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 01-Jul-2021 06:19:56 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9ULZ9/2_msa/Q9ULZ9_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9ULZ9/3_mltree/Q9ULZ9 --seed 2 --threads 6 --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 (6 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9ULZ9/2_msa/Q9ULZ9_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 427 sites

WARNING: Sequences tr_A0A1D5PZ77_A0A1D5PZ77_CHICK_9031 and tr_H0ZNH0_H0ZNH0_TAEGU_59729 are exactly identical!
WARNING: Sequences tr_A0A1D5PZ77_A0A1D5PZ77_CHICK_9031 and tr_U3JRD6_U3JRD6_FICAL_59894 are exactly identical!
WARNING: Sequences tr_A0A1D5PZ77_A0A1D5PZ77_CHICK_9031 and tr_A0A091EJH3_A0A091EJH3_CORBR_85066 are exactly identical!
WARNING: Sequences tr_A0A1D5PZ77_A0A1D5PZ77_CHICK_9031 and tr_A0A091IY01_A0A091IY01_EGRGA_188379 are exactly identical!
WARNING: Sequences tr_A0A1D5PZ77_A0A1D5PZ77_CHICK_9031 and tr_A0A091VE80_A0A091VE80_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A1D5PZ77_A0A1D5PZ77_CHICK_9031 and tr_A0A087QVU2_A0A087QVU2_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A1D5PZ77_A0A1D5PZ77_CHICK_9031 and tr_A0A093JRB4_A0A093JRB4_STRCA_441894 are exactly identical!
WARNING: Sequences tr_A0A1D5PZ77_A0A1D5PZ77_CHICK_9031 and tr_A0A0A0AXT1_A0A0A0AXT1_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A1D5PZ77_A0A1D5PZ77_CHICK_9031 and tr_A0A218V6Q0_A0A218V6Q0_9PASE_299123 are exactly identical!
WARNING: Sequences sp_Q9R0S2_MMP24_MOUSE_10090 and sp_Q99PW6_MMP24_RAT_10116 are exactly identical!
WARNING: Sequences tr_G9KAX2_G9KAX2_MUSPF_9669 and tr_A0A2Y9L3R9_A0A2Y9L3R9_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_Q9W122_Q9W122_DROME_7227 and tr_B4IH69_B4IH69_DROSE_7238 are exactly identical!
WARNING: Sequences tr_A0A2I3GSY2_A0A2I3GSY2_NOMLE_61853 and tr_A0A2I2Y1M9_A0A2I2Y1M9_GORGO_9595 are exactly identical!
WARNING: Sequences tr_A0A2I3GSY2_A0A2I3GSY2_NOMLE_61853 and tr_G1T0W4_G1T0W4_RABIT_9986 are exactly identical!
WARNING: Sequences tr_A0A2I3GSY2_A0A2I3GSY2_NOMLE_61853 and sp_P51512_MMP16_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I3GSY2_A0A2I3GSY2_NOMLE_61853 and tr_F6XP71_F6XP71_MACMU_9544 are exactly identical!
WARNING: Sequences tr_A0A2I3GSY2_A0A2I3GSY2_NOMLE_61853 and tr_F7G1M2_F7G1M2_CALJA_9483 are exactly identical!
WARNING: Sequences tr_A0A2I3GSY2_A0A2I3GSY2_NOMLE_61853 and tr_G7PC63_G7PC63_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A2I3GSY2_A0A2I3GSY2_NOMLE_61853 and tr_A0A2I3MBZ0_A0A2I3MBZ0_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A2I3GSY2_A0A2I3GSY2_NOMLE_61853 and tr_A0A0D9RKH8_A0A0D9RKH8_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A2I3GSY2_A0A2I3GSY2_NOMLE_61853 and tr_A0A2K5N2Y6_A0A2K5N2Y6_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3GSY2_A0A2I3GSY2_NOMLE_61853 and tr_A0A2K6ANU7_A0A2K6ANU7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I3GSY2_A0A2I3GSY2_NOMLE_61853 and tr_A0A2R8ZII6_A0A2R8ZII6_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3GSY2_A0A2I3GSY2_NOMLE_61853 and tr_A0A2U4ALR5_A0A2U4ALR5_TURTR_9739 are exactly identical!
WARNING: Sequences tr_A0A2I3GSY2_A0A2I3GSY2_NOMLE_61853 and tr_A0A2Y9SX66_A0A2Y9SX66_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_A0A2I3GSY2_A0A2I3GSY2_NOMLE_61853 and tr_A0A384A1W3_A0A384A1W3_BALAS_310752 are exactly identical!
WARNING: Sequences tr_A0A2I2ZNE4_A0A2I2ZNE4_GORGO_9595 and tr_H2Q7Z4_H2Q7Z4_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I2ZNE4_A0A2I2ZNE4_GORGO_9595 and sp_P50281_MMP14_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I2ZNE4_A0A2I2ZNE4_GORGO_9595 and tr_A0A2R9BFH7_A0A2R9BFH7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3R8S6_G3R8S6_GORGO_9595 and tr_H2QK91_H2QK91_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3R8S6_G3R8S6_GORGO_9595 and sp_Q9Y5R2_MMP24_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3R8S6_G3R8S6_GORGO_9595 and tr_A0A2R9A2M0_A0A2R9A2M0_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3S700_G3S700_GORGO_9595 and sp_P51511_MMP15_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G1T8Z9_G1T8Z9_RABIT_9986 and sp_P28863_MMP3_RABIT_9986 are exactly identical!
WARNING: Sequences tr_Q28XL6_Q28XL6_DROPS_46245 and tr_B4GGB5_B4GGB5_DROPE_7234 are exactly identical!
WARNING: Sequences tr_F1PLV8_F1PLV8_CANLF_9615 and tr_A0A2U3WW95_A0A2U3WW95_ODORO_9708 are exactly identical!
WARNING: Sequences tr_F1PLV8_F1PLV8_CANLF_9615 and tr_A0A2Y9JAJ2_A0A2Y9JAJ2_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_F1PXM2_F1PXM2_CANLF_9615 and tr_G1LL48_G1LL48_AILME_9646 are exactly identical!
WARNING: Sequences tr_F1Q270_F1Q270_CANLF_9615 and tr_F6RLA7_F6RLA7_HORSE_9796 are exactly identical!
WARNING: Sequences tr_F1Q270_F1Q270_CANLF_9615 and tr_H0V299_H0V299_CAVPO_10141 are exactly identical!
WARNING: Sequences tr_F1Q270_F1Q270_CANLF_9615 and tr_L5JXS3_L5JXS3_PTEAL_9402 are exactly identical!
WARNING: Sequences tr_F1Q270_F1Q270_CANLF_9615 and tr_A0A3Q0EJR9_A0A3Q0EJR9_TARSY_1868482 are exactly identical!
WARNING: Sequences tr_H2Q4N2_H2Q4N2_PANTR_9598 and tr_A0A2R9BCT7_A0A2R9BCT7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QB81_H2QB81_PANTR_9598 and tr_A0A2R9CEF8_A0A2R9CEF8_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F6T9W9_F6T9W9_HORSE_9796 and sp_Q28397_MMP3_HORSE_9796 are exactly identical!
WARNING: Sequences tr_I3MKD7_I3MKD7_ICTTR_43179 and tr_G7PGJ0_G7PGJ0_MACFA_9541 are exactly identical!
WARNING: Sequences tr_I3MKD7_I3MKD7_ICTTR_43179 and tr_A0A096NUQ1_A0A096NUQ1_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_I3MKD7_I3MKD7_ICTTR_43179 and tr_A0A0D9RDJ2_A0A0D9RDJ2_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_I3MKD7_I3MKD7_ICTTR_43179 and tr_A0A2K5LI89_A0A2K5LI89_CERAT_9531 are exactly identical!
WARNING: Sequences tr_I3MKD7_I3MKD7_ICTTR_43179 and tr_A0A2K6B6K0_A0A2K6B6K0_MACNE_9545 are exactly identical!
WARNING: Sequences tr_I3MKD7_I3MKD7_ICTTR_43179 and tr_A0A2K5Z9B5_A0A2K5Z9B5_MANLE_9568 are exactly identical!
WARNING: Sequences tr_H0WLC1_H0WLC1_OTOGA_30611 and tr_A0A2K5XAS8_A0A2K5XAS8_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F7F147_F7F147_MACMU_9544 and tr_A0A096NIY8_A0A096NIY8_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7F147_F7F147_MACMU_9544 and tr_A0A2K5NGB0_A0A2K5NGB0_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7F147_F7F147_MACMU_9544 and tr_A0A2K6CWE1_A0A2K6CWE1_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7F147_F7F147_MACMU_9544 and tr_A0A2K5XY58_A0A2K5XY58_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F7GFT1_F7GFT1_MACMU_9544 and tr_G7P9U2_G7P9U2_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7GFT1_F7GFT1_MACMU_9544 and tr_A0A096NSD0_A0A096NSD0_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7GFT1_F7GFT1_MACMU_9544 and tr_A0A0D9RUM3_A0A0D9RUM3_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F7GFT1_F7GFT1_MACMU_9544 and tr_A0A2K5KJ44_A0A2K5KJ44_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7GFT1_F7GFT1_MACMU_9544 and tr_A0A2K6BNL4_A0A2K6BNL4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7GFT1_F7GFT1_MACMU_9544 and tr_A0A2K5X9Y4_A0A2K5X9Y4_MANLE_9568 are exactly identical!
WARNING: Sequences tr_H9H3A5_H9H3A5_MACMU_9544 and tr_A0A2K5NB72_A0A2K5NB72_CERAT_9531 are exactly identical!
WARNING: Sequences tr_H9H3A5_H9H3A5_MACMU_9544 and tr_A0A2K6BT47_A0A2K6BT47_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A287AQ38_A0A287AQ38_PIG_9823 and tr_A0A1U8CJB1_A0A1U8CJB1_MESAU_10036 are exactly identical!
WARNING: Sequences tr_A0A287AQ38_A0A287AQ38_PIG_9823 and tr_A0A2Y9QHA3_A0A2Y9QHA3_TRIMA_127582 are exactly identical!
WARNING: Sequences tr_A0A287AQ38_A0A287AQ38_PIG_9823 and tr_A0A2Y9EHE1_A0A2Y9EHE1_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_A0A287AQ38_A0A287AQ38_PIG_9823 and tr_A0A384B0R6_A0A384B0R6_BALAS_310752 are exactly identical!
WARNING: Sequences tr_I3LEE9_I3LEE9_PIG_9823 and tr_A0A384A089_A0A384A089_BALAS_310752 are exactly identical!
WARNING: Sequences tr_G7PJG9_G7PJG9_MACFA_9541 and tr_A0A2K5L235_A0A2K5L235_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A091VTZ5_A0A091VTZ5_NIPNI_128390 and tr_A0A091WEJ9_A0A091WEJ9_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_A0A0V1DCQ9_A0A0V1DCQ9_TRIBR_45882 and tr_A0A0V1NVP9_A0A0V1NVP9_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V1DCQ9_A0A0V1DCQ9_TRIBR_45882 and tr_A0A0V0UA13_A0A0V0UA13_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A0V0X6E0_A0A0V0X6E0_9BILA_92179 and tr_A0A0V1LUQ3_A0A0V1LUQ3_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A226N935_A0A226N935_CALSU_9009 and tr_A0A226Q051_A0A226Q051_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0T8J0_A0A2D0T8J0_ICTPU_7998 and tr_A0A2D0T8K1_A0A2D0T8K1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2K5ME47_A0A2K5ME47_CERAT_9531 and tr_A0A2K6AA62_A0A2K6AA62_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2A3E310_A0A2A3E310_APICC_94128 and tr_A0A2A3E4T6_A0A2A3E4T6_APICC_94128 are exactly identical!
WARNING: Duplicate sequences found: 78

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/Q9ULZ9/3_mltree/Q9ULZ9.raxml.reduced.phy

Alignment comprises 1 partitions and 427 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 427 / 427
Gaps: 3.98 %
Invariant sites: 0.47 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9ULZ9/3_mltree/Q9ULZ9.raxml.rba

Parallelization scheme autoconfig: 3 worker(s) x 2 thread(s)

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

[00:00:00] Generating 20 random starting tree(s) with 1001 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 214 / 17120
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -718507.085152] Initial branch length optimization
[00:00:10 -596065.755615] Model parameter optimization (eps = 10.000000)
[00:00:59 -595396.321440] AUTODETECT spr round 1 (radius: 5)
[00:04:33 -402216.868946] AUTODETECT spr round 2 (radius: 10)
[00:08:24 -298555.220418] AUTODETECT spr round 3 (radius: 15)
[00:12:39 -249979.262446] AUTODETECT spr round 4 (radius: 20)
[00:17:11 -219424.766138] AUTODETECT spr round 5 (radius: 25)
[00:22:26 -201361.455582] SPR radius for FAST iterations: 25 (autodetect)
[00:22:26 -201361.455582] Model parameter optimization (eps = 3.000000)
[00:22:56 -201117.912162] FAST spr round 1 (radius: 25)
[00:26:47 -171726.407469] FAST spr round 2 (radius: 25)
[00:29:40 -169912.539876] FAST spr round 3 (radius: 25)
[00:32:16 -169801.123702] FAST spr round 4 (radius: 25)
[00:34:36 -169753.445952] FAST spr round 5 (radius: 25)
[00:36:51 -169740.706006] FAST spr round 6 (radius: 25)
[00:39:02 -169738.144502] FAST spr round 7 (radius: 25)
[00:41:09 -169738.144499] Model parameter optimization (eps = 1.000000)
[00:41:30 -169712.260211] SLOW spr round 1 (radius: 5)
[00:44:23 -169663.060719] SLOW spr round 2 (radius: 5)
[00:47:18 -169645.512263] SLOW spr round 3 (radius: 5)
[00:50:11 -169642.947709] SLOW spr round 4 (radius: 5)
[00:53:00 -169642.558097] SLOW spr round 5 (radius: 5)
[00:58:00 -169642.558076] SLOW spr round 6 (radius: 10)
[01:05:21 -169638.541486] SLOW spr round 7 (radius: 5)
[01:15:11 -169634.856622] SLOW spr round 8 (radius: 5)
[01:19:06] [worker #2] ML tree search #3, logLikelihood: -169633.685115
[01:19:15 -169633.945140] SLOW spr round 9 (radius: 5)
[01:23:27 -169633.945126] SLOW spr round 10 (radius: 10)
[01:27:44 -169633.945125] SLOW spr round 11 (radius: 15)
[01:31:26] [worker #1] ML tree search #2, logLikelihood: -169643.087760
[01:43:48 -169633.945124] SLOW spr round 12 (radius: 20)
[02:02:03 -169633.945123] SLOW spr round 13 (radius: 25)
[02:15:20 -169633.945121] Model parameter optimization (eps = 0.100000)

[02:15:27] [worker #0] ML tree search #1, logLikelihood: -169633.910461

[02:15:28 -715511.276507] Initial branch length optimization
[02:15:42 -591887.514523] Model parameter optimization (eps = 10.000000)
[02:16:54 -591188.698144] AUTODETECT spr round 1 (radius: 5)
[02:23:27 -405545.292691] AUTODETECT spr round 2 (radius: 10)
[02:27:35 -289133.374792] AUTODETECT spr round 3 (radius: 15)
[02:33:36 -248769.857765] AUTODETECT spr round 4 (radius: 20)
[02:40:07 -212442.791795] AUTODETECT spr round 5 (radius: 25)
[02:48:00 -204510.635489] SPR radius for FAST iterations: 25 (autodetect)
[02:48:00 -204510.635489] Model parameter optimization (eps = 3.000000)
[02:48:41 -204250.160663] FAST spr round 1 (radius: 25)
[02:55:15 -171678.750855] FAST spr round 2 (radius: 25)
[03:00:02 -169803.685429] FAST spr round 3 (radius: 25)
[03:02:30 -169691.588602] FAST spr round 4 (radius: 25)
[03:08:39 -169685.777233] FAST spr round 5 (radius: 25)
[03:12:43 -169683.775341] FAST spr round 6 (radius: 25)
[03:16:51 -169683.775337] Model parameter optimization (eps = 1.000000)
[03:17:13 -169679.198532] SLOW spr round 1 (radius: 5)
[03:24:41] [worker #1] ML tree search #5, logLikelihood: -169639.068590
[03:25:00 -169638.250787] SLOW spr round 2 (radius: 5)
[03:32:49 -169635.069245] SLOW spr round 3 (radius: 5)
[03:38:16 -169635.069162] SLOW spr round 4 (radius: 10)
[03:38:54] [worker #2] ML tree search #6, logLikelihood: -169658.364962
[03:44:30 -169632.310610] SLOW spr round 5 (radius: 5)
[03:51:15 -169631.564025] SLOW spr round 6 (radius: 5)
[03:54:31 -169631.563610] SLOW spr round 7 (radius: 10)
[03:57:39 -169631.563609] SLOW spr round 8 (radius: 15)
[04:02:04 -169631.563607] SLOW spr round 9 (radius: 20)
[04:10:47 -169631.563606] SLOW spr round 10 (radius: 25)
[04:22:23 -169631.563605] Model parameter optimization (eps = 0.100000)

[04:22:37] [worker #0] ML tree search #4, logLikelihood: -169631.303419

[04:22:37 -707567.963691] Initial branch length optimization
[04:22:46 -589146.591127] Model parameter optimization (eps = 10.000000)
[04:23:43 -588504.130229] AUTODETECT spr round 1 (radius: 5)
[04:27:24 -387051.609550] AUTODETECT spr round 2 (radius: 10)
[04:31:23 -286990.107276] AUTODETECT spr round 3 (radius: 15)
[04:35:49 -219950.290653] AUTODETECT spr round 4 (radius: 20)
[04:40:44 -203171.942048] AUTODETECT spr round 5 (radius: 25)
[04:47:38 -195709.897113] SPR radius for FAST iterations: 25 (autodetect)
[04:47:38 -195709.897113] Model parameter optimization (eps = 3.000000)
[04:48:05 -195529.014338] FAST spr round 1 (radius: 25)
[04:51:36 -171084.006743] FAST spr round 2 (radius: 25)
[04:54:14 -169814.892583] FAST spr round 3 (radius: 25)
[04:56:40 -169728.712196] FAST spr round 4 (radius: 25)
[04:58:55 -169720.076180] FAST spr round 5 (radius: 25)
[05:01:04 -169720.076111] Model parameter optimization (eps = 1.000000)
[05:01:24 -169712.597434] SLOW spr round 1 (radius: 5)
[05:04:15 -169658.967191] SLOW spr round 2 (radius: 5)
[05:07:07 -169651.635679] SLOW spr round 3 (radius: 5)
[05:09:58 -169647.667675] SLOW spr round 4 (radius: 5)
[05:11:47] [worker #2] ML tree search #9, logLikelihood: -169634.954579
[05:12:47 -169645.909613] SLOW spr round 5 (radius: 5)
[05:12:47] [worker #1] ML tree search #8, logLikelihood: -169635.988052
[05:15:33 -169645.869746] SLOW spr round 6 (radius: 10)
[05:18:22 -169645.869677] SLOW spr round 7 (radius: 15)
[05:22:29 -169645.869676] SLOW spr round 8 (radius: 20)
[05:30:23 -169645.869675] SLOW spr round 9 (radius: 25)
[05:41:25 -169645.869675] Model parameter optimization (eps = 0.100000)

[05:41:36] [worker #0] ML tree search #7, logLikelihood: -169645.739495

[05:41:36 -709247.477197] Initial branch length optimization
[05:41:43 -590700.612515] Model parameter optimization (eps = 10.000000)
[05:42:38 -590043.555973] AUTODETECT spr round 1 (radius: 5)
[05:46:08 -396068.946049] AUTODETECT spr round 2 (radius: 10)
[05:49:58 -290280.410832] AUTODETECT spr round 3 (radius: 15)
[05:54:11 -240533.329083] AUTODETECT spr round 4 (radius: 20)
[05:58:57 -217377.840249] AUTODETECT spr round 5 (radius: 25)
[06:04:09 -204130.039758] SPR radius for FAST iterations: 25 (autodetect)
[06:04:09 -204130.039758] Model parameter optimization (eps = 3.000000)
[06:04:45 -203945.548064] FAST spr round 1 (radius: 25)
[06:08:16 -171253.972659] FAST spr round 2 (radius: 25)
[06:10:55 -169822.466522] FAST spr round 3 (radius: 25)
[06:13:24 -169717.537213] FAST spr round 4 (radius: 25)
[06:15:43 -169712.633775] FAST spr round 5 (radius: 25)
[06:17:54 -169712.633700] Model parameter optimization (eps = 1.000000)
[06:18:14 -169699.914642] SLOW spr round 1 (radius: 5)
[06:21:09 -169663.284767] SLOW spr round 2 (radius: 5)
[06:24:03 -169645.665506] SLOW spr round 3 (radius: 5)
[06:26:53 -169641.636550] SLOW spr round 4 (radius: 5)
[06:29:37 -169641.636328] SLOW spr round 5 (radius: 10)
[06:32:28 -169641.182407] SLOW spr round 6 (radius: 5)
[06:35:24] [worker #1] ML tree search #11, logLikelihood: -169660.461674
[06:35:57 -169641.182362] SLOW spr round 7 (radius: 10)
[06:39:04 -169641.182362] SLOW spr round 8 (radius: 15)
[06:40:29] [worker #2] ML tree search #12, logLikelihood: -169643.075655
[06:43:06 -169641.182362] SLOW spr round 9 (radius: 20)
[06:51:09 -169641.182362] SLOW spr round 10 (radius: 25)
[07:01:56 -169641.182361] Model parameter optimization (eps = 0.100000)

[07:02:11] [worker #0] ML tree search #10, logLikelihood: -169640.752023

[07:02:11 -717295.501742] Initial branch length optimization
[07:02:18 -593808.624596] Model parameter optimization (eps = 10.000000)
[07:03:13 -593093.964811] AUTODETECT spr round 1 (radius: 5)
[07:06:51 -395633.848402] AUTODETECT spr round 2 (radius: 10)
[07:10:48 -286836.493892] AUTODETECT spr round 3 (radius: 15)
[07:14:57 -227510.999308] AUTODETECT spr round 4 (radius: 20)
[07:19:11 -201586.998597] AUTODETECT spr round 5 (radius: 25)
[07:24:24 -197392.970290] SPR radius for FAST iterations: 25 (autodetect)
[07:24:25 -197392.970290] Model parameter optimization (eps = 3.000000)
[07:24:56 -197221.793973] FAST spr round 1 (radius: 25)
[07:28:42 -171346.488043] FAST spr round 2 (radius: 25)
[07:31:18 -169935.923532] FAST spr round 3 (radius: 25)
[07:33:48 -169766.614909] FAST spr round 4 (radius: 25)
[07:36:10 -169739.312416] FAST spr round 5 (radius: 25)
[07:38:24 -169739.312411] Model parameter optimization (eps = 1.000000)
[07:38:48 -169704.895257] SLOW spr round 1 (radius: 5)
[07:41:50 -169656.547227] SLOW spr round 2 (radius: 5)
[07:44:50 -169646.267707] SLOW spr round 3 (radius: 5)
[07:47:43 -169646.267513] SLOW spr round 4 (radius: 10)
[07:50:43 -169645.809866] SLOW spr round 5 (radius: 5)
[07:54:14] [worker #1] ML tree search #14, logLikelihood: -169637.552490
[07:54:19 -169645.809759] SLOW spr round 6 (radius: 10)
[07:57:30 -169645.809757] SLOW spr round 7 (radius: 15)
[08:01:43 -169645.809757] SLOW spr round 8 (radius: 20)
[08:02:33] [worker #2] ML tree search #15, logLikelihood: -169631.334837
[08:10:01 -169645.809756] SLOW spr round 9 (radius: 25)
[08:21:09 -169645.809756] Model parameter optimization (eps = 0.100000)

[08:21:21] [worker #0] ML tree search #13, logLikelihood: -169645.515282

[08:21:22 -712290.086841] Initial branch length optimization
[08:21:28 -591495.839926] Model parameter optimization (eps = 10.000000)
[08:22:14 -590751.072294] AUTODETECT spr round 1 (radius: 5)
[08:25:47 -392337.875404] AUTODETECT spr round 2 (radius: 10)
[08:29:33 -279625.307864] AUTODETECT spr round 3 (radius: 15)
[08:33:23 -243271.499066] AUTODETECT spr round 4 (radius: 20)
[08:38:10 -219066.452939] AUTODETECT spr round 5 (radius: 25)
[08:44:19 -202957.212978] SPR radius for FAST iterations: 25 (autodetect)
[08:44:19 -202957.212978] Model parameter optimization (eps = 3.000000)
[08:44:48 -202829.544665] FAST spr round 1 (radius: 25)
[08:48:17 -171531.163353] FAST spr round 2 (radius: 25)
[08:51:00 -169794.341083] FAST spr round 3 (radius: 25)
[08:53:30 -169693.139892] FAST spr round 4 (radius: 25)
[08:55:44 -169693.139765] Model parameter optimization (eps = 1.000000)
[08:55:58 -169691.196429] SLOW spr round 1 (radius: 5)
[08:59:00 -169643.520813] SLOW spr round 2 (radius: 5)
[09:02:01 -169639.399797] SLOW spr round 3 (radius: 5)
[09:04:53 -169639.399729] SLOW spr round 4 (radius: 10)
[09:07:54 -169634.686573] SLOW spr round 5 (radius: 5)
[09:11:35 -169627.439255] SLOW spr round 6 (radius: 5)
[09:13:55] [worker #1] ML tree search #17, logLikelihood: -169633.825322
[09:14:45 -169627.244218] SLOW spr round 7 (radius: 5)
[09:17:37 -169625.712649] SLOW spr round 8 (radius: 5)
[09:20:32 -169625.264278] SLOW spr round 9 (radius: 5)
[09:23:22 -169625.264267] SLOW spr round 10 (radius: 10)
[09:27:40 -169625.264131] SLOW spr round 11 (radius: 15)
[09:33:06 -169625.264131] SLOW spr round 12 (radius: 20)
[09:33:54] [worker #2] ML tree search #18, logLikelihood: -169634.866992
[09:45:56 -169625.264131] SLOW spr round 13 (radius: 25)
[10:11:37 -169625.264131] Model parameter optimization (eps = 0.100000)

[10:11:52] [worker #0] ML tree search #16, logLikelihood: -169625.174427

[10:11:52 -710470.662734] Initial branch length optimization
[10:12:12 -590659.892624] Model parameter optimization (eps = 10.000000)
[10:14:32 -589947.473866] AUTODETECT spr round 1 (radius: 5)
[10:23:20 -389314.772181] AUTODETECT spr round 2 (radius: 10)
[10:29:04 -288417.306963] AUTODETECT spr round 3 (radius: 15)
[10:34:20 -247999.283455] AUTODETECT spr round 4 (radius: 20)
[10:40:05 -207098.014513] AUTODETECT spr round 5 (radius: 25)
[10:47:47 -201324.796174] SPR radius for FAST iterations: 25 (autodetect)
[10:47:48 -201324.796174] Model parameter optimization (eps = 3.000000)
[10:48:20 -201151.379811] FAST spr round 1 (radius: 25)
[10:51:57 -170979.988927] FAST spr round 2 (radius: 25)
[10:54:33 -169932.192389] FAST spr round 3 (radius: 25)
[10:57:00 -169728.936161] FAST spr round 4 (radius: 25)
[10:59:15 -169711.324901] FAST spr round 5 (radius: 25)
[11:01:24 -169707.884162] FAST spr round 6 (radius: 25)
[11:03:29 -169707.884142] Model parameter optimization (eps = 1.000000)
[11:03:43 -169699.441062] SLOW spr round 1 (radius: 5)
[11:06:34 -169650.354960] SLOW spr round 2 (radius: 5)
[11:09:23 -169646.567060] SLOW spr round 3 (radius: 5)
[11:12:07 -169646.566930] SLOW spr round 4 (radius: 10)
[11:13:04] [worker #1] ML tree search #20, logLikelihood: -169633.366744
[11:14:56 -169646.090169] SLOW spr round 5 (radius: 5)
[11:18:20 -169646.090119] SLOW spr round 6 (radius: 10)
[11:21:21 -169646.090117] SLOW spr round 7 (radius: 15)
[11:25:16 -169646.090097] SLOW spr round 8 (radius: 20)
[11:32:56 -169646.090095] SLOW spr round 9 (radius: 25)
[11:43:09 -169646.090093] Model parameter optimization (eps = 0.100000)

[11:43:18] [worker #0] ML tree search #19, logLikelihood: -169645.958801


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.141066,0.299052) (0.217844,0.452724) (0.332513,0.882375) (0.308577,1.833543) 
   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: -169625.174427

AIC score: 343260.348855 / AICc score: 8387320.348855 / BIC score: 351394.200801
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=427).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 164 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9ULZ9/3_mltree/Q9ULZ9.raxml.bestTreeCollapsed
Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9ULZ9/3_mltree/Q9ULZ9.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9ULZ9/3_mltree/Q9ULZ9.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9ULZ9/3_mltree/Q9ULZ9.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9ULZ9/3_mltree/Q9ULZ9.raxml.log

Analysis started: 01-Jul-2021 06:19:56 / finished: 01-Jul-2021 18:03:15

Elapsed time: 42198.901 seconds