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 12-Jul-2021 03:57:26 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9GZR5/2_msa/Q9GZR5_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9GZR5/3_mltree/Q9GZR5 --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/Q9GZR5/2_msa/Q9GZR5_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 228 sites

WARNING: Sequences tr_B4QPP5_B4QPP5_DROSI_7240 and tr_B4HDW0_B4HDW0_DROSE_7238 are exactly identical!
WARNING: Sequences tr_B4R0L9_B4R0L9_DROSI_7240 and tr_Q9VCZ0_Q9VCZ0_DROME_7227 are exactly identical!
WARNING: Sequences tr_B4R0L9_B4R0L9_DROSI_7240 and tr_B4HEA8_B4HEA8_DROSE_7238 are exactly identical!
WARNING: Sequences tr_B4R0L9_B4R0L9_DROSI_7240 and tr_A0A1W4VRB8_A0A1W4VRB8_DROFC_30025 are exactly identical!
WARNING: Sequences tr_E3VVM5_E3VVM5_CHICK_9031 and tr_G1NBS6_G1NBS6_MELGA_9103 are exactly identical!
WARNING: Sequences tr_E3VVZ7_E3VVZ7_CHICK_9031 and tr_G1NLX4_G1NLX4_MELGA_9103 are exactly identical!
WARNING: Sequences tr_E3VVZ7_E3VVZ7_CHICK_9031 and tr_A0A226NE72_A0A226NE72_CALSU_9009 are exactly identical!
WARNING: Sequences tr_E3VVZ7_E3VVZ7_CHICK_9031 and tr_A0A226P061_A0A226P061_COLVI_9014 are exactly identical!
WARNING: Sequences tr_Q9VCY6_Q9VCY6_DROME_7227 and tr_B4HEP7_B4HEP7_DROSE_7238 are exactly identical!
WARNING: Sequences tr_Q9VHX7_Q9VHX7_DROME_7227 and tr_B4I4Z7_B4I4Z7_DROSE_7238 are exactly identical!
WARNING: Sequences tr_A0A2I3G665_A0A2I3G665_NOMLE_61853 and tr_A0A2I3SUS4_A0A2I3SUS4_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I3G665_A0A2I3G665_NOMLE_61853 and tr_A0A2R9CAN2_A0A2R9CAN2_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3H726_G3H726_CRIGR_10029 and tr_A0A1U7QJT1_A0A1U7QJT1_MESAU_10036 are exactly identical!
WARNING: Sequences tr_G3QWW6_G3QWW6_GORGO_9595 and tr_H2PHX6_H2PHX6_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3QWW6_G3QWW6_GORGO_9595 and tr_A0A2I3RLM7_A0A2I3RLM7_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3QWW6_G3QWW6_GORGO_9595 and sp_Q9NXB9_ELOV2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3QWW6_G3QWW6_GORGO_9595 and tr_A0A2R9BFK1_A0A2R9BFK1_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3R1R5_G3R1R5_GORGO_9595 and tr_A0A2I3T3A6_A0A2I3T3A6_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3R1R5_G3R1R5_GORGO_9595 and sp_Q9GZR5_ELOV4_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3R1R5_G3R1R5_GORGO_9595 and tr_A0A2R9CF78_A0A2R9CF78_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3S6X0_G3S6X0_GORGO_9595 and tr_A0A2I3T7B5_A0A2I3T7B5_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3S6X0_G3S6X0_GORGO_9595 and sp_Q9NYP7_ELOV5_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3S6X0_G3S6X0_GORGO_9595 and tr_F7HUC8_F7HUC8_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G3S6X0_G3S6X0_GORGO_9595 and tr_G7P2V6_G7P2V6_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G3S6X0_G3S6X0_GORGO_9595 and tr_A0A096NJ95_A0A096NJ95_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G3S6X0_G3S6X0_GORGO_9595 and tr_A0A0D9RL39_A0A0D9RL39_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G3S6X0_G3S6X0_GORGO_9595 and tr_A0A2K5NGQ5_A0A2K5NGQ5_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G3S6X0_G3S6X0_GORGO_9595 and tr_A0A2K6E3N5_A0A2K6E3N5_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G3S6X0_G3S6X0_GORGO_9595 and tr_A0A2K6A232_A0A2K6A232_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G3S6X0_G3S6X0_GORGO_9595 and tr_A0A2R9BBN2_A0A2R9BBN2_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A0R3NLI7_A0A0R3NLI7_DROPS_46245 and tr_B4G2U1_B4G2U1_DROPE_7234 are exactly identical!
WARNING: Sequences tr_A0A0R3NP99_A0A0R3NP99_DROPS_46245 and tr_B4GDW9_B4GDW9_DROPE_7234 are exactly identical!
WARNING: Sequences tr_B5DPB4_B5DPB4_DROPS_46245 and tr_B4GRK8_B4GRK8_DROPE_7234 are exactly identical!
WARNING: Sequences tr_B5DYD8_B5DYD8_DROPS_46245 and tr_B4GP39_B4GP39_DROPE_7234 are exactly identical!
WARNING: Sequences tr_Q295G9_Q295G9_DROPS_46245 and tr_B4GDX0_B4GDX0_DROPE_7234 are exactly identical!
WARNING: Sequences tr_Q295G9_Q295G9_DROPS_46245 and tr_A0A1W4VZ90_A0A1W4VZ90_DROFC_30025 are exactly identical!
WARNING: Sequences tr_Q29BK2_Q29BK2_DROPS_46245 and tr_B4GP34_B4GP34_DROPE_7234 are exactly identical!
WARNING: Sequences tr_Q29BK5_Q29BK5_DROPS_46245 and tr_B4GP38_B4GP38_DROPE_7234 are exactly identical!
WARNING: Sequences tr_J9PBB9_J9PBB9_CANLF_9615 and tr_A0A2Y9JJ28_A0A2Y9JJ28_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_A0A2J8KKV3_A0A2J8KKV3_PANTR_9598 and tr_A0A2R9CE84_A0A2R9CE84_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A088A435_A0A088A435_APIME_7460 and tr_A0A2A3ELV1_A0A2A3ELV1_APICC_94128 are exactly identical!
WARNING: Sequences tr_A0A158N9L8_A0A158N9L8_ATTCE_12957 and tr_A0A195BNJ4_A0A195BNJ4_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A158NN75_A0A158NN75_ATTCE_12957 and tr_A0A151I3V6_A0A151I3V6_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A1D5R3E1_A0A1D5R3E1_MACMU_9544 and tr_G7P7K6_G7P7K6_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A1D5R3E1_A0A1D5R3E1_MACMU_9544 and tr_A0A0D9RU57_A0A0D9RU57_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A1D5R3E1_A0A1D5R3E1_MACMU_9544 and tr_A0A2K5Z4M3_A0A2K5Z4M3_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F6QW21_F6QW21_MACMU_9544 and tr_A0A2R8MBJ5_A0A2R8MBJ5_CALJA_9483 are exactly identical!
WARNING: Sequences tr_F6QW21_F6QW21_MACMU_9544 and tr_G7P4E7_G7P4E7_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F6QW21_F6QW21_MACMU_9544 and tr_A0A096NKX3_A0A096NKX3_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F6QW21_F6QW21_MACMU_9544 and tr_A0A2K5MD24_A0A2K5MD24_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F6QW21_F6QW21_MACMU_9544 and tr_A0A2K6DRW2_A0A2K6DRW2_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F6QW21_F6QW21_MACMU_9544 and tr_A0A2K6A6Z4_A0A2K6A6Z4_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F7FUS0_F7FUS0_MACMU_9544 and tr_G7NUX0_G7NUX0_MACFA_9541 are exactly identical!
WARNING: Sequences sp_Q3S8M4_ELOV4_MACMU_9544 and tr_G7P3H7_G7P3H7_MACFA_9541 are exactly identical!
WARNING: Sequences sp_Q3S8M4_ELOV4_MACMU_9544 and tr_A0A096NQ85_A0A096NQ85_PAPAN_9555 are exactly identical!
WARNING: Sequences sp_Q3S8M4_ELOV4_MACMU_9544 and tr_A0A0D9RXW1_A0A0D9RXW1_CHLSB_60711 are exactly identical!
WARNING: Sequences sp_Q3S8M4_ELOV4_MACMU_9544 and tr_A0A2K5MG52_A0A2K5MG52_CERAT_9531 are exactly identical!
WARNING: Sequences sp_Q3S8M4_ELOV4_MACMU_9544 and tr_A0A2K6CXC5_A0A2K6CXC5_MACNE_9545 are exactly identical!
WARNING: Sequences sp_Q3S8M4_ELOV4_MACMU_9544 and tr_A0A2K5ZJQ4_A0A2K5ZJQ4_MANLE_9568 are exactly identical!
WARNING: Sequences tr_H0ZQR1_H0ZQR1_TAEGU_59729 and tr_A0A218UF02_A0A218UF02_9PASE_299123 are exactly identical!
WARNING: Sequences tr_H0ZRK3_H0ZRK3_TAEGU_59729 and tr_A0A218VCJ1_A0A218VCJ1_9PASE_299123 are exactly identical!
WARNING: Sequences tr_D2H3V6_D2H3V6_AILME_9646 and tr_A0A2U3VWW1_A0A2U3VWW1_ODORO_9708 are exactly identical!
WARNING: Sequences sp_A0JNC4_ELOV7_BOVIN_9913 and tr_G5E592_G5E592_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_U3JSR8_U3JSR8_FICAL_59894 and tr_A0A218VFA9_A0A218VFA9_9PASE_299123 are exactly identical!
WARNING: Sequences tr_U3I7D9_U3I7D9_ANAPL_8839 and tr_A0A0Q3X7N1_A0A0Q3X7N1_AMAAE_12930 are exactly identical!
WARNING: Sequences tr_U3I7D9_U3I7D9_ANAPL_8839 and tr_A0A091J4T0_A0A091J4T0_EGRGA_188379 are exactly identical!
WARNING: Sequences tr_U3I7D9_U3I7D9_ANAPL_8839 and tr_A0A091VWT9_A0A091VWT9_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_U3I7D9_U3I7D9_ANAPL_8839 and tr_A0A091GIU1_A0A091GIU1_9AVES_55661 are exactly identical!
WARNING: Sequences tr_U3I7D9_U3I7D9_ANAPL_8839 and tr_A0A091I207_A0A091I207_CALAN_9244 are exactly identical!
WARNING: Sequences tr_U3IDT1_U3IDT1_ANAPL_8839 and tr_A0A093S4X9_A0A093S4X9_9PASS_328815 are exactly identical!
WARNING: Sequences tr_U3IDT1_U3IDT1_ANAPL_8839 and tr_A0A091W7A1_A0A091W7A1_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_U3IDT1_U3IDT1_ANAPL_8839 and tr_A0A099YVH1_A0A099YVH1_TINGU_94827 are exactly identical!
WARNING: Sequences tr_U3IDT1_U3IDT1_ANAPL_8839 and tr_A0A0A0AMQ7_A0A0A0AMQ7_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A2I3LME4_A0A2I3LME4_PAPAN_9555 and tr_A0A2K5L7V9_A0A2K5L7V9_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3LME4_A0A2I3LME4_PAPAN_9555 and tr_A0A2K6C664_A0A2K6C664_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I3LME4_A0A2I3LME4_PAPAN_9555 and tr_A0A2K5YPE6_A0A2K5YPE6_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A151MU47_A0A151MU47_ALLMI_8496 and tr_A0A1U8DS60_A0A1U8DS60_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A151PDG7_A0A151PDG7_ALLMI_8496 and tr_A0A1U7S2N2_A0A1U7S2N2_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A2I0MUW5_A0A2I0MUW5_COLLI_8932 and tr_A0A1V4JMQ9_A0A1V4JMQ9_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A1S3H7U6_A0A1S3H7U6_LINUN_7574 and tr_A0A1S3JLJ9_A0A1S3JLJ9_LINUN_7574 are exactly identical!
WARNING: Sequences tr_B9ELL1_B9ELL1_SALSA_8030 and tr_A0A060WDI8_A0A060WDI8_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A1D1VE85_A0A1D1VE85_RAMVA_947166 and tr_A0A1D1VHU7_A0A1D1VHU7_RAMVA_947166 are exactly identical!
WARNING: Sequences tr_A0A226N6H8_A0A226N6H8_CALSU_9009 and tr_A0A226P945_A0A226P945_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A226N735_A0A226N735_CALSU_9009 and tr_A0A226PWT6_A0A226PWT6_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A226NME5_A0A226NME5_CALSU_9009 and tr_A0A226PKP6_A0A226PKP6_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0S1N1_A0A2D0S1N1_ICTPU_7998 and tr_W5UJS2_W5UJS2_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2U4AVQ8_A0A2U4AVQ8_TURTR_9739 and tr_A0A2Y9PJU9_A0A2Y9PJU9_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A2U4AX76_A0A2U4AX76_TURTR_9739 and tr_A0A2Y9Q5C7_A0A2Y9Q5C7_DELLE_9749 are exactly identical!
WARNING: Duplicate sequences found: 88

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/Q9GZR5/3_mltree/Q9GZR5.raxml.reduced.phy

Alignment comprises 1 partitions and 227 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 228 / 227
Gaps: 0.83 %
Invariant sites: 0.88 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9GZR5/3_mltree/Q9GZR5.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 1001 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 227 / 18160
[00:00:00] Data distribution: max. searches per worker: 4

Starting ML tree search with 20 distinct starting trees

[00:00:00 -386094.982391] Initial branch length optimization
[00:00:10 -330400.931370] Model parameter optimization (eps = 10.000000)
[00:01:16 -329426.759427] AUTODETECT spr round 1 (radius: 5)
[00:04:45 -212928.196723] AUTODETECT spr round 2 (radius: 10)
[00:08:22 -153692.798713] AUTODETECT spr round 3 (radius: 15)
[00:12:16 -127794.407418] AUTODETECT spr round 4 (radius: 20)
[00:17:03 -116005.147636] AUTODETECT spr round 5 (radius: 25)
[00:22:09 -113866.577547] SPR radius for FAST iterations: 25 (autodetect)
[00:22:09 -113866.577547] Model parameter optimization (eps = 3.000000)
[00:22:39 -113820.022099] FAST spr round 1 (radius: 25)
[00:26:15 -98161.679133] FAST spr round 2 (radius: 25)
[00:28:55 -97403.618624] FAST spr round 3 (radius: 25)
[00:31:20 -97366.446529] FAST spr round 4 (radius: 25)
[00:33:35 -97363.738449] FAST spr round 5 (radius: 25)
[00:35:43 -97363.738439] Model parameter optimization (eps = 1.000000)
[00:36:08 -97360.177613] SLOW spr round 1 (radius: 5)
[00:39:10 -97330.894168] SLOW spr round 2 (radius: 5)
[00:42:03 -97318.700603] SLOW spr round 3 (radius: 5)
[00:44:47 -97317.911707] SLOW spr round 4 (radius: 5)
[00:47:27 -97314.707121] SLOW spr round 5 (radius: 5)
[00:50:06 -97314.707087] SLOW spr round 6 (radius: 10)
[00:52:55 -97309.513860] SLOW spr round 7 (radius: 5)
[00:56:34 -97305.493081] SLOW spr round 8 (radius: 5)
[00:59:39 -97305.493074] SLOW spr round 9 (radius: 10)
[01:02:29 -97305.493074] SLOW spr round 10 (radius: 15)
[01:06:53 -97305.493074] SLOW spr round 11 (radius: 20)
[01:14:52 -97305.493074] SLOW spr round 12 (radius: 25)
[01:15:01] [worker #3] ML tree search #4, logLikelihood: -97300.554988
[01:15:33] [worker #1] ML tree search #2, logLikelihood: -97308.878594
[01:17:57] [worker #4] ML tree search #5, logLikelihood: -97296.649903
[01:24:50 -97305.493074] Model parameter optimization (eps = 0.100000)

[01:25:00] [worker #0] ML tree search #1, logLikelihood: -97305.337244

[01:25:00 -389649.085923] Initial branch length optimization
[01:25:06 -333106.691372] Model parameter optimization (eps = 10.000000)
[01:26:09 -332086.207033] AUTODETECT spr round 1 (radius: 5)
[01:29:41 -209544.265420] AUTODETECT spr round 2 (radius: 10)
[01:31:13] [worker #2] ML tree search #3, logLikelihood: -97309.122134
[01:33:13 -144603.491694] AUTODETECT spr round 3 (radius: 15)
[01:37:05 -114756.832860] AUTODETECT spr round 4 (radius: 20)
[01:41:35 -109631.881281] AUTODETECT spr round 5 (radius: 25)
[01:46:42 -108610.981713] SPR radius for FAST iterations: 25 (autodetect)
[01:46:42 -108610.981713] Model parameter optimization (eps = 3.000000)
[01:47:06 -108573.143416] FAST spr round 1 (radius: 25)
[01:50:48 -98080.213401] FAST spr round 2 (radius: 25)
[01:53:43 -97463.293680] FAST spr round 3 (radius: 25)
[01:56:14 -97401.756124] FAST spr round 4 (radius: 25)
[01:58:28 -97395.231539] FAST spr round 5 (radius: 25)
[02:00:36 -97395.231516] Model parameter optimization (eps = 1.000000)
[02:01:01 -97390.505680] SLOW spr round 1 (radius: 5)
[02:04:06 -97361.071939] SLOW spr round 2 (radius: 5)
[02:07:02 -97342.164879] SLOW spr round 3 (radius: 5)
[02:09:50 -97338.434094] SLOW spr round 4 (radius: 5)
[02:12:32 -97338.434033] SLOW spr round 5 (radius: 10)
[02:15:21 -97329.608865] SLOW spr round 6 (radius: 5)
[02:19:02 -97320.005714] SLOW spr round 7 (radius: 5)
[02:22:17 -97319.438426] SLOW spr round 8 (radius: 5)
[02:25:12 -97319.437645] SLOW spr round 9 (radius: 10)
[02:28:00 -97311.825346] SLOW spr round 10 (radius: 5)
[02:31:41 -97310.741522] SLOW spr round 11 (radius: 5)
[02:31:42] [worker #1] ML tree search #7, logLikelihood: -97298.724653
[02:31:46] [worker #4] ML tree search #10, logLikelihood: -97330.099537
[02:34:49 -97310.741397] SLOW spr round 12 (radius: 10)
[02:37:43 -97310.741394] SLOW spr round 13 (radius: 15)
[02:42:18 -97310.079275] SLOW spr round 14 (radius: 5)
[02:46:06 -97309.341986] SLOW spr round 15 (radius: 5)
[02:49:19 -97309.341967] SLOW spr round 16 (radius: 10)
[02:52:14 -97308.276847] SLOW spr round 17 (radius: 5)
[02:54:26] [worker #3] ML tree search #9, logLikelihood: -97301.269295
[02:55:16] [worker #2] ML tree search #8, logLikelihood: -97301.046467
[02:55:45 -97307.185706] SLOW spr round 18 (radius: 5)
[02:58:53 -97306.704038] SLOW spr round 19 (radius: 5)
[03:01:46 -97306.704038] SLOW spr round 20 (radius: 10)
[03:04:35 -97306.704038] SLOW spr round 21 (radius: 15)
[03:09:19 -97306.704038] SLOW spr round 22 (radius: 20)
[03:17:25 -97306.704038] SLOW spr round 23 (radius: 25)
[03:27:38 -97306.704038] Model parameter optimization (eps = 0.100000)

[03:27:53] [worker #0] ML tree search #6, logLikelihood: -97306.022891

[03:27:53 -386746.883369] Initial branch length optimization
[03:27:59 -330866.859758] Model parameter optimization (eps = 10.000000)
[03:29:06 -329796.955218] AUTODETECT spr round 1 (radius: 5)
[03:32:35 -213285.674633] AUTODETECT spr round 2 (radius: 10)
[03:36:08 -143011.763944] AUTODETECT spr round 3 (radius: 15)
[03:39:54 -121228.550035] AUTODETECT spr round 4 (radius: 20)
[03:43:56 -112993.188185] AUTODETECT spr round 5 (radius: 25)
[03:45:50] [worker #4] ML tree search #15, logLikelihood: -97307.913893
[03:46:21] [worker #1] ML tree search #12, logLikelihood: -97301.148650
[03:49:56 -109864.307323] SPR radius for FAST iterations: 25 (autodetect)
[03:49:56 -109864.307323] Model parameter optimization (eps = 3.000000)
[03:50:22 -109829.596289] FAST spr round 1 (radius: 25)
[03:53:59 -98339.448336] FAST spr round 2 (radius: 25)
[03:56:48 -97431.135243] FAST spr round 3 (radius: 25)
[03:59:19 -97343.368071] FAST spr round 4 (radius: 25)
[04:01:32 -97335.210220] FAST spr round 5 (radius: 25)
[04:03:39 -97335.210188] Model parameter optimization (eps = 1.000000)
[04:03:53 -97332.023637] SLOW spr round 1 (radius: 5)
[04:06:40] [worker #3] ML tree search #14, logLikelihood: -97317.847402
[04:06:51 -97309.175147] SLOW spr round 2 (radius: 5)
[04:09:51 -97305.069817] SLOW spr round 3 (radius: 5)
[04:12:35 -97303.519865] SLOW spr round 4 (radius: 5)
[04:15:16 -97302.858654] SLOW spr round 5 (radius: 5)
[04:15:43] [worker #2] ML tree search #13, logLikelihood: -97322.577700
[04:17:56 -97302.858618] SLOW spr round 6 (radius: 10)
[04:20:40 -97301.225276] SLOW spr round 7 (radius: 5)
[04:24:18 -97301.225276] SLOW spr round 8 (radius: 10)
[04:27:27 -97301.225276] SLOW spr round 9 (radius: 15)
[04:31:51 -97301.225276] SLOW spr round 10 (radius: 20)
[04:40:18 -97301.225276] SLOW spr round 11 (radius: 25)
[04:50:20 -97301.225276] Model parameter optimization (eps = 0.100000)

[04:50:29] [worker #0] ML tree search #11, logLikelihood: -97301.199179

[04:50:29 -385292.508923] Initial branch length optimization
[04:50:38 -329223.401953] Model parameter optimization (eps = 10.000000)
[04:51:33 -328231.816591] AUTODETECT spr round 1 (radius: 5)
[04:55:04 -208685.668147] AUTODETECT spr round 2 (radius: 10)
[04:58:40 -141835.312359] AUTODETECT spr round 3 (radius: 15)
[05:02:32 -120501.411023] AUTODETECT spr round 4 (radius: 20)
[05:04:21] [worker #4] ML tree search #20, logLikelihood: -97305.077528
[05:07:10 -110725.087045] AUTODETECT spr round 5 (radius: 25)
[05:11:18] [worker #1] ML tree search #17, logLikelihood: -97298.203763
[05:12:22 -110078.315456] SPR radius for FAST iterations: 25 (autodetect)
[05:12:22 -110078.315456] Model parameter optimization (eps = 3.000000)
[05:12:50 -110055.078120] FAST spr round 1 (radius: 25)
[05:13:09] [worker #3] ML tree search #19, logLikelihood: -97316.614157
[05:16:32 -98010.117716] FAST spr round 2 (radius: 25)
[05:19:12 -97459.257466] FAST spr round 3 (radius: 25)
[05:21:33 -97405.979225] FAST spr round 4 (radius: 25)
[05:23:44 -97398.006608] FAST spr round 5 (radius: 25)
[05:25:48 -97398.006581] Model parameter optimization (eps = 1.000000)
[05:26:07 -97372.674239] SLOW spr round 1 (radius: 5)
[05:29:10 -97343.932535] SLOW spr round 2 (radius: 5)
[05:32:00 -97339.039070] SLOW spr round 3 (radius: 5)
[05:34:48 -97332.499125] SLOW spr round 4 (radius: 5)
[05:37:31 -97332.013484] SLOW spr round 5 (radius: 5)
[05:40:09 -97332.013476] SLOW spr round 6 (radius: 10)
[05:40:59] [worker #2] ML tree search #18, logLikelihood: -97310.797560
[05:42:51 -97332.013471] SLOW spr round 7 (radius: 15)
[05:47:27 -97332.013471] SLOW spr round 8 (radius: 20)
[05:55:15 -97332.013471] SLOW spr round 9 (radius: 25)
[06:05:38 -97332.013471] Model parameter optimization (eps = 0.100000)

[06:05:57] [worker #0] ML tree search #16, logLikelihood: -97331.743921


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.166092,0.279366) (0.381002,0.521323) (0.369957,1.474154) (0.082950,2.526849) 
   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: -97296.649903

AIC score: 198603.299805 / AICc score: 8242663.299805 / BIC score: 205479.137791
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=228).
         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/Q9GZR5/3_mltree/Q9GZR5.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9GZR5/3_mltree/Q9GZR5.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9GZR5/3_mltree/Q9GZR5.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9GZR5/3_mltree/Q9GZR5.raxml.log

Analysis started: 12-Jul-2021 03:57:26 / finished: 12-Jul-2021 10:03:24

Elapsed time: 21957.931 seconds