: 20)
[02:05:12 -133829.152574] SLOW spr round 14 (radius: 25)
[02:21:06 -133828.450503] SLOW spr round 15 (radius: 5)
[02:26:05 -133828.450015] SLOW spr round 16 (radius: 10)
[02:31:06 -133828.449915] SLOW spr round 17 (radius: 15)
[02:38:19 -133828.449851] SLOW spr round 18 (radius: 20)
[02:39:55] [worker #4] ML tree search #5, logLikelihood: -133667.249361
[02:47:41] [worker #3] ML tree search #4, logLikelihood: -133668.129570
[02:51:25 -133828.449797] SLOW spr round 19 (radius: 25)
[02:55:07] [worker #1] ML tree search #2, logLikelihood: -133668.252095
[03:07:18 -133828.449749] Model parameter optimization (eps = 0.100000)

[03:07:35] [worker #0] ML tree search #1, logLikelihood: -133828.274173

[03:07:36 -505151.689652] Initial branch length optimization
[03:07:51 -423842.963838] Model parameter optimization (eps = 10.000000)
[03:09:01 -422476.667119] AUTODETECT spr round 1 (radius: 5)
[03:12:25] [worker #2] ML tree search #3, logLikelihood: -133687.959527
[03:13:15 -287948.042116] AUTODETECT spr round 2 (radius: 10)
[03:17:45 -205095.709770] AUTODETECT spr round 3 (radius: 15)
[03:22:36 -169395.659068] AUTODETECT spr round 4 (radius: 20)
[03:28:01 -155051.254350] AUTODETECT spr round 5 (radius: 25)
[03:34:32 -151818.466859] SPR radius for FAST iterations: 25 (autodetect)
[03:34:32 -151818.466859] Model parameter optimization (eps = 3.000000)
[03:35:15 -151587.703809] FAST spr round 1 (radius: 25)
[03:41:17 -134617.551790] FAST spr round 2 (radius: 25)
[03:45:37 -133849.989892] FAST spr round 3 (radius: 25)
[03:49:13 -133752.700767] FAST spr round 4 (radius: 25)
[03:52:25 -133729.533636] FAST spr round 5 (radius: 25)
[03:55:25 -133722.892523] FAST spr round 6 (radius: 25)
[03:58:15 -133722.306481] FAST spr round 7 (radius: 25)
[04:01:00 -133722.031167] FAST spr round 8 (radius: 25)
[04:03:42 -133722.028239] Model parameter optimization (eps = 1.000000)
[04:04:17 -133719.998809] SLOW spr round 1 (radius: 5)
[04:08:01 -133704.293040] SLOW spr round 2 (radius: 5)
[04:11:46 -133693.041518] SLOW spr round 3 (radius: 5)
[04:15:29 -133689.922498] SLOW spr round 4 (radius: 5)
[04:19:04 -133689.922045] SLOW spr round 5 (radius: 10)
[04:22:53 -133689.355887] SLOW spr round 6 (radius: 5)
[04:27:35 -133689.328278] SLOW spr round 7 (radius: 10)
[04:32:06 -133689.327454] SLOW spr round 8 (radius: 15)
[04:39:26 -133689.327201] SLOW spr round 9 (radius: 20)
[04:52:18 -133689.327119] SLOW spr round 10 (radius: 25)
[05:04:07] [worker #4] ML tree search #10, logLikelihood: -133691.104268
[05:08:19 -133689.327092] Model parameter optimization (eps = 0.100000)

[05:08:30] [worker #0] ML tree search #6, logLikelihood: -133689.296597

[05:08:30 -505154.249740] Initial branch length optimization
[05:08:40 -421433.125835] Model parameter optimization (eps = 10.000000)
[05:10:01 -420032.418510] AUTODETECT spr round 1 (radius: 5)
[05:14:17 -286559.562647] AUTODETECT spr round 2 (radius: 10)
[05:16:37] [worker #1] ML tree search #7, logLikelihood: -133666.261958
[05:18:43 -216881.802428] AUTODETECT spr round 3 (radius: 15)
[05:20:36] [worker #2] ML tree search #8, logLikelihood: -133682.006522
[05:23:33 -180213.330468] AUTODETECT spr round 4 (radius: 20)
[05:26:57] [worker #3] ML tree search #9, logLikelihood: -133706.398422
[05:29:20 -155103.592688] AUTODETECT spr round 5 (radius: 25)
[05:35:35 -152533.273552] SPR radius for FAST iterations: 25 (autodetect)
[05:35:36 -152533.273552] Model parameter optimization (eps = 3.000000)
[05:36:28 -152359.677918] FAST spr round 1 (radius: 25)
[05:42:38 -134880.209705] FAST spr round 2 (radius: 25)
[05:47:06 -133865.406144] FAST spr round 3 (radius: 25)
[05:50:43 -133746.060632] FAST spr round 4 (radius: 25)
[05:53:58 -133730.538510] FAST spr round 5 (radius: 25)
[05:56:52 -133728.787968] FAST spr round 6 (radius: 25)
[05:59:38 -133728.786269] Model parameter optimization (eps = 1.000000)
[06:00:04 -133722.817891] SLOW spr round 1 (radius: 5)
[06:03:51 -133693.673687] SLOW spr round 2 (radius: 5)
[06:07:41 -133685.109554] SLOW spr round 3 (radius: 5)
[06:11:21 -133685.109142] SLOW spr round 4 (radius: 10)
[06:15:07 -133684.224454] SLOW spr round 5 (radius: 5)
[06:19:46 -133684.223686] SLOW spr round 6 (radius: 10)
[06:24:11 -133684.223594] SLOW spr round 7 (radius: 15)
[06:31:09 -133684.223538] SLOW spr round 8 (radius: 20)
[06:43:19 -133683.822666] SLOW spr round 9 (radius: 5)
[06:48:23 -133682.356871] SLOW spr round 10 (radius: 5)
[06:52:40 -133682.354747] SLOW spr round 11 (radius: 10)
[06:56:44 -133682.353180] SLOW spr round 12 (radius: 15)
[07:00:12] [worker #4] ML tree search #15, logLikelihood: -133680.883977
[07:04:01 -133682.352016] SLOW spr round 13 (radius: 20)
[07:16:08 -133681.843151] SLOW spr round 14 (radius: 5)
[07:21:14 -133681.176843] SLOW spr round 15 (radius: 5)
[07:25:31 -133681.173213] SLOW spr round 16 (radius: 10)
[07:29:34 -133681.172642] SLOW spr round 17 (radius: 15)
[07:36:50 -133681.172491] SLOW spr round 18 (radius: 20)
[07:43:03] [worker #1] ML tree search #12, logLikelihood: -133665.264562
[07:48:57 -133681.172440] SLOW spr round 19 (radius: 25)
[07:56:51] [worker #2] ML tree search #13, logLikelihood: -133680.863823
[08:03:54 -133681.172414] Model parameter optimization (eps = 0.100000)

[08:04:08] [worker #0] ML tree search #11, logLikelihood: -133681.111326

[08:04:08 -501608.292060] Initial branch length optimization
[08:04:18 -419135.338179] Model parameter optimization (eps = 10.000000)
[08:05:41 -417825.310710] AUTODETECT spr round 1 (radius: 5)
[08:09:57 -287487.344538] AUTODETECT spr round 2 (radius: 10)
[08:14:29 -201774.897544] AUTODETECT spr round 3 (radius: 15)
[08:18:52] [worker #3] ML tree search #14, logLikelihood: -133670.408834
[08:19:37 -172042.329344] AUTODETECT spr round 4 (radius: 20)
[08:25:47 -157698.902005] AUTODETECT spr round 5 (radius: 25)
[08:33:09 -152911.930267] SPR radius for FAST iterations: 25 (autodetect)
[08:33:09 -152911.930267] Model parameter optimization (eps = 3.000000)
[08:33:54 -152725.658257] FAST spr round 1 (radius: 25)
[08:40:19 -135121.683159] FAST spr round 2 (radius: 25)
[08:44:54 -133810.325047] FAST spr round 3 (radius: 25)
[08:48:41 -133743.398941] FAST spr round 4 (radius: 25)
[08:51:52 -133735.630348] FAST spr round 5 (radius: 25)
[08:54:46 -133733.873302] FAST spr round 6 (radius: 25)
[08:57:31 -133733.861545] Model parameter optimization (eps = 1.000000)
[08:58:01 -133727.432057] SLOW spr round 1 (radius: 5)
[09:02:00 -133686.256891] SLOW spr round 2 (radius: 5)
[09:05:47 -133682.386828] SLOW spr round 3 (radius: 5)
[09:09:25 -133682.355163] SLOW spr round 4 (radius: 10)
[09:13:11 -133678.346912] SLOW spr round 5 (radius: 5)
[09:17:54 -133675.925466] SLOW spr round 6 (radius: 5)
[09:22:00 -133675.913922] SLOW spr round 7 (radius: 10)
[09:25:59 -133675.913602] SLOW spr round 8 (radius: 15)
[09:33:48 -133673.228656] SLOW spr round 9 (radius: 5)
[09:36:53] [worker #4] ML tree search #20, logLikelihood: -133698.619859
[09:38:40 -133672.308870] SLOW spr round 10 (radius: 5)
[09:42:52 -133672.298265] SLOW spr round 11 (radius: 10)
[09:46:03] [worker #2] ML tree search #18, logLikelihood: -133843.094666
[09:46:56 -133671.200518] SLOW spr round 12 (radius: 5)
[09:51:32 -133670.686005] SLOW spr round 13 (radius: 5)
[09:52:27] [worker #1] ML tree search #17, logLikelihood: -133706.158471
[09:55:33 -133670.685532] SLOW spr round 14 (radius: 10)
[09:59:29 -133670.685363] SLOW spr round 15 (radius: 15)
[10:07:20 -133670.685298] SLOW spr round 16 (radius: 20)
[10:19:47 -133670.685272] SLOW spr round 17 (radius: 25)
[10:24:46] [worker #3] ML tree search #19, logLikelihood: -133689.573645
[10:35:27 -133670.685262] Model parameter optimization (eps = 0.100000)

[10:35:41] [worker #0] ML tree search #16, logLikelihood: -133670.657978


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.113940,0.386014) (0.091033,1.059689) (0.478720,0.792702) (0.316307,1.517730) 
   Base frequencies (model): 
M0: 0.147383 0.017579 0.058208 0.017707 0.026331 0.041582 0.017494 0.027859 0.011849 0.076971 0.147823 0.019535 0.037132 0.029940 0.008059 0.088179 0.089653 0.006477 0.032308 0.097931 
M1: 0.063139 0.066357 0.011586 0.066571 0.010800 0.009276 0.053984 0.146986 0.034214 0.088822 0.098196 0.032390 0.021263 0.072697 0.016761 0.020711 0.020797 0.025463 0.045615 0.094372 
M2: 0.062457 0.066826 0.049332 0.065270 0.006513 0.041231 0.058965 0.080852 0.028024 0.037024 0.075925 0.064131 0.019620 0.028710 0.104579 0.056388 0.062027 0.008241 0.033124 0.050760 
M3: 0.106471 0.074171 0.044513 0.096390 0.002148 0.066733 0.158908 0.037625 0.020691 0.014608 0.028797 0.105352 0.007864 0.007477 0.083595 0.055726 0.047711 0.003975 0.010088 0.027159 
   Substitution rates (model): 
M 0: 0.295719 0.067388 0.253712 1.029289 0.107964 0.514644 10.868848 0.380498 0.084223 0.086976 0.188789 0.286389 0.155567 1.671061 2.132922 0.529591 0.115551 0.102453 0.916683 0.448317 0.457483 0.576016 1.741924 0.736017 0.704334 5.658311 0.123387 0.221777 93.433377 0.382175 0.235965 6.535048 0.525521 0.303537 0.641259 0.289466 0.102065 2.358429 0.251987 0.216561 0.503084 0.435271 4.873453 0.090748 0.033310 0.746537 0.128905 0.127321 0.904011 0.939733 0.435450 0.046646 0.262076 0.043986 0.189008 0.599450 109.901504 1.070052 5.229858 0.052764 0.021407 0.621146 0.081091 0.205164 5.164456 0.747330 0.308078 0.260889 0.185083 0.080708 0.029955 0.084794 1.862626 0.553477 0.151733 0.230320 0.096955 0.352526 0.590018 0.386853 1.559564 0.606648 0.587531 0.592318 0.885230 4.117654 0.246260 6.508329 0.054187 0.195703 1.669092 0.810168 0.066081 2.437439 0.165666 0.106333 0.093417 0.035149 0.072549 1.202023 1.634845 0.060194 0.069359 2.448827 0.232297 0.064822 3.537387 0.435384 0.290413 0.280695 0.105999 0.206603 0.404968 0.048984 0.069963 0.256662 0.228519 0.241077 4.320442 3.656545 0.290216 0.307466 0.096556 0.306067 0.204296 0.504221 1.991533 0.655465 6.799829 11.291065 0.961142 0.448965 6.227274 20.304886 0.205944 1.495537 0.091940 1.994320 0.754940 0.170343 0.050315 0.372166 0.206332 0.097050 5.381403 0.122332 3.256485 2.261319 0.848067 0.064441 0.102493 0.459041 0.133091 0.561215 0.457430 0.163849 5.260446 0.360946 0.389413 0.033291 0.115301 0.112593 1.559944 0.426508 0.132547 0.498634 0.559069 0.264728 0.693307 0.438856 0.306683 0.109129 18.392863 66.647302 0.400021 4.586081 2.099355 0.411347 0.476350 0.584622 3.634276 0.101797 0.148995 0.089177 0.034710 0.063603 0.755865 20.561407 0.133790 0.154902 
M 1: 0.066142 0.590377 0.069930 9.850951 1.101363 0.150375 0.568586 0.051668 0.127170 0.292429 0.071458 1.218562 0.075144 7.169085 30.139501 13.461692 0.021372 0.045779 4.270235 0.468325 0.013688 0.302287 1.353957 0.028386 0.037750 0.262130 0.016923 0.064289 0.855973 0.079621 0.011169 0.161937 0.276530 0.161053 0.081472 0.036742 0.030342 2.851667 3.932151 8.159169 0.219934 0.421974 2.468752 0.344765 0.210724 1.172204 0.763553 0.082464 0.726566 11.149790 4.782635 0.058046 0.498072 0.258487 0.146882 0.249672 0.560142 0.046719 0.106259 0.003656 0.004200 0.014189 0.009876 0.002656 0.040244 0.267322 0.053740 0.006597 0.027639 0.012745 0.582670 0.005035 0.275844 0.098208 0.445038 1.217010 0.033969 1.988516 0.681161 0.825960 18.762977 11.949233 0.286794 0.534219 4.336817 3.054085 0.129551 4.210126 0.165753 1.088704 1.889645 3.344809 0.111063 2.067758 3.547017 2.466507 0.188236 0.203493 0.281953 0.037250 0.029788 0.008541 0.014768 0.125869 0.056702 0.004186 0.110993 0.201148 0.139705 0.009201 0.012095 0.043812 0.013513 0.002533 0.005848 0.031390 0.021612 0.004854 0.129497 0.976631 0.053397 0.019475 0.004964 0.015539 0.031779 0.064558 0.065585 0.079927 0.095591 0.196886 0.408834 0.126088 0.037226 0.452302 0.016212 7.278994 0.029917 7.918203 0.450964 0.169797 0.104288 1.578530 0.015909 0.094365 16.179952 0.042762 14.799537 1.506485 0.637893 0.123793 0.641351 0.154810 0.140750 3.416059 0.259400 0.009457 0.090576 0.292108 0.297913 0.017172 0.021976 0.032578 1.375871 0.457399 0.598048 4.418398 0.239749 0.168432 2.950318 0.143327 0.328689 0.125011 0.562720 1.414883 0.227807 3.478333 2.984862 0.061299 0.077470 1.050562 13.974326 0.154326 0.224675 0.112000 0.060703 0.123480 5.294490 0.447011 0.033381 0.045528 
M 2: 0.733336 0.558955 0.503360 4.149599 1.415369 1.367574 1.263002 0.994098 0.517204 0.775054 0.763094 1.890137 0.540460 0.200122 4.972745 1.825593 0.450842 0.526135 3.839269 0.597671 0.058964 2.863355 2.872594 0.258365 0.366868 2.578946 0.358350 0.672023 5.349861 0.691594 0.063347 0.032875 0.821562 0.580847 0.661866 0.265730 0.395134 5.581680 1.279881 1.335650 0.397108 1.840061 5.739035 0.284730 0.109781 1.612642 0.466979 0.141582 0.019509 4.670980 1.967383 0.088064 0.581928 0.145401 0.225860 0.434096 2.292917 1.024707 0.821921 0.027824 0.021443 0.088850 0.060820 0.018288 0.042687 1.199607 0.420710 0.037642 0.141233 0.090101 1.043232 0.209978 0.823594 3.039380 1.463390 1.983693 0.397640 2.831098 4.102068 0.059723 5.901348 2.034980 2.600668 5.413080 4.193725 4.534772 0.377181 4.877840 0.370939 1.298542 3.509873 2.646440 0.087872 0.072299 1.139018 0.864479 0.390688 0.322761 0.625409 0.496780 0.532488 0.232460 0.169219 0.755219 0.379926 0.020447 0.023282 0.503875 0.577513 0.109318 0.153776 0.696533 0.398817 0.008940 0.043707 0.436013 0.087640 0.064863 0.036426 1.673207 0.124068 0.218118 0.039217 0.104335 0.349195 0.838324 0.888693 0.488389 1.385133 0.050226 0.962470 0.502294 1.065585 8.351808 0.377304 5.102837 0.561690 7.010411 3.054968 0.039318 0.204155 2.653232 0.564368 0.854294 15.559906 0.401070 8.929538 5.525874 0.067505 0.273372 0.437116 1.927515 0.940458 2.508169 1.357738 0.043394 0.023126 0.567639 1.048288 0.120994 0.180650 0.449074 3.135353 0.012695 0.570771 2.319555 1.856122 0.975427 3.404087 0.015631 0.458799 0.151684 4.154750 11.429924 1.457957 0.233109 0.077004 0.011074 0.026268 0.052132 8.113282 0.377578 0.429221 0.260296 0.222293 0.273138 2.903836 4.731579 0.564762 0.681215 
M 3: 0.658412 0.566269 0.854111 0.884454 1.309554 1.272639 1.874713 0.552007 0.227683 0.581512 0.695190 0.967985 0.344015 0.978992 3.427163 2.333253 0.154701 0.221089 2.088785 0.540749 0.058015 5.851132 2.294145 0.182966 0.684164 3.192521 0.528161 1.128882 3.010922 1.012866 0.227296 0.156635 0.878405 0.802754 0.830884 0.431617 0.456530 3.060574 1.279257 1.438430 0.431464 2.075952 4.840271 0.644656 0.266076 2.084975 0.720060 0.291854 0.028961 4.071574 2.258357 0.073037 1.238426 0.199728 0.160296 0.482619 2.992763 1.296206 0.841829 0.031467 0.048542 0.132774 0.133055 0.056045 0.209188 0.925172 0.360522 0.094591 0.313945 0.118104 0.992259 0.086318 2.149634 5.103188 3.775817 3.954021 0.190734 1.776095 4.495841 0.264277 7.063879 2.221150 3.017954 8.558815 4.310199 2.130054 0.571406 4.137385 0.437589 2.071689 2.498630 1.763546 0.116381 0.296578 1.033710 1.283423 0.312579 0.305772 0.681277 0.507160 0.351381 0.189152 0.217780 0.767361 0.278392 0.092075 0.177263 0.451893 0.653836 0.074620 0.181992 0.752277 0.679853 0.025780 0.082005 0.326441 0.343977 0.195877 0.217424 3.057583 0.377558 0.401252 0.072258 0.241015 0.665865 1.266791 0.680174 0.717301 4.001286 0.362942 1.189259 0.964545 1.350568 12.869737 0.531100 8.904999 0.652629 10.091413 2.671718 0.086367 0.359932 4.797423 0.336801 1.021885 23.029406 0.440178 14.013035 5.069337 0.539010 0.742569 0.780580 1.331875 1.531589 4.414850 1.082703 0.091278 0.172734 0.693405 1.422571 0.068958 0.163829 0.481711 4.643214 0.121821 0.584083 4.216178 1.677263 1.575754 5.046403 0.161015 1.531223 0.599244 5.832025 33.873091 1.914768 1.287474 0.444362 0.076328 0.079916 0.466823 5.231362 0.548763 0.831890 0.382271 0.208791 0.307846 3.717971 5.910440 0.282540 0.964421 


Final LogLikelihood: -133665.264562

AIC score: 271328.529124 / AICc score: 8267328.529124 / BIC score: 278758.867499
Free parameters (model + branch lengths): 1999

WARNING: Number of free parameters (K=1999) is larger than alignment size (n=304).
         This might lead to overfitting and compromise tree inference results!


Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P22897/3_mltree/P22897.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P22897/3_mltree/P22897.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P22897/3_mltree/P22897.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P22897/3_mltree/P22897.raxml.log

Analysis started: 03-Jul-2021 06:01:57 / finished: 03-Jul-2021 16:37:38

Elapsed time: 38141.593 seconds