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 02-Jul-2021 13:44:27 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P81274/2_msa/P81274_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P81274/3_mltree/P81274 --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/P81274/2_msa/P81274_trimmed_msa.fasta
[00:00:00] Loaded alignment with 798 taxa and 426 sites

WARNING: Sequences tr_B4QXH8_B4QXH8_DROSI_7240 and tr_B4IGT6_B4IGT6_DROSE_7238 are exactly identical!
WARNING: Sequences tr_M3XUI6_M3XUI6_MUSPF_9669 and tr_F6V2B9_F6V2B9_CANLF_9615 are exactly identical!
WARNING: Sequences tr_M3XUI6_M3XUI6_MUSPF_9669 and tr_A0A2Y9J1Z9_A0A2Y9J1Z9_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3YA20_M3YA20_MUSPF_9669 and tr_A0A2Y9L8G8_A0A2Y9L8G8_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3YJH2_M3YJH2_MUSPF_9669 and tr_A0A2Y9JIN2_A0A2Y9JIN2_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G1QNT0_G1QNT0_NOMLE_61853 and tr_G3QPV4_G3QPV4_GORGO_9595 are exactly identical!
WARNING: Sequences tr_G1QNT0_G1QNT0_NOMLE_61853 and tr_A0A096MPG4_A0A096MPG4_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G1QNT0_G1QNT0_NOMLE_61853 and tr_A0A0D9S6K4_A0A0D9S6K4_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G1QNT0_G1QNT0_NOMLE_61853 and tr_A0A2K5MZU8_A0A2K5MZU8_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G1QNT0_G1QNT0_NOMLE_61853 and tr_A0A2K5ZDN7_A0A2K5ZDN7_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I2YLX2_A0A2I2YLX2_GORGO_9595 and tr_A0A2I3S6T2_A0A2I3S6T2_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I2YLX2_A0A2I2YLX2_GORGO_9595 and sp_Q86YR5_GPSM1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I2YLX2_A0A2I2YLX2_GORGO_9595 and tr_A0A1D5RHW7_A0A1D5RHW7_MACMU_9544 are exactly identical!
WARNING: Sequences tr_A0A2I2YLX2_A0A2I2YLX2_GORGO_9595 and tr_A0A2K6DNB5_A0A2K6DNB5_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I2YLX2_A0A2I2YLX2_GORGO_9595 and tr_A0A2K5Y9V7_A0A2K5Y9V7_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I2Z2Z3_A0A2I2Z2Z3_GORGO_9595 and tr_H2QF67_H2QF67_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I2Z2Z3_A0A2I2Z2Z3_GORGO_9595 and sp_Q8IVA1_PCP2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I2Z2Z3_A0A2I2Z2Z3_GORGO_9595 and tr_A0A0D9R7L3_A0A0D9R7L3_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A2I2Z2Z3_A0A2I2Z2Z3_GORGO_9595 and tr_A0A2K5XIJ1_A0A2K5XIJ1_MANLE_9568 are exactly identical!
WARNING: Sequences tr_H2P3X5_H2P3X5_PONAB_9601 and sp_Q96AY4_TTC28_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_Q29BH6_Q29BH6_DROPS_46245 and tr_B4GNY6_B4GNY6_DROPE_7234 are exactly identical!
WARNING: Sequences tr_H2PZJ5_H2PZJ5_PANTR_9598 and sp_P81274_GPSM2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2R056_H2R056_PANTR_9598 and tr_A0A2R9CCI0_A0A2R9CCI0_PANPA_9597 are exactly identical!
WARNING: Sequences tr_M3ZI88_M3ZI88_XIPMA_8083 and tr_A0A087Y6S1_A0A087Y6S1_POEFO_48698 are exactly identical!
WARNING: Sequences tr_A0A088AH84_A0A088AH84_APIME_7460 and tr_A0A2A3ESD1_A0A2A3ESD1_APICC_94128 are exactly identical!
WARNING: Sequences tr_A0A1D5QXF2_A0A1D5QXF2_MACMU_9544 and tr_G7PQ94_G7PQ94_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A1D5QXF2_A0A1D5QXF2_MACMU_9544 and tr_A0A096N391_A0A096N391_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A1D5QXF2_A0A1D5QXF2_MACMU_9544 and tr_A0A0D9R0F1_A0A0D9R0F1_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A1D5QXF2_A0A1D5QXF2_MACMU_9544 and tr_A0A2K5NVN1_A0A2K5NVN1_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A1D5QXF2_A0A1D5QXF2_MACMU_9544 and tr_A0A2K6BER0_A0A2K6BER0_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A1D5QXF2_A0A1D5QXF2_MACMU_9544 and tr_A0A2K5ZHM1_A0A2K5ZHM1_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F6QN66_F6QN66_MACMU_9544 and tr_A0A096NRH6_A0A096NRH6_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F6QN66_F6QN66_MACMU_9544 and tr_A0A0D9RC91_A0A0D9RC91_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F6QN66_F6QN66_MACMU_9544 and tr_A0A2K5LRW8_A0A2K5LRW8_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G7NN97_G7NN97_MACMU_9544 and tr_A0A2K6CZ80_A0A2K6CZ80_MACNE_9545 are exactly identical!
WARNING: Sequences tr_H9FTK2_H9FTK2_MACMU_9544 and tr_G7NV46_G7NV46_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F4X2Q8_F4X2Q8_ACREC_103372 and tr_A0A195BLK8_A0A195BLK8_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A087XZ75_A0A087XZ75_POEFO_48698 and tr_A0A087XZN7_A0A087XZN7_POEFO_48698 are exactly identical!
WARNING: Sequences tr_A0A087R8S7_A0A087R8S7_APTFO_9233 and tr_A0A0A0ANF2_A0A0A0ANF2_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A087R8S7_A0A087R8S7_APTFO_9233 and tr_A0A226MUX3_A0A226MUX3_CALSU_9009 are exactly identical!
WARNING: Sequences tr_A0A087R8S7_A0A087R8S7_APTFO_9233 and tr_A0A226PZV8_A0A226PZV8_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A0V1DAK3_A0A0V1DAK3_TRIBR_45882 and tr_A0A0V0X029_A0A0V0X029_9BILA_92179 are exactly identical!
WARNING: Sequences tr_A0A0V1DAK3_A0A0V1DAK3_TRIBR_45882 and tr_A0A0V1L6Y6_A0A0V1L6Y6_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V1DAK3_A0A0V1DAK3_TRIBR_45882 and tr_A0A0V0ZZK2_A0A0V0ZZK2_9BILA_990121 are exactly identical!
WARNING: Sequences tr_A0A0V1DAK3_A0A0V1DAK3_TRIBR_45882 and tr_A0A0V0TZY1_A0A0V0TZY1_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A151X9H2_A0A151X9H2_9HYME_64791 and tr_A0A151J940_A0A151J940_9HYME_471704 are exactly identical!
WARNING: Sequences tr_A0A151X9H2_A0A151X9H2_9HYME_64791 and tr_A0A195BF00_A0A195BF00_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A151X9H2_A0A151X9H2_9HYME_64791 and tr_A0A195FEE0_A0A195FEE0_9HYME_34720 are exactly identical!
WARNING: Sequences tr_A0A2I4CFR9_A0A2I4CFR9_9TELE_52670 and tr_A0A2I4CTL2_A0A2I4CTL2_9TELE_52670 are exactly identical!
WARNING: Sequences tr_A0A060WGQ7_A0A060WGQ7_ONCMY_8022 and tr_A0A060Z5L0_A0A060Z5L0_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A226NM09_A0A226NM09_CALSU_9009 and tr_A0A226PWW6_A0A226PWW6_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0SR43_A0A2D0SR43_ICTPU_7998 and tr_A0A2D0SR57_A0A2D0SR57_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0SR43_A0A2D0SR43_ICTPU_7998 and tr_A0A2D0SR60_A0A2D0SR60_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0T768_A0A2D0T768_ICTPU_7998 and tr_A0A2D0T7B5_A0A2D0T7B5_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2U4A2N2_A0A2U4A2N2_TURTR_9739 and tr_A0A2Y9SGP5_A0A2Y9SGP5_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_A0A2U4A2N2_A0A2U4A2N2_TURTR_9739 and tr_A0A383Z394_A0A383Z394_BALAS_310752 are exactly identical!
WARNING: Sequences tr_A0A2U3WNU8_A0A2U3WNU8_ODORO_9708 and tr_A0A2U3YJV8_A0A2U3YJV8_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_A0A2Y9LA86_A0A2Y9LA86_DELLE_9749 and tr_A0A2Y9SLY7_A0A2Y9SLY7_PHYCD_9755 are exactly identical!
WARNING: Duplicate sequences found: 58

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/P81274/3_mltree/P81274.raxml.reduced.phy

Alignment comprises 1 partitions and 426 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 426 / 426
Gaps: 20.59 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P81274/3_mltree/P81274.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 798 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 213 / 17040
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -504127.265097] Initial branch length optimization
[00:00:05 -403878.433372] Model parameter optimization (eps = 10.000000)
[00:01:01 -401245.595460] AUTODETECT spr round 1 (radius: 5)
[00:03:04 -285502.107675] AUTODETECT spr round 2 (radius: 10)
[00:05:16 -212531.586716] AUTODETECT spr round 3 (radius: 15)
[00:07:43 -181804.972985] AUTODETECT spr round 4 (radius: 20)
[00:10:36 -164600.499923] AUTODETECT spr round 5 (radius: 25)
[00:13:40 -160235.056248] SPR radius for FAST iterations: 25 (autodetect)
[00:13:40 -160235.056248] Model parameter optimization (eps = 3.000000)
[00:14:18 -159382.847580] FAST spr round 1 (radius: 25)
[00:17:11 -144688.048560] FAST spr round 2 (radius: 25)
[00:19:13 -143956.102950] FAST spr round 3 (radius: 25)
[00:21:02 -143902.244449] FAST spr round 4 (radius: 25)
[00:22:36 -143900.605860] FAST spr round 5 (radius: 25)
[00:24:07 -143899.061068] FAST spr round 6 (radius: 25)
[00:25:34 -143896.817420] FAST spr round 7 (radius: 25)
[00:27:00 -143896.817016] Model parameter optimization (eps = 1.000000)
[00:27:15 -143894.102196] SLOW spr round 1 (radius: 5)
[00:29:19 -143846.342046] SLOW spr round 2 (radius: 5)
[00:31:24 -143835.922601] SLOW spr round 3 (radius: 5)
[00:33:27 -143832.928977] SLOW spr round 4 (radius: 5)
[00:35:26 -143832.926326] SLOW spr round 5 (radius: 10)
[00:37:28 -143832.911787] SLOW spr round 6 (radius: 15)
[00:41:15 -143832.676946] SLOW spr round 7 (radius: 5)
[00:43:54 -143832.675662] SLOW spr round 8 (radius: 10)
[00:46:25 -143832.675500] SLOW spr round 9 (radius: 15)
[00:49:50 -143831.691455] SLOW spr round 10 (radius: 5)
[00:52:31 -143830.518455] SLOW spr round 11 (radius: 5)
[00:54:51 -143830.318438] SLOW spr round 12 (radius: 5)
[00:56:57 -143830.318069] SLOW spr round 13 (radius: 10)
[00:59:02 -143830.317943] SLOW spr round 14 (radius: 15)
[01:02:45 -143830.243769] SLOW spr round 15 (radius: 20)
[01:08:21 -143830.223067] SLOW spr round 16 (radius: 25)
[01:11:30] [worker #2] ML tree search #3, logLikelihood: -143819.438869
[01:15:29 -143830.217615] Model parameter optimization (eps = 0.100000)

[01:15:36] [worker #0] ML tree search #1, logLikelihood: -143830.187786

[01:15:37 -506279.813047] Initial branch length optimization
[01:15:42 -403897.172645] Model parameter optimization (eps = 10.000000)
[01:16:32 -401202.306229] AUTODETECT spr round 1 (radius: 5)
[01:18:36 -276516.312505] AUTODETECT spr round 2 (radius: 10)
[01:20:47 -216986.127487] AUTODETECT spr round 3 (radius: 15)
[01:23:20 -183336.924898] AUTODETECT spr round 4 (radius: 20)
[01:26:03 -165816.873476] AUTODETECT spr round 5 (radius: 25)
[01:29:25 -162901.842344] SPR radius for FAST iterations: 25 (autodetect)
[01:29:25 -162901.842344] Model parameter optimization (eps = 3.000000)
[01:30:02 -162231.139666] FAST spr round 1 (radius: 25)
[01:31:34] [worker #1] ML tree search #2, logLikelihood: -143813.137666
[01:33:10 -144832.652586] FAST spr round 2 (radius: 25)
[01:35:24 -143958.090119] FAST spr round 3 (radius: 25)
[01:37:11 -143873.061182] FAST spr round 4 (radius: 25)
[01:38:50 -143858.144184] FAST spr round 5 (radius: 25)
[01:40:21 -143855.786104] FAST spr round 6 (radius: 25)
[01:41:51 -143853.734544] FAST spr round 7 (radius: 25)
[01:43:17 -143853.732243] Model parameter optimization (eps = 1.000000)
[01:43:34 -143843.330405] SLOW spr round 1 (radius: 5)
[01:45:40 -143808.305112] SLOW spr round 2 (radius: 5)
[01:47:44 -143805.444447] SLOW spr round 3 (radius: 5)
[01:49:42 -143805.356901] SLOW spr round 4 (radius: 10)
[01:51:46 -143801.174896] SLOW spr round 5 (radius: 5)
[01:54:20 -143794.534188] SLOW spr round 6 (radius: 5)
[01:56:33 -143794.531533] SLOW spr round 7 (radius: 10)
[01:58:42 -143794.530783] SLOW spr round 8 (radius: 15)
[02:02:08 -143794.530495] SLOW spr round 9 (radius: 20)
[02:07:27 -143794.530358] SLOW spr round 10 (radius: 25)
[02:14:16 -143794.530274] Model parameter optimization (eps = 0.100000)

[02:14:33] [worker #0] ML tree search #4, logLikelihood: -143794.187113

[02:14:33 -506151.256662] Initial branch length optimization
[02:14:38 -403051.413979] Model parameter optimization (eps = 10.000000)
[02:15:21 -400443.514972] AUTODETECT spr round 1 (radius: 5)
[02:17:25 -279572.338627] AUTODETECT spr round 2 (radius: 10)
[02:19:35 -208141.370246] AUTODETECT spr round 3 (radius: 15)
[02:22:05 -175722.171317] AUTODETECT spr round 4 (radius: 20)
[02:24:48 -168274.018231] AUTODETECT spr round 5 (radius: 25)
[02:25:58] [worker #2] ML tree search #6, logLikelihood: -143806.231847
[02:28:06 -163541.473083] SPR radius for FAST iterations: 25 (autodetect)
[02:28:06 -163541.473083] Model parameter optimization (eps = 3.000000)
[02:28:40 -162903.220479] FAST spr round 1 (radius: 25)
[02:29:23] [worker #1] ML tree search #5, logLikelihood: -143826.043293
[02:31:45 -144963.796017] FAST spr round 2 (radius: 25)
[02:34:03 -143983.309942] FAST spr round 3 (radius: 25)
[02:35:58 -143921.950634] FAST spr round 4 (radius: 25)
[02:37:34 -143918.116355] FAST spr round 5 (radius: 25)
[02:39:04 -143918.113290] Model parameter optimization (eps = 1.000000)
[02:39:26 -143896.508562] SLOW spr round 1 (radius: 5)
[02:41:33 -143852.275481] SLOW spr round 2 (radius: 5)
[02:43:41 -143845.916113] SLOW spr round 3 (radius: 5)
[02:45:46 -143842.971714] SLOW spr round 4 (radius: 5)
[02:47:50 -143836.526802] SLOW spr round 5 (radius: 5)
[02:49:49 -143836.526270] SLOW spr round 6 (radius: 10)
[02:51:56 -143828.016570] SLOW spr round 7 (radius: 5)
[02:54:31 -143823.550304] SLOW spr round 8 (radius: 5)
[02:56:46 -143823.550231] SLOW spr round 9 (radius: 10)
[02:58:59 -143823.550182] SLOW spr round 10 (radius: 15)
[03:02:43 -143823.550136] SLOW spr round 11 (radius: 20)
[03:08:36 -143823.550091] SLOW spr round 12 (radius: 25)
[03:16:44 -143823.550046] Model parameter optimization (eps = 0.100000)

[03:16:56] [worker #0] ML tree search #7, logLikelihood: -143823.366446

[03:16:56 -508766.793671] Initial branch length optimization
[03:17:02 -406197.707242] Model parameter optimization (eps = 10.000000)
[03:17:49 -403281.826019] AUTODETECT spr round 1 (radius: 5)
[03:19:55 -281778.750557] AUTODETECT spr round 2 (radius: 10)
[03:22:06 -218189.010791] AUTODETECT spr round 3 (radius: 15)
[03:24:38 -181038.633780] AUTODETECT spr round 4 (radius: 20)
[03:27:30 -164706.636923] AUTODETECT spr round 5 (radius: 25)
[03:31:00 -160486.879615] SPR radius for FAST iterations: 25 (autodetect)
[03:31:00 -160486.879615] Model parameter optimization (eps = 3.000000)
[03:31:39 -159698.697196] FAST spr round 1 (radius: 25)
[03:34:40 -145404.793216] FAST spr round 2 (radius: 25)
[03:36:44 -144019.427610] FAST spr round 3 (radius: 25)
[03:38:36 -143941.701069] FAST spr round 4 (radius: 25)
[03:39:35] [worker #1] ML tree search #8, logLikelihood: -143816.555334
[03:39:39] [worker #2] ML tree search #9, logLikelihood: -143792.550160
[03:40:13 -143928.980310] FAST spr round 5 (radius: 25)
[03:41:43 -143927.307356] FAST spr round 6 (radius: 25)
[03:43:10 -143927.304223] Model parameter optimization (eps = 1.000000)
[03:43:27 -143915.799898] SLOW spr round 1 (radius: 5)
[03:45:37 -143858.119090] SLOW spr round 2 (radius: 5)
[03:47:44 -143853.742123] SLOW spr round 3 (radius: 5)
[03:49:47 -143853.006240] SLOW spr round 4 (radius: 5)
[03:51:49 -143850.832010] SLOW spr round 5 (radius: 5)
[03:53:52 -143842.421826] SLOW spr round 6 (radius: 5)
[03:55:55 -143835.939908] SLOW spr round 7 (radius: 5)
[03:57:55 -143834.908669] SLOW spr round 8 (radius: 5)
[03:59:53 -143834.908229] SLOW spr round 9 (radius: 10)
[04:02:03 -143825.216264] SLOW spr round 10 (radius: 5)
[04:04:37 -143820.689277] SLOW spr round 11 (radius: 5)
[04:06:52 -143820.686008] SLOW spr round 12 (radius: 10)
[04:09:04 -143820.684491] SLOW spr round 13 (radius: 15)
[04:12:27 -143820.125575] SLOW spr round 14 (radius: 5)
[04:15:11 -143817.787319] SLOW spr round 15 (radius: 5)
[04:17:31 -143817.716802] SLOW spr round 16 (radius: 10)
[04:19:44 -143817.714363] SLOW spr round 17 (radius: 15)
[04:23:02 -143817.713191] SLOW spr round 18 (radius: 20)
[04:28:01 -143817.712626] SLOW spr round 19 (radius: 25)
[04:33:03] [worker #1] ML tree search #11, logLikelihood: -143815.332260
[04:34:10 -143817.712380] Model parameter optimization (eps = 0.100000)

[04:34:19] [worker #0] ML tree search #10, logLikelihood: -143817.603677

[04:34:20 -504817.179548] Initial branch length optimization
[04:34:25 -405924.704692] Model parameter optimization (eps = 10.000000)
[04:35:08 -402988.987425] AUTODETECT spr round 1 (radius: 5)
[04:37:14 -281388.692152] AUTODETECT spr round 2 (radius: 10)
[04:39:25 -207735.296680] AUTODETECT spr round 3 (radius: 15)
[04:41:58 -166649.996967] AUTODETECT spr round 4 (radius: 20)
[04:45:02 -157174.112580] AUTODETECT spr round 5 (radius: 25)
[04:48:20 -156475.242395] SPR radius for FAST iterations: 25 (autodetect)
[04:48:20 -156475.242395] Model parameter optimization (eps = 3.000000)
[04:48:55 -155781.245365] FAST spr round 1 (radius: 25)
[04:51:49 -144488.542058] FAST spr round 2 (radius: 25)
[04:54:00 -143926.837596] FAST spr round 3 (radius: 25)
[04:55:53 -143895.574600] FAST spr round 4 (radius: 25)
[04:57:27 -143894.421895] FAST spr round 5 (radius: 25)
[04:58:40] [worker #2] ML tree search #12, logLikelihood: -143807.727026
[04:58:57 -143894.421225] Model parameter optimization (eps = 1.000000)
[04:59:15 -143886.863973] SLOW spr round 1 (radius: 5)
[05:01:22 -143847.622524] SLOW spr round 2 (radius: 5)
[05:03:28 -143843.178161] SLOW spr round 3 (radius: 5)
[05:05:34 -143839.677390] SLOW spr round 4 (radius: 5)
[05:07:34 -143839.677181] SLOW spr round 5 (radius: 10)
[05:09:36 -143839.677101] SLOW spr round 6 (radius: 15)
[05:13:11 -143838.857170] SLOW spr round 7 (radius: 5)
[05:15:51 -143838.855285] SLOW spr round 8 (radius: 10)
[05:18:20 -143838.855054] SLOW spr round 9 (radius: 15)
[05:21:38 -143838.444835] SLOW spr round 10 (radius: 5)
[05:24:21 -143835.130963] SLOW spr round 11 (radius: 5)
[05:26:42 -143833.481461] SLOW spr round 12 (radius: 5)
[05:28:49 -143833.479270] SLOW spr round 13 (radius: 10)
[05:30:54 -143833.478592] SLOW spr round 14 (radius: 15)
[05:34:25 -143832.299110] SLOW spr round 15 (radius: 5)
[05:37:05 -143831.811345] SLOW spr round 16 (radius: 5)
[05:39:22 -143831.810574] SLOW spr round 17 (radius: 10)
[05:41:34 -143831.810505] SLOW spr round 18 (radius: 15)
[05:41:48] [worker #1] ML tree search #14, logLikelihood: -143813.750332
[05:45:01 -143831.810441] SLOW spr round 19 (radius: 20)
[05:50:30 -143831.635496] SLOW spr round 20 (radius: 5)
[05:53:14 -143831.630850] SLOW spr round 21 (radius: 10)
[05:55:47 -143831.630725] SLOW spr round 22 (radius: 15)
[05:59:08 -143831.630638] SLOW spr round 23 (radius: 20)
[06:04:39 -143831.630566] SLOW spr round 24 (radius: 25)
[06:11:50 -143831.630499] Model parameter optimization (eps = 0.100000)

[06:11:59] [worker #0] ML tree search #13, logLikelihood: -143831.388899

[06:11:59 -506988.074386] Initial branch length optimization
[06:12:04 -406329.419037] Model parameter optimization (eps = 10.000000)
[06:12:44 -403443.199206] AUTODETECT spr round 1 (radius: 5)
[06:14:49 -270682.809843] AUTODETECT spr round 2 (radius: 10)
[06:16:58 -212662.300331] AUTODETECT spr round 3 (radius: 15)
[06:19:24 -184517.933536] AUTODETECT spr round 4 (radius: 20)
[06:22:28 -165759.163443] AUTODETECT spr round 5 (radius: 25)
[06:25:42 -161036.178640] SPR radius for FAST iterations: 25 (autodetect)
[06:25:42 -161036.178640] Model parameter optimization (eps = 3.000000)
[06:26:23 -160253.273596] FAST spr round 1 (radius: 25)
[06:29:28 -145150.273770] FAST spr round 2 (radius: 25)
[06:31:49 -144222.451485] FAST spr round 3 (radius: 25)
[06:33:49 -143937.926867] FAST spr round 4 (radius: 25)
[06:35:31 -143896.410828] FAST spr round 5 (radius: 25)
[06:37:03 -143892.632361] FAST spr round 6 (radius: 25)
[06:38:31 -143892.630335] Model parameter optimization (eps = 1.000000)
[06:38:45 -143890.111688] SLOW spr round 1 (radius: 5)
[06:40:54 -143847.891059] SLOW spr round 2 (radius: 5)
[06:42:59 -143847.595578] SLOW spr round 3 (radius: 5)
[06:44:58 -143847.594456] SLOW spr round 4 (radius: 10)
[06:47:05 -143841.430602] SLOW spr round 5 (radius: 5)
[06:47:26] [worker #1] ML tree search #17, logLikelihood: -143847.238069
[06:49:42 -143836.599106] SLOW spr round 6 (radius: 5)
[06:51:56 -143836.586968] SLOW spr round 7 (radius: 10)
[06:52:57] [worker #2] ML tree search #15, logLikelihood: -143795.636422
[06:54:08 -143836.584730] SLOW spr round 8 (radius: 15)
[06:57:32 -143836.584296] SLOW spr round 9 (radius: 20)
[07:02:27 -143836.584181] SLOW spr round 10 (radius: 25)
[07:08:40 -143836.584121] Model parameter optimization (eps = 0.100000)

[07:08:50] [worker #0] ML tree search #16, logLikelihood: -143836.457244

[07:08:50 -505375.077241] Initial branch length optimization
[07:08:55 -405353.397144] Model parameter optimization (eps = 10.000000)
[07:09:40 -402516.787002] AUTODETECT spr round 1 (radius: 5)
[07:11:45 -281456.397526] AUTODETECT spr round 2 (radius: 10)
[07:13:56 -211347.388818] AUTODETECT spr round 3 (radius: 15)
[07:16:27 -175552.278206] AUTODETECT spr round 4 (radius: 20)
[07:19:39 -161395.551920] AUTODETECT spr round 5 (radius: 25)
[07:23:23 -159343.834842] SPR radius for FAST iterations: 25 (autodetect)
[07:23:23 -159343.834842] Model parameter optimization (eps = 3.000000)
[07:24:04 -158590.861496] FAST spr round 1 (radius: 25)
[07:26:55 -144622.577340] FAST spr round 2 (radius: 25)
[07:28:59 -143913.059713] FAST spr round 3 (radius: 25)
[07:30:48 -143888.869919] FAST spr round 4 (radius: 25)
[07:32:24 -143885.881717] FAST spr round 5 (radius: 25)
[07:33:55 -143882.091304] FAST spr round 6 (radius: 25)
[07:35:23 -143882.091160] Model parameter optimization (eps = 1.000000)
[07:35:40 -143876.306234] SLOW spr round 1 (radius: 5)
[07:37:49 -143848.106680] SLOW spr round 2 (radius: 5)
[07:39:58 -143839.815163] SLOW spr round 3 (radius: 5)
[07:42:00 -143838.936178] SLOW spr round 4 (radius: 5)
[07:44:01 -143838.935081] SLOW spr round 5 (radius: 10)
[07:46:07 -143836.051047] SLOW spr round 6 (radius: 5)
[07:46:45] [worker #1] ML tree search #20, logLikelihood: -143818.826310
[07:48:44 -143830.371982] SLOW spr round 7 (radius: 5)
[07:51:00 -143829.015331] SLOW spr round 8 (radius: 5)
[07:53:04 -143829.014842] SLOW spr round 9 (radius: 10)
[07:55:09 -143829.014784] SLOW spr round 10 (radius: 15)
[07:58:43 -143828.002485] SLOW spr round 11 (radius: 5)
[08:01:24 -143827.988775] SLOW spr round 12 (radius: 10)
[08:01:36] [worker #2] ML tree search #18, logLikelihood: -143802.684070
[08:03:57 -143827.988531] SLOW spr round 13 (radius: 15)
[08:07:14 -143827.988480] SLOW spr round 14 (radius: 20)
[08:12:38 -143827.988432] SLOW spr round 15 (radius: 25)
[08:19:27 -143827.988384] Model parameter optimization (eps = 0.100000)

[08:19:33] [worker #0] ML tree search #19, logLikelihood: -143827.933439


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.121981,0.682716) (0.032241,0.652532) (0.567984,0.822785) (0.277794,1.541986) 
   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: -143792.550160

AIC score: 290783.100320 / AICc score: 5407583.100320 / BIC score: 297266.148835
Free parameters (model + branch lengths): 1599

WARNING: Number of free parameters (K=1599) is larger than alignment size (n=426).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 107 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P81274/3_mltree/P81274.raxml.bestTreeCollapsed
Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P81274/3_mltree/P81274.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P81274/3_mltree/P81274.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P81274/3_mltree/P81274.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P81274/3_mltree/P81274.raxml.log

Analysis started: 02-Jul-2021 13:44:27 / finished: 02-Jul-2021 22:04:00

Elapsed time: 29973.667 seconds