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 19-Jul-2021 15:48:00 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P19532/2_msa/P19532_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P19532/3_mltree/P19532 --seed 2 --threads 7 --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 (7 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P19532/2_msa/P19532_trimmed_msa.fasta
[00:00:00] Loaded alignment with 903 taxa and 462 sites

WARNING: Sequences sp_Q64705_USF2_MOUSE_10090 and sp_Q63665_USF2_RAT_10116 are exactly identical!
WARNING: Sequences tr_M3YQ82_M3YQ82_MUSPF_9669 and tr_A0A2Y9JDZ6_A0A2Y9JDZ6_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G1QYE3_G1QYE3_NOMLE_61853 and tr_F7FXN6_F7FXN6_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G1QYE3_G1QYE3_NOMLE_61853 and tr_A0A2K5LZY5_A0A2K5LZY5_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G1QYE3_G1QYE3_NOMLE_61853 and tr_A0A2K6CP29_A0A2K6CP29_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I2YS93_A0A2I2YS93_GORGO_9595 and sp_P19532_TFE3_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I2YXN7_A0A2I2YXN7_GORGO_9595 and tr_G7NZ88_G7NZ88_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A2I2YXN7_A0A2I2YXN7_GORGO_9595 and tr_A0A2K5ZRN7_A0A2K5ZRN7_MANLE_9568 are exactly identical!
WARNING: Sequences tr_B8P4X4_B8P4X4_POSPM_561896 and tr_A0A1X6MPE3_A0A1X6MPE3_9APHY_670580 are exactly identical!
WARNING: Sequences tr_A0A2I3SGI9_A0A2I3SGI9_PANTR_9598 and tr_A0A2R9AUX9_A0A2R9AUX9_PANPA_9597 are exactly identical!
WARNING: Sequences sp_Q15853_USF2_HUMAN_9606 and tr_I0FUV2_I0FUV2_MACMU_9544 are exactly identical!
WARNING: Sequences tr_A0A1D5QUV2_A0A1D5QUV2_MACMU_9544 and tr_G7P2I1_G7P2I1_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A1D5QUV2_A0A1D5QUV2_MACMU_9544 and tr_A0A2K6ALQ3_A0A2K6ALQ3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A1D5QWQ4_A0A1D5QWQ4_MACMU_9544 and tr_A0A096P323_A0A096P323_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F6UXQ5_F6UXQ5_MACMU_9544 and tr_A0A2K5MJT8_A0A2K5MJT8_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7E2P9_F7E2P9_MACMU_9544 and tr_G7Q2P5_G7Q2P5_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7E2P9_F7E2P9_MACMU_9544 and tr_A0A0D9RKQ6_A0A0D9RKQ6_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F7E2P9_F7E2P9_MACMU_9544 and tr_A0A2K5LC64_A0A2K5LC64_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7E2P9_F7E2P9_MACMU_9544 and tr_A0A2K6CFN5_A0A2K6CFN5_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7E2P9_F7E2P9_MACMU_9544 and tr_A0A2K5ZD31_A0A2K5ZD31_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F7FA74_F7FA74_CALJA_9483 and tr_A0A2I3M2E5_A0A2I3M2E5_PAPAN_9555 are exactly identical!
WARNING: Sequences sp_A4IFU7_TFEC_BOVIN_9913 and tr_F1ML66_F1ML66_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_A0A337SGF3_A0A337SGF3_FELCA_9685 and tr_A0A2U3X4F1_A0A2U3X4F1_ODORO_9708 are exactly identical!
WARNING: Sequences tr_A0A337SGF3_A0A337SGF3_FELCA_9685 and tr_A0A2Y9L605_A0A2Y9L605_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_V2XHX0_V2XHX0_MONRO_1381753 and tr_A0A0W0FMJ9_A0A0W0FMJ9_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_A0A0A1MH28_A0A0A1MH28_9FUNG_58291 and tr_A0A367KBH5_A0A367KBH5_9FUNG_86630 are exactly identical!
WARNING: Sequences tr_A0A091KDI0_A0A091KDI0_EGRGA_188379 and tr_A0A087RBZ2_A0A087RBZ2_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A2D0PPZ9_A0A2D0PPZ9_ICTPU_7998 and tr_A0A2D0PSM2_A0A2D0PSM2_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2U3V0J3_A0A2U3V0J3_TURTR_9739 and tr_A0A2U3V0J9_A0A2U3V0J9_TURTR_9739 are exactly identical!
WARNING: Sequences tr_A0A2U4CCY7_A0A2U4CCY7_TURTR_9739 and tr_A0A2U4CCZ3_A0A2U4CCZ3_TURTR_9739 are exactly identical!
WARNING: Sequences tr_A0A2Y9NU69_A0A2Y9NU69_DELLE_9749 and tr_A0A2Y9FDH8_A0A2Y9FDH8_PHYCD_9755 are exactly identical!
WARNING: Duplicate sequences found: 31

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/P19532/3_mltree/P19532.raxml.reduced.phy

Alignment comprises 1 partitions and 462 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 462 / 462
Gaps: 34.48 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P19532/3_mltree/P19532.raxml.rba

Parallelization scheme autoconfig: 1 worker(s) x 7 thread(s)

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

[00:00:00] Generating 20 random starting tree(s) with 903 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 66 / 5280
[00:00:00] Data distribution: max. searches per worker: 20

Starting ML tree search with 20 distinct starting trees

[00:00:00 -539090.045975] Initial branch length optimization
[00:00:03 -442856.393088] Model parameter optimization (eps = 10.000000)
[00:00:35 -440869.627015] AUTODETECT spr round 1 (radius: 5)
[00:01:56 -323347.512430] AUTODETECT spr round 2 (radius: 10)
[00:03:24 -240139.581565] AUTODETECT spr round 3 (radius: 15)
[00:05:01 -200582.514144] AUTODETECT spr round 4 (radius: 20)
[00:06:51 -182709.642980] AUTODETECT spr round 5 (radius: 25)
[00:08:51 -180123.972596] SPR radius for FAST iterations: 25 (autodetect)
[00:08:51 -180123.972596] Model parameter optimization (eps = 3.000000)
[00:09:14 -179409.269365] FAST spr round 1 (radius: 25)
[00:11:00 -159448.965085] FAST spr round 2 (radius: 25)
[00:12:22 -158658.498561] FAST spr round 3 (radius: 25)
[00:13:38 -158588.732755] FAST spr round 4 (radius: 25)
[00:14:50 -158568.796000] FAST spr round 5 (radius: 25)
[00:15:59 -158559.280743] FAST spr round 6 (radius: 25)
[00:17:05 -158559.279844] Model parameter optimization (eps = 1.000000)
[00:17:17 -158552.829032] SLOW spr round 1 (radius: 5)
[00:18:47 -158532.320086] SLOW spr round 2 (radius: 5)
[00:20:14 -158525.155043] SLOW spr round 3 (radius: 5)
[00:21:39 -158522.715336] SLOW spr round 4 (radius: 5)
[00:23:03 -158516.917713] SLOW spr round 5 (radius: 5)
[00:24:26 -158516.917585] SLOW spr round 6 (radius: 10)
[00:25:50 -158516.098921] SLOW spr round 7 (radius: 5)
[00:27:32 -158510.100856] SLOW spr round 8 (radius: 5)
[00:29:03 -158510.100814] SLOW spr round 9 (radius: 10)
[00:30:32 -158510.100772] SLOW spr round 10 (radius: 15)
[00:32:44 -158509.761593] SLOW spr round 11 (radius: 5)
[00:34:28 -158509.761079] SLOW spr round 12 (radius: 10)
[00:36:09 -158509.761005] SLOW spr round 13 (radius: 15)
[00:38:15 -158509.760960] SLOW spr round 14 (radius: 20)
[00:41:43 -158509.760918] SLOW spr round 15 (radius: 25)
[00:46:12 -158509.760877] Model parameter optimization (eps = 0.100000)

[00:46:22] ML tree search #1, logLikelihood: -158508.469780

[00:46:22 -539959.550954] Initial branch length optimization
[00:46:25 -442043.653135] Model parameter optimization (eps = 10.000000)
[00:46:49 -440166.983631] AUTODETECT spr round 1 (radius: 5)
[00:48:10 -318923.550676] AUTODETECT spr round 2 (radius: 10)
[00:49:38 -234869.015670] AUTODETECT spr round 3 (radius: 15)
[00:51:17 -193077.303580] AUTODETECT spr round 4 (radius: 20)
[00:53:13 -178218.698186] AUTODETECT spr round 5 (radius: 25)
[00:55:32 -175107.823655] SPR radius for FAST iterations: 25 (autodetect)
[00:55:32 -175107.823655] Model parameter optimization (eps = 3.000000)
[00:55:54 -174540.171793] FAST spr round 1 (radius: 25)
[00:57:45 -159370.373397] FAST spr round 2 (radius: 25)
[00:59:14 -158665.935685] FAST spr round 3 (radius: 25)
[01:00:35 -158605.765555] FAST spr round 4 (radius: 25)
[01:01:46 -158604.690360] FAST spr round 5 (radius: 25)
[01:02:55 -158600.221550] FAST spr round 6 (radius: 25)
[01:04:02 -158600.220947] Model parameter optimization (eps = 1.000000)
[01:04:12 -158596.572885] SLOW spr round 1 (radius: 5)
[01:05:43 -158553.360208] SLOW spr round 2 (radius: 5)
[01:07:10 -158550.349071] SLOW spr round 3 (radius: 5)
[01:08:34 -158550.348407] SLOW spr round 4 (radius: 10)
[01:10:00 -158548.936139] SLOW spr round 5 (radius: 5)
[01:11:40 -158548.935842] SLOW spr round 6 (radius: 10)
[01:13:16 -158548.935774] SLOW spr round 7 (radius: 15)
[01:15:28 -158548.383597] SLOW spr round 8 (radius: 5)
[01:17:13 -158548.383531] SLOW spr round 9 (radius: 10)
[01:18:56 -158548.383492] SLOW spr round 10 (radius: 15)
[01:21:06 -158548.383455] SLOW spr round 11 (radius: 20)
[01:24:55 -158548.383419] SLOW spr round 12 (radius: 25)
[01:29:59 -158548.383384] Model parameter optimization (eps = 0.100000)

[01:30:04] ML tree search #2, logLikelihood: -158548.291023

[01:30:04 -540260.492642] Initial branch length optimization
[01:30:07 -441375.750291] Model parameter optimization (eps = 10.000000)
[01:30:31 -439411.575096] AUTODETECT spr round 1 (radius: 5)
[01:31:52 -320956.863393] AUTODETECT spr round 2 (radius: 10)
[01:33:22 -243027.333658] AUTODETECT spr round 3 (radius: 15)
[01:35:04 -199668.221798] AUTODETECT spr round 4 (radius: 20)
[01:37:11 -182718.074604] AUTODETECT spr round 5 (radius: 25)
[01:39:32 -181258.255411] SPR radius for FAST iterations: 25 (autodetect)
[01:39:32 -181258.255411] Model parameter optimization (eps = 3.000000)
[01:39:53 -180718.643257] FAST spr round 1 (radius: 25)
[01:41:45 -159771.393552] FAST spr round 2 (radius: 25)
[01:43:12 -158769.807351] FAST spr round 3 (radius: 25)
[01:44:27 -158683.727248] FAST spr round 4 (radius: 25)
[01:45:38 -158672.717620] FAST spr round 5 (radius: 25)
[01:46:46 -158671.051154] FAST spr round 6 (radius: 25)
[01:47:53 -158671.050549] Model parameter optimization (eps = 1.000000)
[01:48:10 -158609.793252] SLOW spr round 1 (radius: 5)
[01:49:39 -158556.201116] SLOW spr round 2 (radius: 5)
[01:51:07 -158549.630637] SLOW spr round 3 (radius: 5)
[01:52:32 -158540.595071] SLOW spr round 4 (radius: 5)
[01:53:57 -158540.408067] SLOW spr round 5 (radius: 5)
[01:55:20 -158540.407931] SLOW spr round 6 (radius: 10)
[01:56:45 -158538.143416] SLOW spr round 7 (radius: 5)
[01:58:29 -158532.690233] SLOW spr round 8 (radius: 5)
[02:00:02 -158531.738053] SLOW spr round 9 (radius: 5)
[02:01:29 -158531.737388] SLOW spr round 10 (radius: 10)
[02:02:55 -158528.586640] SLOW spr round 11 (radius: 5)
[02:04:37 -158525.394284] SLOW spr round 12 (radius: 5)
[02:06:09 -158525.393233] SLOW spr round 13 (radius: 10)
[02:07:36 -158525.393009] SLOW spr round 14 (radius: 15)
[02:09:52 -158525.111180] SLOW spr round 15 (radius: 5)
[02:11:39 -158518.362870] SLOW spr round 16 (radius: 5)
[02:13:14 -158514.286175] SLOW spr round 17 (radius: 5)
[02:14:42 -158514.286141] SLOW spr round 18 (radius: 10)
[02:16:09 -158514.165174] SLOW spr round 19 (radius: 5)
[02:17:49 -158514.165140] SLOW spr round 20 (radius: 10)
[02:19:24 -158514.165106] SLOW spr round 21 (radius: 15)
[02:21:34 -158514.165072] SLOW spr round 22 (radius: 20)
[02:25:16 -158514.165038] SLOW spr round 23 (radius: 25)
[02:30:07 -158514.165004] Model parameter optimization (eps = 0.100000)

[02:30:15] ML tree search #3, logLikelihood: -158513.500966

[02:30:15 -540755.335902] Initial branch length optimization
[02:30:18 -442618.123979] Model parameter optimization (eps = 10.000000)
[02:30:46 -440911.881247] AUTODETECT spr round 1 (radius: 5)
[02:32:09 -318937.463117] AUTODETECT spr round 2 (radius: 10)
[02:33:38 -236685.596454] AUTODETECT spr round 3 (radius: 15)
[02:35:17 -205222.358255] AUTODETECT spr round 4 (radius: 20)
[02:37:07 -191879.685036] AUTODETECT spr round 5 (radius: 25)
[02:39:19 -181626.839485] SPR radius for FAST iterations: 25 (autodetect)
[02:39:19 -181626.839485] Model parameter optimization (eps = 3.000000)
[02:39:40 -181172.261264] FAST spr round 1 (radius: 25)
[02:41:28 -159615.643395] FAST spr round 2 (radius: 25)
[02:42:56 -158651.208583] FAST spr round 3 (radius: 25)
[02:44:15 -158587.986652] FAST spr round 4 (radius: 25)
[02:45:26 -158575.406686] FAST spr round 5 (radius: 25)
[02:46:35 -158574.957002] FAST spr round 6 (radius: 25)
[02:47:43 -158574.956895] Model parameter optimization (eps = 1.000000)
[02:47:59 -158547.157668] SLOW spr round 1 (radius: 5)
[02:49:29 -158502.217657] SLOW spr round 2 (radius: 5)
[02:50:56 -158497.156718] SLOW spr round 3 (radius: 5)
[02:52:21 -158497.155475] SLOW spr round 4 (radius: 10)
[02:53:46 -158489.879979] SLOW spr round 5 (radius: 5)
[02:55:28 -158489.879609] SLOW spr round 6 (radius: 10)
[02:57:03 -158489.879370] SLOW spr round 7 (radius: 15)
[02:59:11 -158489.879201] SLOW spr round 8 (radius: 20)
[03:02:42 -158489.879072] SLOW spr round 9 (radius: 25)
[03:07:21 -158489.878966] Model parameter optimization (eps = 0.100000)

[03:07:26] ML tree search #4, logLikelihood: -158489.653402

[03:07:27 -538345.277791] Initial branch length optimization
[03:07:29 -442838.306279] Model parameter optimization (eps = 10.000000)
[03:07:54 -440863.773905] AUTODETECT spr round 1 (radius: 5)
[03:09:16 -325007.960852] AUTODETECT spr round 2 (radius: 10)
[03:10:45 -240485.855265] AUTODETECT spr round 3 (radius: 15)
[03:12:24 -201487.823935] AUTODETECT spr round 4 (radius: 20)
[03:14:13 -186131.262778] AUTODETECT spr round 5 (radius: 25)
[03:16:21 -180654.436662] SPR radius for FAST iterations: 25 (autodetect)
[03:16:21 -180654.436662] Model parameter optimization (eps = 3.000000)
[03:16:42 -180022.823370] FAST spr round 1 (radius: 25)
[03:18:35 -159589.277625] FAST spr round 2 (radius: 25)
[03:20:06 -158648.290249] FAST spr round 3 (radius: 25)
[03:21:24 -158565.000051] FAST spr round 4 (radius: 25)
[03:22:37 -158560.699873] FAST spr round 5 (radius: 25)
[03:23:46 -158560.439324] FAST spr round 6 (radius: 25)
[03:24:53 -158560.439241] Model parameter optimization (eps = 1.000000)
[03:24:59 -158559.541572] SLOW spr round 1 (radius: 5)
[03:26:30 -158513.407566] SLOW spr round 2 (radius: 5)
[03:27:57 -158512.707803] SLOW spr round 3 (radius: 5)
[03:29:20 -158512.707723] SLOW spr round 4 (radius: 10)
[03:30:46 -158511.292465] SLOW spr round 5 (radius: 5)
[03:32:30 -158505.522704] SLOW spr round 6 (radius: 5)
[03:34:05 -158499.246448] SLOW spr round 7 (radius: 5)
[03:35:33 -158496.983277] SLOW spr round 8 (radius: 5)
[03:36:58 -158496.983132] SLOW spr round 9 (radius: 10)
[03:38:22 -158496.983126] SLOW spr round 10 (radius: 15)
[03:40:35 -158496.776080] SLOW spr round 11 (radius: 5)
[03:42:20 -158496.775054] SLOW spr round 12 (radius: 10)
[03:44:01 -158496.775039] SLOW spr round 13 (radius: 15)
[03:46:03 -158496.775039] SLOW spr round 14 (radius: 20)
[03:49:33 -158496.775038] SLOW spr round 15 (radius: 25)
[03:54:15 -158496.775038] Model parameter optimization (eps = 0.100000)

[03:54:24] ML tree search #5, logLikelihood: -158496.427630

[03:54:24 -539341.173003] Initial branch length optimization
[03:54:26 -443172.864071] Model parameter optimization (eps = 10.000000)
[03:54:58 -441286.855707] AUTODETECT spr round 1 (radius: 5)
[03:56:20 -323986.475047] AUTODETECT spr round 2 (radius: 10)
[03:57:50 -241107.909220] AUTODETECT spr round 3 (radius: 15)
[03:59:31 -207706.207968] AUTODETECT spr round 4 (radius: 20)
[04:01:26 -185912.140986] AUTODETECT spr round 5 (radius: 25)
[04:03:41 -180783.689322] SPR radius for FAST iterations: 25 (autodetect)
[04:03:41 -180783.689322] Model parameter optimization (eps = 3.000000)
[04:04:05 -180082.887614] FAST spr round 1 (radius: 25)
[04:05:52 -159440.545975] FAST spr round 2 (radius: 25)
[04:07:17 -158654.016105] FAST spr round 3 (radius: 25)
[04:08:35 -158611.679632] FAST spr round 4 (radius: 25)
[04:09:48 -158593.002369] FAST spr round 5 (radius: 25)
[04:10:58 -158591.138258] FAST spr round 6 (radius: 25)
[04:12:06 -158590.420379] FAST spr round 7 (radius: 25)
[04:13:13 -158590.419384] Model parameter optimization (eps = 1.000000)
[04:13:26 -158582.496648] SLOW spr round 1 (radius: 5)
[04:14:57 -158548.212058] SLOW spr round 2 (radius: 5)
[04:16:24 -158535.322095] SLOW spr round 3 (radius: 5)
[04:17:49 -158534.029994] SLOW spr round 4 (radius: 5)
[04:19:13 -158534.029801] SLOW spr round 5 (radius: 10)
[04:20:39 -158524.377305] SLOW spr round 6 (radius: 5)
[04:22:22 -158523.621461] SLOW spr round 7 (radius: 5)
[04:23:54 -158522.989543] SLOW spr round 8 (radius: 5)
[04:25:23 -158522.989376] SLOW spr round 9 (radius: 10)
[04:26:50 -158515.679015] SLOW spr round 10 (radius: 5)
[04:28:32 -158515.345792] SLOW spr round 11 (radius: 5)
[04:30:04 -158515.345343] SLOW spr round 12 (radius: 10)
[04:31:32 -158515.345294] SLOW spr round 13 (radius: 15)
[04:33:46 -158514.743185] SLOW spr round 14 (radius: 5)
[04:35:34 -158514.743151] SLOW spr round 15 (radius: 10)
[04:37:16 -158514.743117] SLOW spr round 16 (radius: 15)
[04:39:22 -158514.743084] SLOW spr round 17 (radius: 20)
[04:43:10 -158514.743051] SLOW spr round 18 (radius: 25)
[04:48:13 -158514.743018] Model parameter optimization (eps = 0.100000)

[04:48:19] ML tree search #6, logLikelihood: -158514.562847

[04:48:19 -538997.746374] Initial branch length optimization
[04:48:22 -441727.085733] Model parameter optimization (eps = 10.000000)
[04:48:51 -439769.524101] AUTODETECT spr round 1 (radius: 5)
[04:50:11 -317327.472041] AUTODETECT spr round 2 (radius: 10)
[04:51:40 -238058.472095] AUTODETECT spr round 3 (radius: 15)
[04:53:22 -199941.957894] AUTODETECT spr round 4 (radius: 20)
[04:55:04 -188182.622702] AUTODETECT spr round 5 (radius: 25)
[04:57:08 -182260.474500] SPR radius for FAST iterations: 25 (autodetect)
[04:57:08 -182260.474500] Model parameter optimization (eps = 3.000000)
[04:57:28 -181522.897653] FAST spr round 1 (radius: 25)
[04:59:19 -159570.033189] FAST spr round 2 (radius: 25)
[05:00:48 -158661.783075] FAST spr round 3 (radius: 25)
[05:02:08 -158596.650265] FAST spr round 4 (radius: 25)
[05:03:20 -158590.458705] FAST spr round 5 (radius: 25)
[05:04:30 -158576.530583] FAST spr round 6 (radius: 25)
[05:05:36 -158576.530307] Model parameter optimization (eps = 1.000000)
[05:05:45 -158575.598859] SLOW spr round 1 (radius: 5)
[05:07:19 -158535.045444] SLOW spr round 2 (radius: 5)
[05:08:48 -158527.607522] SLOW spr round 3 (radius: 5)
[05:10:13 -158526.050401] SLOW spr round 4 (radius: 5)
[05:11:36 -158526.048892] SLOW spr round 5 (radius: 10)
[05:13:00 -158518.778760] SLOW spr round 6 (radius: 5)
[05:14:40 -158518.778716] SLOW spr round 7 (radius: 10)
[05:16:15 -158518.778680] SLOW spr round 8 (radius: 15)
[05:18:23 -158518.580635] SLOW spr round 9 (radius: 5)
[05:20:07 -158518.580169] SLOW spr round 10 (radius: 10)
[05:21:48 -158518.580133] SLOW spr round 11 (radius: 15)
[05:23:55 -158518.580098] SLOW spr round 12 (radius: 20)
[05:27:23 -158518.580064] SLOW spr round 13 (radius: 25)
[05:31:55 -158518.580030] Model parameter optimization (eps = 0.100000)

[05:32:00] ML tree search #7, logLikelihood: -158518.501289

[05:32:00 -537308.073717] Initial branch length optimization
[05:32:03 -441668.041521] Model parameter optimization (eps = 10.000000)
[05:32:42 -439401.884645] AUTODETECT spr round 1 (radius: 5)
[05:34:05 -315415.489512] AUTODETECT spr round 2 (radius: 10)
[05:35:37 -238113.917565] AUTODETECT spr round 3 (radius: 15)
[05:37:18 -200684.022212] AUTODETECT spr round 4 (radius: 20)
[05:39:02 -180612.254950] AUTODETECT spr round 5 (radius: 25)
[05:40:59 -178241.541682] SPR radius for FAST iterations: 25 (autodetect)
[05:40:59 -178241.541682] Model parameter optimization (eps = 3.000000)
[05:41:21 -177765.614347] FAST spr round 1 (radius: 25)
[05:43:13 -160272.797001] FAST spr round 2 (radius: 25)
[05:44:46 -158814.954698] FAST spr round 3 (radius: 25)
[05:46:08 -158614.920917] FAST spr round 4 (radius: 25)
[05:47:24 -158597.768056] FAST spr round 5 (radius: 25)
[05:48:34 -158595.976563] FAST spr round 6 (radius: 25)
[05:49:40 -158595.950093] Model parameter optimization (eps = 1.000000)
[05:49:58 -158566.291945] SLOW spr round 1 (radius: 5)
[05:51:31 -158516.835894] SLOW spr round 2 (radius: 5)
[05:53:00 -158513.421674] SLOW spr round 3 (radius: 5)
[05:54:24 -158511.807943] SLOW spr round 4 (radius: 5)
[05:55:48 -158510.810922] SLOW spr round 5 (radius: 5)
[05:57:12 -158510.808280] SLOW spr round 6 (radius: 10)
[05:58:38 -158507.261160] SLOW spr round 7 (radius: 5)
[06:00:19 -158505.231280] SLOW spr round 8 (radius: 5)
[06:01:51 -158504.987710] SLOW spr round 9 (radius: 5)
[06:03:20 -158502.480589] SLOW spr round 10 (radius: 5)
[06:04:45 -158501.164316] SLOW spr round 11 (radius: 5)
[06:06:12 -158499.194301] SLOW spr round 12 (radius: 5)
[06:07:35 -158499.193856] SLOW spr round 13 (radius: 10)
[06:09:01 -158499.193814] SLOW spr round 14 (radius: 15)
[06:11:18 -158499.193784] SLOW spr round 15 (radius: 20)
[06:14:41 -158499.193758] SLOW spr round 16 (radius: 25)
[06:19:23 -158499.193734] Model parameter optimization (eps = 0.100000)

[06:19:31] ML tree search #8, logLikelihood: -158498.972545

[06:19:31 -535783.134872] Initial branch length optimization
[06:19:33 -439574.027401] Model parameter optimization (eps = 10.000000)
[06:19:57 -437566.491457] AUTODETECT spr round 1 (radius: 5)
[06:21:19 -311992.294159] AUTODETECT spr round 2 (radius: 10)
[06:22:50 -239702.257516] AUTODETECT spr round 3 (radius: 15)
[06:24:28 -206932.242457] AUTODETECT spr round 4 (radius: 20)
[06:26:18 -185823.276608] AUTODETECT spr round 5 (radius: 25)
[06:28:22 -180422.087000] SPR radius for FAST iterations: 25 (autodetect)
[06:28:22 -180422.087000] Model parameter optimization (eps = 3.000000)
[06:28:40 -179921.001060] FAST spr round 1 (radius: 25)
[06:30:34 -159484.222388] FAST spr round 2 (radius: 25)
[06:32:03 -158735.091956] FAST spr round 3 (radius: 25)
[06:33:25 -158659.961141] FAST spr round 4 (radius: 25)
[06:34:39 -158640.406776] FAST spr round 5 (radius: 25)
[06:35:47 -158639.104237] FAST spr round 6 (radius: 25)
[06:36:54 -158639.103755] Model parameter optimization (eps = 1.000000)
[06:37:12 -158584.151889] SLOW spr round 1 (radius: 5)
[06:38:42 -158531.306174] SLOW spr round 2 (radius: 5)
[06:40:11 -158525.248112] SLOW spr round 3 (radius: 5)
[06:41:35 -158525.247994] SLOW spr round 4 (radius: 10)
[06:43:02 -158517.996968] SLOW spr round 5 (radius: 5)
[06:44:46 -158513.063285] SLOW spr round 6 (radius: 5)
[06:46:18 -158513.062800] SLOW spr round 7 (radius: 10)
[06:47:47 -158506.360685] SLOW spr round 8 (radius: 5)
[06:49:27 -158506.360624] SLOW spr round 9 (radius: 10)
[06:51:02 -158506.360588] SLOW spr round 10 (radius: 15)
[06:53:07 -158506.360554] SLOW spr round 11 (radius: 20)
[06:56:34 -158506.360519] SLOW spr round 12 (radius: 25)
[07:01:01 -158506.360485] Model parameter optimization (eps = 0.100000)

[07:01:13] ML tree search #9, logLikelihood: -158505.364562

[07:01:13 -536578.957580] Initial branch length optimization
[07:01:15 -440695.562661] Model parameter optimization (eps = 10.000000)
[07:01:48 -438745.289656] AUTODETECT spr round 1 (radius: 5)
[07:03:10 -317869.035365] AUTODETECT spr round 2 (radius: 10)
[07:04:40 -236573.329636] AUTODETECT spr round 3 (radius: 15)
[07:06:22 -198822.883769] AUTODETECT spr round 4 (radius: 20)
[07:08:22 -180386.235743] AUTODETECT spr round 5 (radius: 25)
[07:10:31 -179298.363195] SPR radius for FAST iterations: 25 (autodetect)
[07:10:31 -179298.363195] Model parameter optimization (eps = 3.000000)
[07:10:55 -178713.636091] FAST spr round 1 (radius: 25)
[07:12:46 -159429.121968] FAST spr round 2 (radius: 25)
[07:14:14 -158629.879280] FAST spr round 3 (radius: 25)
[07:15:31 -158588.469073] FAST spr round 4 (radius: 25)
[07:16:44 -158576.610550] FAST spr round 5 (radius: 25)
[07:17:52 -158576.096625] FAST spr round 6 (radius: 25)
[07:18:59 -158576.096032] Model parameter optimization (eps = 1.000000)
[07:19:12 -158568.421899] SLOW spr round 1 (radius: 5)
[07:20:43 -158536.236890] SLOW spr round 2 (radius: 5)
[07:22:10 -158533.143774] SLOW spr round 3 (radius: 5)
[07:23:34 -158525.866348] SLOW spr round 4 (radius: 5)
[07:24:58 -158525.863517] SLOW spr round 5 (radius: 10)
[07:26:23 -158515.805854] SLOW spr round 6 (radius: 5)
[07:28:09 -158510.388777] SLOW spr round 7 (radius: 5)
[07:29:41 -158510.070117] SLOW spr round 8 (radius: 5)
[07:31:09 -158509.171965] SLOW spr round 9 (radius: 5)
[07:32:34 -158509.171942] SLOW spr round 10 (radius: 10)
[07:33:58 -158509.171941] SLOW spr round 11 (radius: 15)
[07:36:14 -158509.171941] SLOW spr round 12 (radius: 20)
[07:39:43 -158509.171941] SLOW spr round 13 (radius: 25)
[07:44:29 -158509.171941] Model parameter optimization (eps = 0.100000)

[07:44:35] ML tree search #10, logLikelihood: -158509.064563

[07:44:35 -536262.279410] Initial branch length optimization
[07:44:38 -437849.461269] Model parameter optimization (eps = 10.000000)
[07:44:57 -436009.217815] AUTODETECT spr round 1 (radius: 5)
[07:46:18 -324876.360182] AUTODETECT spr round 2 (radius: 10)
[07:47:48 -233779.728506] AUTODETECT spr round 3 (radius: 15)
[07:49:25 -196815.888068] AUTODETECT spr round 4 (radius: 20)
[07:51:13 -182884.155551] AUTODETECT spr round 5 (radius: 25)
[07:53:26 -179224.671812] SPR radius for FAST iterations: 25 (autodetect)
[07:53:26 -179224.671812] Model parameter optimization (eps = 3.000000)
[07:53:52 -178581.516859] FAST spr round 1 (radius: 25)
[07:55:40 -159422.691531] FAST spr round 2 (radius: 25)
[07:57:05 -158655.361088] FAST spr round 3 (radius: 25)
[07:58:21 -158616.507112] FAST spr round 4 (radius: 25)
[07:59:33 -158595.875904] FAST spr round 5 (radius: 25)
[08:00:41 -158590.096762] FAST spr round 6 (radius: 25)
[08:01:48 -158589.356689] FAST spr round 7 (radius: 25)
[08:02:54 -158589.356433] Model parameter optimization (eps = 1.000000)
[08:03:07 -158573.546848] SLOW spr round 1 (radius: 5)
[08:04:41 -158528.642122] SLOW spr round 2 (radius: 5)
[08:06:09 -158514.729564] SLOW spr round 3 (radius: 5)
[08:07:34 -158514.019494] SLOW spr round 4 (radius: 5)
[08:08:58 -158514.018000] SLOW spr round 5 (radius: 10)
[08:10:24 -158498.717461] SLOW spr round 6 (radius: 5)
[08:12:05 -158496.413702] SLOW spr round 7 (radius: 5)
[08:13:37 -158495.691070] SLOW spr round 8 (radius: 5)
[08:15:03 -158495.690231] SLOW spr round 9 (radius: 10)
[08:16:29 -158495.689468] SLOW spr round 10 (radius: 15)
[08:18:42 -158495.687854] SLOW spr round 11 (radius: 20)
[08:22:09 -158495.687799] SLOW spr round 12 (radius: 25)
[08:26:46 -158495.687746] Model parameter optimization (eps = 0.100000)

[08:26:52] ML tree search #11, logLikelihood: -158495.499883

[08:26:52 -541870.559665] Initial branch length optimization
[08:26:55 -442080.326754] Model parameter optimization (eps = 10.000000)
[08:27:20 -440134.409062] AUTODETECT spr round 1 (radius: 5)
[08:28:42 -320603.686442] AUTODETECT spr round 2 (radius: 10)
[08:30:11 -230011.105129] AUTODETECT spr round 3 (radius: 15)
[08:31:58 -195104.591796] AUTODETECT spr round 4 (radius: 20)
[08:34:05 -179266.578530] AUTODETECT spr round 5 (radius: 25)
[08:36:32 -176272.332280] SPR radius for FAST iterations: 25 (autodetect)
[08:36:32 -176272.332280] Model parameter optimization (eps = 3.000000)
[08:36:56 -175658.605571] FAST spr round 1 (radius: 25)
[08:38:54 -159495.912253] FAST spr round 2 (radius: 25)
[08:40:27 -158630.161944] FAST spr round 3 (radius: 25)
[08:41:49 -158588.798972] FAST spr round 4 (radius: 25)
[08:43:03 -158576.520289] FAST spr round 5 (radius: 25)
[08:44:13 -158574.018542] FAST spr round 6 (radius: 25)
[08:45:21 -158574.015973] Model parameter optimization (eps = 1.000000)
[08:45:32 -158572.611920] SLOW spr round 1 (radius: 5)
[08:47:04 -158531.492875] SLOW spr round 2 (radius: 5)
[08:48:33 -158524.891196] SLOW spr round 3 (radius: 5)
[08:50:00 -158522.698431] SLOW spr round 4 (radius: 5)
[08:51:28 -158522.093080] SLOW spr round 5 (radius: 5)
[08:52:53 -158521.855101] SLOW spr round 6 (radius: 5)
[08:54:19 -158521.671179] SLOW spr round 7 (radius: 5)
[08:55:44 -158521.669781] SLOW spr round 8 (radius: 10)
[08:57:12 -158513.694926] SLOW spr round 9 (radius: 5)
[08:58:59 -158509.401110] SLOW spr round 10 (radius: 5)
[09:00:32 -158509.007460] SLOW spr round 11 (radius: 5)
[09:02:01 -158509.006241] SLOW spr round 12 (radius: 10)
[09:03:29 -158509.006092] SLOW spr round 13 (radius: 15)
[09:05:48 -158509.006046] SLOW spr round 14 (radius: 20)
[09:09:25 -158509.006010] SLOW spr round 15 (radius: 25)
[09:14:28 -158509.005976] Model parameter optimization (eps = 0.100000)

[09:14:34] ML tree search #12, logLikelihood: -158508.844960

[09:14:34 -543183.228783] Initial branch length optimization
[09:14:37 -443391.420393] Model parameter optimization (eps = 10.000000)
[09:15:04 -441468.086368] AUTODETECT spr round 1 (radius: 5)
[09:16:26 -325636.053261] AUTODETECT spr round 2 (radius: 10)
[09:17:58 -239171.422271] AUTODETECT spr round 3 (radius: 15)
[09:19:37 -199529.627974] AUTODETECT spr round 4 (radius: 20)
[09:21:28 -181492.465370] AUTODETECT spr round 5 (radius: 25)
[09:23:34 -179781.493331] SPR radius for FAST iterations: 25 (autodetect)
[09:23:34 -179781.493331] Model parameter optimization (eps = 3.000000)
[09:24:02 -179224.845046] FAST spr round 1 (radius: 25)
[09:25:56 -159503.096166] FAST spr round 2 (radius: 25)
[09:27:26 -158621.314182] FAST spr round 3 (radius: 25)
[09:28:47 -158570.198596] FAST spr round 4 (radius: 25)
[09:29:59 -158563.974201] FAST spr round 5 (radius: 25)
[09:31:06 -158563.971738] Model parameter optimization (eps = 1.000000)
[09:31:15 -158562.005204] SLOW spr round 1 (radius: 5)
[09:32:46 -158532.695330] SLOW spr round 2 (radius: 5)
[09:34:14 -158525.027401] SLOW spr round 3 (radius: 5)
[09:35:39 -158525.026392] SLOW spr round 4 (radius: 10)
[09:37:03 -158523.880062] SLOW spr round 5 (radius: 5)
[09:38:45 -158523.371870] SLOW spr round 6 (radius: 5)
[09:40:16 -158523.103691] SLOW spr round 7 (radius: 5)
[09:41:43 -158523.103578] SLOW spr round 8 (radius: 10)
[09:43:09 -158521.013180] SLOW spr round 9 (radius: 5)
[09:44:50 -158518.783048] SLOW spr round 10 (radius: 5)
[09:46:21 -158518.781008] SLOW spr round 11 (radius: 10)
[09:47:48 -158518.780904] SLOW spr round 12 (radius: 15)
[09:50:00 -158518.131698] SLOW spr round 13 (radius: 5)
[09:51:44 -158518.131634] SLOW spr round 14 (radius: 10)
[09:53:24 -158518.131632] SLOW spr round 15 (radius: 15)
[09:55:29 -158517.416893] SLOW spr round 16 (radius: 5)
[09:57:16 -158513.563664] SLOW spr round 17 (radius: 5)
[09:58:50 -158513.561415] SLOW spr round 18 (radius: 10)
[10:00:20 -158513.561386] SLOW spr round 19 (radius: 15)
[10:02:29 -158513.561384] SLOW spr round 20 (radius: 20)
[10:05:54 -158513.561383] SLOW spr round 21 (radius: 25)
[10:10:25 -158513.561383] Model parameter optimization (eps = 0.100000)

[10:10:33] ML tree search #13, logLikelihood: -158513.359330

[10:10:33 -541221.418936] Initial branch length optimization
[10:10:37 -441104.613059] Model parameter optimization (eps = 10.000000)
[10:11:14 -439097.451206] AUTODETECT spr round 1 (radius: 5)
[10:12:35 -327119.992430] AUTODETECT spr round 2 (radius: 10)
[10:14:04 -240202.772948] AUTODETECT spr round 3 (radius: 15)
[10:15:40 -200693.869478] AUTODETECT spr round 4 (radius: 20)
[10:17:27 -188035.682065] AUTODETECT spr round 5 (radius: 25)
[10:19:30 -180609.499741] SPR radius for FAST iterations: 25 (autodetect)
[10:19:30 -180609.499741] Model parameter optimization (eps = 3.000000)
[10:19:52 -179997.122797] FAST spr round 1 (radius: 25)
[10:21:47 -159465.281601] FAST spr round 2 (radius: 25)
[10:23:18 -158664.692485] FAST spr round 3 (radius: 25)
[10:24:36 -158604.738121] FAST spr round 4 (radius: 25)
[10:25:47 -158597.650444] FAST spr round 5 (radius: 25)
[10:26:55 -158597.649328] Model parameter optimization (eps = 1.000000)
[10:27:09 -158585.748605] SLOW spr round 1 (radius: 5)
[10:28:41 -158556.236608] SLOW spr round 2 (radius: 5)
[10:30:09 -158550.806364] SLOW spr round 3 (radius: 5)
[10:31:34 -158550.696058] SLOW spr round 4 (radius: 5)
[10:32:57 -158550.694619] SLOW spr round 5 (radius: 10)
[10:34:26 -158538.022014] SLOW spr round 6 (radius: 5)
[10:36:09 -158536.147137] SLOW spr round 7 (radius: 5)
[10:37:40 -158536.146512] SLOW spr round 8 (radius: 10)
[10:39:09 -158536.146462] SLOW spr round 9 (radius: 15)
[10:41:24 -158535.464577] SLOW spr round 10 (radius: 5)
[10:43:10 -158535.464497] SLOW spr round 11 (radius: 10)
[10:44:52 -158535.464460] SLOW spr round 12 (radius: 15)
[10:47:02 -158535.464427] SLOW spr round 13 (radius: 20)
[10:51:01 -158535.464393] SLOW spr round 14 (radius: 25)
[10:56:07 -158535.464360] Model parameter optimization (eps = 0.100000)

[10:56:14] ML tree search #14, logLikelihood: -158535.351610

[10:56:14 -543382.613416] Initial branch length optimization
[10:56:18 -443686.282112] Model parameter optimization (eps = 10.000000)
[10:57:00 -441606.343206] AUTODETECT spr round 1 (radius: 5)
[10:58:22 -321276.850770] AUTODETECT spr round 2 (radius: 10)
[10:59:51 -240347.475361] AUTODETECT spr round 3 (radius: 15)
[11:01:25 -204049.528451] AUTODETECT spr round 4 (radius: 20)
[11:03:28 -189895.631174] AUTODETECT spr round 5 (radius: 25)
[11:05:40 -187642.278025] SPR radius for FAST iterations: 25 (autodetect)
[11:05:40 -187642.278025] Model parameter optimization (eps = 3.000000)
[11:06:01 -186781.397857] FAST spr round 1 (radius: 25)
[11:07:56 -160223.808640] FAST spr round 2 (radius: 25)
[11:09:28 -158757.014338] FAST spr round 3 (radius: 25)
[11:10:49 -158678.186910] FAST spr round 4 (radius: 25)
[11:12:02 -158662.926003] FAST spr round 5 (radius: 25)
[11:13:10 -158662.294565] FAST spr round 6 (radius: 25)
[11:14:17 -158662.293833] Model parameter optimization (eps = 1.000000)
[11:14:35 -158600.501481] SLOW spr round 1 (radius: 5)
[11:16:08 -158529.084230] SLOW spr round 2 (radius: 5)
[11:17:37 -158524.092791] SLOW spr round 3 (radius: 5)
[11:19:01 -158524.092573] SLOW spr round 4 (radius: 10)
[11:20:26 -158520.568451] SLOW spr round 5 (radius: 5)
[11:22:08 -158520.143224] SLOW spr round 6 (radius: 5)
[11:23:40 -158519.414642] SLOW spr round 7 (radius: 5)
[11:25:07 -158519.414443] SLOW spr round 8 (radius: 10)
[11:26:36 -158511.349878] SLOW spr round 9 (radius: 5)
[11:28:17 -158511.078790] SLOW spr round 10 (radius: 5)
[11:29:48 -158511.078422] SLOW spr round 11 (radius: 10)
[11:31:16 -158511.078392] SLOW spr round 12 (radius: 15)
[11:33:28 -158511.078133] SLOW spr round 13 (radius: 20)
[11:36:54 -158511.078103] SLOW spr round 14 (radius: 25)
[11:41:37 -158511.078073] Model parameter optimization (eps = 0.100000)

[11:41:47] ML tree search #15, logLikelihood: -158510.430694

[11:41:47 -542474.526993] Initial branch length optimization
[11:41:50 -445147.218829] Model parameter optimization (eps = 10.000000)
[11:42:12 -443164.556515] AUTODETECT spr round 1 (radius: 5)
[11:43:33 -315772.415421] AUTODETECT spr round 2 (radius: 10)
[11:45:03 -224778.043588] AUTODETECT spr round 3 (radius: 15)
[11:46:39 -194438.342823] AUTODETECT spr round 4 (radius: 20)
[11:48:33 -179868.939880] AUTODETECT spr round 5 (radius: 25)
[11:50:46 -178220.378537] SPR radius for FAST iterations: 25 (autodetect)
[11:50:46 -178220.378537] Model parameter optimization (eps = 3.000000)
[11:51:10 -177565.552388] FAST spr round 1 (radius: 25)
[11:52:56 -159419.144171] FAST spr round 2 (radius: 25)
[11:54:21 -158648.911138] FAST spr round 3 (radius: 25)
[11:55:38 -158574.385257] FAST spr round 4 (radius: 25)
[11:56:50 -158563.777252] FAST spr round 5 (radius: 25)
[11:57:58 -158563.754510] Model parameter optimization (eps = 1.000000)
[11:58:07 -158561.951449] SLOW spr round 1 (radius: 5)
[11:59:37 -158532.277739] SLOW spr round 2 (radius: 5)
[12:01:04 -158531.378347] SLOW spr round 3 (radius: 5)
[12:02:28 -158531.378055] SLOW spr round 4 (radius: 10)
[12:03:52 -158531.256841] SLOW spr round 5 (radius: 5)
[12:05:31 -158531.256623] SLOW spr round 6 (radius: 10)
[12:07:06 -158531.256400] SLOW spr round 7 (radius: 15)
[12:09:14 -158527.189540] SLOW spr round 8 (radius: 5)
[12:11:00 -158519.265018] SLOW spr round 9 (radius: 5)
[12:12:34 -158519.264046] SLOW spr round 10 (radius: 10)
[12:14:03 -158519.263983] SLOW spr round 11 (radius: 15)
[12:16:13 -158519.263948] SLOW spr round 12 (radius: 20)
[12:19:37 -158519.263914] SLOW spr round 13 (radius: 25)
[12:24:07 -158519.263879] Model parameter optimization (eps = 0.100000)

[12:24:13] ML tree search #16, logLikelihood: -158519.035227

[12:24:14 -538455.513314] Initial branch length optimization
[12:24:17 -442269.828523] Model parameter optimization (eps = 10.000000)
[12:24:39 -440300.420399] AUTODETECT spr round 1 (radius: 5)
[12:26:02 -320061.819579] AUTODETECT spr round 2 (radius: 10)
[12:27:29 -230209.199726] AUTODETECT spr round 3 (radius: 15)
[12:29:10 -202512.813752] AUTODETECT spr round 4 (radius: 20)
[12:31:04 -184006.493021] AUTODETECT spr round 5 (radius: 25)
[12:33:15 -179524.290723] SPR radius for FAST iterations: 25 (autodetect)
[12:33:15 -179524.290723] Model parameter optimization (eps = 3.000000)
[12:33:40 -178893.177715] FAST spr round 1 (radius: 25)
[12:35:34 -159369.676292] FAST spr round 2 (radius: 25)
[12:37:04 -158678.692253] FAST spr round 3 (radius: 25)
[12:38:23 -158618.137927] FAST spr round 4 (radius: 25)
[12:39:35 -158606.896733] FAST spr round 5 (radius: 25)
[12:40:43 -158606.046204] FAST spr round 6 (radius: 25)
[12:41:49 -158606.046151] Model parameter optimization (eps = 1.000000)
[12:42:03 -158602.775953] SLOW spr round 1 (radius: 5)
[12:43:32 -158556.415281] SLOW spr round 2 (radius: 5)
[12:44:59 -158547.797932] SLOW spr round 3 (radius: 5)
[12:46:23 -158547.796761] SLOW spr round 4 (radius: 10)
[12:47:47 -158542.637679] SLOW spr round 5 (radius: 5)
[12:49:28 -158542.281415] SLOW spr round 6 (radius: 5)
[12:50:59 -158542.281128] SLOW spr round 7 (radius: 10)
[12:52:27 -158542.281085] SLOW spr round 8 (radius: 15)
[12:54:37 -158536.910388] SLOW spr round 9 (radius: 5)
[12:56:22 -158531.707653] SLOW spr round 10 (radius: 5)
[12:57:56 -158531.707618] SLOW spr round 11 (radius: 10)
[12:59:25 -158531.707584] SLOW spr round 12 (radius: 15)
[13:01:34 -158531.134044] SLOW spr round 13 (radius: 5)
[13:03:18 -158531.134007] SLOW spr round 14 (radius: 10)
[13:04:58 -158531.133973] SLOW spr round 15 (radius: 15)
[13:07:02 -158531.133939] SLOW spr round 16 (radius: 20)
[13:10:29 -158531.133905] SLOW spr round 17 (radius: 25)
[13:15:05 -158531.133871] Model parameter optimization (eps = 0.100000)

[13:15:11] ML tree search #17, logLikelihood: -158530.946272

[13:15:11 -535943.964394] Initial branch length optimization
[13:15:14 -440900.022511] Model parameter optimization (eps = 10.000000)
[13:15:41 -438997.796018] AUTODETECT spr round 1 (radius: 5)
[13:17:00 -317737.426182] AUTODETECT spr round 2 (radius: 10)
[13:18:30 -231798.489145] AUTODETECT spr round 3 (radius: 15)
[13:20:11 -202254.504771] AUTODETECT spr round 4 (radius: 20)
[13:21:58 -185799.004946] AUTODETECT spr round 5 (radius: 25)
[13:24:02 -180919.734557] SPR radius for FAST iterations: 25 (autodetect)
[13:24:02 -180919.734557] Model parameter optimization (eps = 3.000000)
[13:24:21 -180284.457943] FAST spr round 1 (radius: 25)
[13:26:14 -159440.528483] FAST spr round 2 (radius: 25)
[13:27:45 -158663.476221] FAST spr round 3 (radius: 25)
[13:29:08 -158618.508358] FAST spr round 4 (radius: 25)
[13:30:19 -158613.267894] FAST spr round 5 (radius: 25)
[13:31:26 -158613.266860] Model parameter optimization (eps = 1.000000)
[13:31:45 -158599.895375] SLOW spr round 1 (radius: 5)
[13:33:16 -158551.816101] SLOW spr round 2 (radius: 5)
[13:34:47 -158540.456733] SLOW spr round 3 (radius: 5)
[13:36:11 -158540.342048] SLOW spr round 4 (radius: 5)
[13:37:34 -158540.341920] SLOW spr round 5 (radius: 10)
[13:38:58 -158540.341842] SLOW spr round 6 (radius: 15)
[13:41:14 -158536.066165] SLOW spr round 7 (radius: 5)
[13:43:00 -158535.283131] SLOW spr round 8 (radius: 5)
[13:44:34 -158535.282000] SLOW spr round 9 (radius: 10)
[13:46:03 -158535.281916] SLOW spr round 10 (radius: 15)
[13:48:13 -158535.281857] SLOW spr round 11 (radius: 20)
[13:51:45 -158535.281801] SLOW spr round 12 (radius: 25)
[13:56:27 -158535.281747] Model parameter optimization (eps = 0.100000)

[13:56:35] ML tree search #18, logLikelihood: -158534.872876

[13:56:35 -535358.764889] Initial branch length optimization
[13:56:38 -435222.538078] Model parameter optimization (eps = 10.000000)
[13:57:18 -433413.501547] AUTODETECT spr round 1 (radius: 5)
[13:58:39 -318317.810184] AUTODETECT spr round 2 (radius: 10)
[14:00:08 -243473.108600] AUTODETECT spr round 3 (radius: 15)
[14:01:47 -203880.148406] AUTODETECT spr round 4 (radius: 20)
[14:03:49 -179774.997322] AUTODETECT spr round 5 (radius: 25)
[14:06:12 -177866.865573] SPR radius for FAST iterations: 25 (autodetect)
[14:06:12 -177866.865573] Model parameter optimization (eps = 3.000000)
[14:06:34 -177432.709614] FAST spr round 1 (radius: 25)
[14:08:26 -159334.876753] FAST spr round 2 (radius: 25)
[14:09:51 -158659.943442] FAST spr round 3 (radius: 25)
[14:11:08 -158603.049606] FAST spr round 4 (radius: 25)
[14:12:20 -158588.871750] FAST spr round 5 (radius: 25)
[14:13:28 -158586.336809] FAST spr round 6 (radius: 25)
[14:14:35 -158586.336755] Model parameter optimization (eps = 1.000000)
[14:14:48 -158582.539284] SLOW spr round 1 (radius: 5)
[14:16:18 -158532.694502] SLOW spr round 2 (radius: 5)
[14:17:46 -158527.780359] SLOW spr round 3 (radius: 5)
[14:19:11 -158526.414553] SLOW spr round 4 (radius: 5)
[14:20:34 -158526.414424] SLOW spr round 5 (radius: 10)
[14:21:59 -158517.194093] SLOW spr round 6 (radius: 5)
[14:23:41 -158517.192975] SLOW spr round 7 (radius: 10)
[14:25:16 -158517.192936] SLOW spr round 8 (radius: 15)
[14:27:22 -158517.192897] SLOW spr round 9 (radius: 20)
[14:30:55 -158517.192858] SLOW spr round 10 (radius: 25)
[14:35:37 -158517.192820] Model parameter optimization (eps = 0.100000)

[14:35:42] ML tree search #19, logLikelihood: -158517.131267

[14:35:42 -540969.632590] Initial branch length optimization
[14:35:45 -442806.595208] Model parameter optimization (eps = 10.000000)
[14:36:16 -440828.459547] AUTODETECT spr round 1 (radius: 5)
[14:37:37 -314817.654671] AUTODETECT spr round 2 (radius: 10)
[14:39:05 -234834.310223] AUTODETECT spr round 3 (radius: 15)
[14:40:44 -199492.214215] AUTODETECT spr round 4 (radius: 20)
[14:42:46 -181930.610555] AUTODETECT spr round 5 (radius: 25)
[14:45:22 -179066.498601] SPR radius for FAST iterations: 25 (autodetect)
[14:45:22 -179066.498601] Model parameter optimization (eps = 3.000000)
[14:45:46 -178493.692132] FAST spr round 1 (radius: 25)
[14:47:31 -159889.655497] FAST spr round 2 (radius: 25)
[14:48:55 -158628.454674] FAST spr round 3 (radius: 25)
[14:50:12 -158575.179889] FAST spr round 4 (radius: 25)
[14:51:21 -158573.116121] FAST spr round 5 (radius: 25)
[14:52:29 -158570.116471] FAST spr round 6 (radius: 25)
[14:53:36 -158567.065599] FAST spr round 7 (radius: 25)
[14:54:43 -158567.065445] Model parameter optimization (eps = 1.000000)
[14:54:54 -158562.496090] SLOW spr round 1 (radius: 5)
[14:56:24 -158539.617470] SLOW spr round 2 (radius: 5)
[14:57:52 -158534.710346] SLOW spr round 3 (radius: 5)
[14:59:16 -158534.700413] SLOW spr round 4 (radius: 10)
[15:00:41 -158517.932568] SLOW spr round 5 (radius: 5)
[15:02:23 -158517.104317] SLOW spr round 6 (radius: 5)
[15:03:55 -158517.103191] SLOW spr round 7 (radius: 10)
[15:05:22 -158517.103163] SLOW spr round 8 (radius: 15)
[15:07:36 -158517.102932] SLOW spr round 9 (radius: 20)
[15:11:04 -158517.102929] SLOW spr round 10 (radius: 25)
[15:15:45 -158517.102927] Model parameter optimization (eps = 0.100000)

[15:15:51] ML tree search #20, logLikelihood: -158516.982331


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.078747,0.325482) (0.095705,0.863287) (0.326266,0.746527) (0.499282,1.298228) 
   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: -158489.653402

AIC score: 320597.306804 / AICc score: 6869177.306804 / BIC score: 328078.543692
Free parameters (model + branch lengths): 1809

WARNING: Number of free parameters (K=1809) is larger than alignment size (n=462).
         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/P19532/3_mltree/P19532.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P19532/3_mltree/P19532.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P19532/3_mltree/P19532.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P19532/3_mltree/P19532.raxml.log

Analysis started: 19-Jul-2021 15:48:00 / finished: 20-Jul-2021 07:03:52

Elapsed time: 54951.256 seconds