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 14:36:29 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P17735/2_msa/P17735_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P17735/3_mltree/P17735 --seed 2 --threads 7 --tree rand{20} pars{20}

Analysis options:
  run mode: ML tree search
  start tree(s): random (20)
  random seed: 2
  tip-inner: OFF
  pattern compression: ON
  per-rate scalers: OFF
  site repeats: ON
  fast spr radius: AUTO
  spr subtree cutoff: 1.000000
  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
  SIMD kernels: AVX2
  parallelization: coarse-grained (auto), PTHREADS (7 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P17735/2_msa/P17735_trimmed_msa.fasta
[00:00:00] Loaded alignment with 941 taxa and 445 sites

WARNING: Sequences tr_H2QBH3_H2QBH3_PANTR_9598 and tr_A0A2R9BXN4_A0A2R9BXN4_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A0E0G5C0_A0A0E0G5C0_ORYNI_4536 and tr_A2X3T3_A2X3T3_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0G5C0_A0A0E0G5C0_ORYNI_4536 and tr_A0A0E0NDH8_A0A0E0NDH8_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0G5D1_A0A0E0G5D1_ORYNI_4536 and tr_A2X3V3_A2X3V3_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0G5D1_A0A0E0G5D1_ORYNI_4536 and tr_I1NZQ1_I1NZQ1_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_A0A0E0G5D1_A0A0E0G5D1_ORYNI_4536 and tr_A0A0E0NDK4_A0A0E0NDK4_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0G5D1_A0A0E0G5D1_ORYNI_4536 and tr_A0A0P0VI36_A0A0P0VI36_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A5AAC2_A5AAC2_ASPNC_425011 and tr_A0A319AJT0_A0A319AJT0_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_F6TEF9_F6TEF9_MACMU_9544 and tr_A0A2K5P6F4_A0A2K5P6F4_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F6TEF9_F6TEF9_MACMU_9544 and tr_A0A2K6ALY2_A0A2K6ALY2_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F6TEF9_F6TEF9_MACMU_9544 and tr_A0A2K5ZK55_A0A2K5ZK55_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F6TMN5_F6TMN5_MACMU_9544 and tr_G7Q1K1_G7Q1K1_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F6TMN5_F6TMN5_MACMU_9544 and tr_A0A2K6AUW7_A0A2K6AUW7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_I1NZN5_I1NZN5_ORYGL_4538 and tr_A0A0E0NDH5_A0A0E0NDH5_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_B3RJH2_B3RJH2_TRIAD_10228 and tr_A0A369S2K8_A0A369S2K8_9METZ_287889 are exactly identical!
WARNING: Sequences tr_M4E600_M4E600_BRARP_51351 and tr_A0A078GXQ6_A0A078GXQ6_BRANA_3708 are exactly identical!
WARNING: Sequences tr_W2PWU2_W2PWU2_PHYPN_761204 and tr_W2KQ23_W2KQ23_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A067D4U0_A0A067D4U0_CITSI_2711 and tr_V4U3I2_V4U3I2_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A096NSH7_A0A096NSH7_PAPAN_9555 and tr_A0A2K5NR21_A0A2K5NR21_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096NSH7_A0A096NSH7_PAPAN_9555 and tr_A0A2K5XTQ3_A0A2K5XTQ3_MANLE_9568 are exactly identical!
WARNING: Sequences tr_V4URA3_V4URA3_9ROSI_85681 and tr_A0A2H5PU18_A0A2H5PU18_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A1S3ZNW9_A0A1S3ZNW9_TOBAC_4097 and tr_A0A1U7Y8Q5_A0A1U7Y8Q5_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3ZS23_A0A1S3ZS23_TOBAC_4097 and tr_A0A1U7VA27_A0A1U7VA27_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4B421_A0A1S4B421_TOBAC_4097 and tr_A0A1U7VC55_A0A1U7VC55_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4B499_A0A1S4B499_TOBAC_4097 and tr_A0A1U7V361_A0A1U7V361_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A226NCA0_A0A226NCA0_CALSU_9009 and tr_A0A226PFK5_A0A226PFK5_COLVI_9014 are exactly identical!
WARNING: Duplicate sequences found: 26

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/P17735/3_mltree/P17735.raxml.reduced.phy

Alignment comprises 1 partitions and 445 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 445 / 445
Gaps: 14.85 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P17735/3_mltree/P17735.raxml.rba

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

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

[00:00:00] Generating 20 random starting tree(s) with 941 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 64 / 5120
[00:00:00] Data distribution: max. searches per worker: 20

Starting ML tree search with 20 distinct starting trees

[00:00:00 -687478.011161] Initial branch length optimization
[00:00:02 -576588.858493] Model parameter optimization (eps = 10.000000)
[00:00:40 -572710.065281] AUTODETECT spr round 1 (radius: 5)
[00:02:07 -451940.035377] AUTODETECT spr round 2 (radius: 10)
[00:03:46 -348479.089960] AUTODETECT spr round 3 (radius: 15)
[00:05:34 -297645.058405] AUTODETECT spr round 4 (radius: 20)
[00:08:02 -261027.773065] AUTODETECT spr round 5 (radius: 25)
[00:10:40 -258305.074909] SPR radius for FAST iterations: 25 (autodetect)
[00:10:40 -258305.074909] Model parameter optimization (eps = 3.000000)
[00:10:54 -258185.896660] FAST spr round 1 (radius: 25)
[00:12:57 -223121.494647] FAST spr round 2 (radius: 25)
[00:14:35 -222031.440094] FAST spr round 3 (radius: 25)
[00:16:03 -221970.211105] FAST spr round 4 (radius: 25)
[00:17:20 -221968.414762] FAST spr round 5 (radius: 25)
[00:18:38 -221962.745215] FAST spr round 6 (radius: 25)
[00:19:51 -221962.722096] Model parameter optimization (eps = 1.000000)
[00:20:04 -221953.087165] SLOW spr round 1 (radius: 5)
[00:21:41 -221900.511890] SLOW spr round 2 (radius: 5)
[00:23:16 -221889.508527] SLOW spr round 3 (radius: 5)
[00:24:48 -221889.508142] SLOW spr round 4 (radius: 10)
[00:26:28 -221881.486321] SLOW spr round 5 (radius: 5)
[00:28:23 -221872.800825] SLOW spr round 6 (radius: 5)
[00:30:03 -221869.490225] SLOW spr round 7 (radius: 5)
[00:31:40 -221868.789051] SLOW spr round 8 (radius: 5)
[00:33:12 -221868.788583] SLOW spr round 9 (radius: 10)
[00:34:53 -221867.578663] SLOW spr round 10 (radius: 5)
[00:36:44 -221865.739122] SLOW spr round 11 (radius: 5)
[00:38:23 -221865.738759] SLOW spr round 12 (radius: 10)
[00:40:07 -221865.738620] SLOW spr round 13 (radius: 15)
[00:42:56 -221865.738494] SLOW spr round 14 (radius: 20)
[00:47:09 -221865.738368] SLOW spr round 15 (radius: 25)
[00:51:50 -221865.738240] Model parameter optimization (eps = 0.100000)

[00:51:57] ML tree search #1, logLikelihood: -221865.455746

[00:51:57 -686067.570281] Initial branch length optimization
[00:52:00 -577679.061890] Model parameter optimization (eps = 10.000000)
[00:52:35 -574005.253423] AUTODETECT spr round 1 (radius: 5)
[00:54:02 -458547.958357] AUTODETECT spr round 2 (radius: 10)
[00:55:42 -349610.895195] AUTODETECT spr round 3 (radius: 15)
[00:57:34 -283780.079340] AUTODETECT spr round 4 (radius: 20)
[00:59:45 -262997.019074] AUTODETECT spr round 5 (radius: 25)
[01:02:31 -257208.815656] SPR radius for FAST iterations: 25 (autodetect)
[01:02:31 -257208.815656] Model parameter optimization (eps = 3.000000)
[01:02:44 -257100.834145] FAST spr round 1 (radius: 25)
[01:04:49 -223308.056303] FAST spr round 2 (radius: 25)
[01:06:28 -222059.247849] FAST spr round 3 (radius: 25)
[01:08:00 -221941.875683] FAST spr round 4 (radius: 25)
[01:09:19 -221933.247397] FAST spr round 5 (radius: 25)
[01:10:35 -221932.977832] FAST spr round 6 (radius: 25)
[01:11:49 -221932.977758] Model parameter optimization (eps = 1.000000)
[01:11:58 -221928.166718] SLOW spr round 1 (radius: 5)
[01:13:37 -221869.077622] SLOW spr round 2 (radius: 5)
[01:15:14 -221849.667043] SLOW spr round 3 (radius: 5)
[01:16:47 -221847.882694] SLOW spr round 4 (radius: 5)
[01:18:20 -221844.956611] SLOW spr round 5 (radius: 5)
[01:19:51 -221844.956580] SLOW spr round 6 (radius: 10)
[01:21:30 -221844.956580] SLOW spr round 7 (radius: 15)
[01:24:19 -221844.956580] SLOW spr round 8 (radius: 20)
[01:28:05 -221844.956580] SLOW spr round 9 (radius: 25)
[01:32:23 -221844.956580] Model parameter optimization (eps = 0.100000)

[01:32:32] ML tree search #2, logLikelihood: -221844.449998

[01:32:33 -688011.381716] Initial branch length optimization
[01:32:36 -578865.978313] Model parameter optimization (eps = 10.000000)
[01:33:09 -575159.241787] AUTODETECT spr round 1 (radius: 5)
[01:34:38 -458186.072179] AUTODETECT spr round 2 (radius: 10)
[01:36:19 -344454.381051] AUTODETECT spr round 3 (radius: 15)
[01:38:10 -294309.657512] AUTODETECT spr round 4 (radius: 20)
[01:40:29 -263531.207295] AUTODETECT spr round 5 (radius: 25)
[01:42:48 -256541.247509] SPR radius for FAST iterations: 25 (autodetect)
[01:42:48 -256541.247509] Model parameter optimization (eps = 3.000000)
[01:43:01 -256454.194804] FAST spr round 1 (radius: 25)
[01:45:01 -223193.906584] FAST spr round 2 (radius: 25)
[01:46:38 -222069.036327] FAST spr round 3 (radius: 25)
[01:48:06 -221944.118678] FAST spr round 4 (radius: 25)
[01:49:26 -221934.559019] FAST spr round 5 (radius: 25)
[01:50:41 -221934.547636] Model parameter optimization (eps = 1.000000)
[01:50:52 -221922.660690] SLOW spr round 1 (radius: 5)
[01:52:34 -221881.362565] SLOW spr round 2 (radius: 5)
[01:54:11 -221879.291490] SLOW spr round 3 (radius: 5)
[01:55:44 -221879.291369] SLOW spr round 4 (radius: 10)
[01:57:23 -221879.291273] SLOW spr round 5 (radius: 15)
[02:00:16 -221879.291176] SLOW spr round 6 (radius: 20)
[02:04:31 -221879.291078] SLOW spr round 7 (radius: 25)
[02:09:16 -221879.290979] Model parameter optimization (eps = 0.100000)

[02:09:20] ML tree search #3, logLikelihood: -221879.226280

[02:09:20 -691859.716839] Initial branch length optimization
[02:09:23 -582130.321374] Model parameter optimization (eps = 10.000000)
[02:09:57 -578397.673799] AUTODETECT spr round 1 (radius: 5)
[02:11:24 -459920.284100] AUTODETECT spr round 2 (radius: 10)
[02:13:05 -357602.220499] AUTODETECT spr round 3 (radius: 15)
[02:14:56 -308048.799109] AUTODETECT spr round 4 (radius: 20)
[02:17:14 -265277.532576] AUTODETECT spr round 5 (radius: 25)
[02:19:53 -258057.536089] SPR radius for FAST iterations: 25 (autodetect)
[02:19:53 -258057.536089] Model parameter optimization (eps = 3.000000)
[02:20:06 -257969.808270] FAST spr round 1 (radius: 25)
[02:22:12 -223336.762851] FAST spr round 2 (radius: 25)
[02:23:52 -222151.368154] FAST spr round 3 (radius: 25)
[02:25:22 -222000.115345] FAST spr round 4 (radius: 25)
[02:26:43 -221947.403753] FAST spr round 5 (radius: 25)
[02:28:00 -221945.395772] FAST spr round 6 (radius: 25)
[02:29:15 -221945.395299] Model parameter optimization (eps = 1.000000)
[02:29:25 -221935.920445] SLOW spr round 1 (radius: 5)
[02:31:05 -221867.021145] SLOW spr round 2 (radius: 5)
[02:32:41 -221859.922209] SLOW spr round 3 (radius: 5)
[02:34:15 -221859.664259] SLOW spr round 4 (radius: 5)
[02:35:46 -221859.663819] SLOW spr round 5 (radius: 10)
[02:37:25 -221857.738705] SLOW spr round 6 (radius: 5)
[02:39:18 -221849.528918] SLOW spr round 7 (radius: 5)
[02:40:59 -221846.121479] SLOW spr round 8 (radius: 5)
[02:42:33 -221846.120878] SLOW spr round 9 (radius: 10)
[02:44:14 -221846.120679] SLOW spr round 10 (radius: 15)
[02:47:02 -221846.120561] SLOW spr round 11 (radius: 20)
[02:50:52 -221846.120464] SLOW spr round 12 (radius: 25)
[02:55:15 -221846.120372] Model parameter optimization (eps = 0.100000)

[02:55:22] ML tree search #4, logLikelihood: -221846.002407

[02:55:22 -686195.253523] Initial branch length optimization
[02:55:24 -578140.299538] Model parameter optimization (eps = 10.000000)
[02:55:54 -574362.026244] AUTODETECT spr round 1 (radius: 5)
[02:57:22 -454035.441089] AUTODETECT spr round 2 (radius: 10)
[02:59:01 -350160.879551] AUTODETECT spr round 3 (radius: 15)
[03:00:53 -280604.272572] AUTODETECT spr round 4 (radius: 20)
[03:03:09 -260016.989686] AUTODETECT spr round 5 (radius: 25)
[03:05:50 -256393.783131] SPR radius for FAST iterations: 25 (autodetect)
[03:05:50 -256393.783131] Model parameter optimization (eps = 3.000000)
[03:06:02 -256314.192799] FAST spr round 1 (radius: 25)
[03:08:07 -223430.853228] FAST spr round 2 (radius: 25)
[03:09:47 -222029.963261] FAST spr round 3 (radius: 25)
[03:11:16 -221965.181875] FAST spr round 4 (radius: 25)
[03:12:36 -221955.379222] FAST spr round 5 (radius: 25)
[03:13:54 -221952.399213] FAST spr round 6 (radius: 25)
[03:15:10 -221950.560948] FAST spr round 7 (radius: 25)
[03:16:25 -221950.560819] Model parameter optimization (eps = 1.000000)
[03:16:36 -221941.228426] SLOW spr round 1 (radius: 5)
[03:18:15 -221880.887972] SLOW spr round 2 (radius: 5)
[03:19:51 -221870.540307] SLOW spr round 3 (radius: 5)
[03:21:25 -221868.583799] SLOW spr round 4 (radius: 5)
[03:22:58 -221867.531449] SLOW spr round 5 (radius: 5)
[03:24:30 -221867.530805] SLOW spr round 6 (radius: 10)
[03:26:10 -221865.213049] SLOW spr round 7 (radius: 5)
[03:28:04 -221853.534525] SLOW spr round 8 (radius: 5)
[03:29:48 -221845.874635] SLOW spr round 9 (radius: 5)
[03:31:24 -221845.874092] SLOW spr round 10 (radius: 10)
[03:33:05 -221845.874072] SLOW spr round 11 (radius: 15)
[03:35:52 -221845.874070] SLOW spr round 12 (radius: 20)
[03:39:42 -221845.874069] SLOW spr round 13 (radius: 25)
[03:44:01 -221843.972535] SLOW spr round 14 (radius: 5)
[03:46:02 -221840.005460] SLOW spr round 15 (radius: 5)
[03:47:47 -221840.002259] SLOW spr round 16 (radius: 10)
[03:49:36 -221840.001554] SLOW spr round 17 (radius: 15)
[03:52:18 -221840.001393] SLOW spr round 18 (radius: 20)
[03:56:20 -221840.001355] SLOW spr round 19 (radius: 25)
[04:00:56 -221840.001346] Model parameter optimization (eps = 0.100000)

[04:01:03] ML tree search #5, logLikelihood: -221839.445138

[04:01:03 -687054.433721] Initial branch length optimization
[04:01:06 -576969.248796] Model parameter optimization (eps = 10.000000)
[04:01:39 -573324.316061] AUTODETECT spr round 1 (radius: 5)
[04:03:09 -451574.624847] AUTODETECT spr round 2 (radius: 10)
[04:04:51 -338621.486445] AUTODETECT spr round 3 (radius: 15)
[04:06:38 -293387.296677] AUTODETECT spr round 4 (radius: 20)
[04:08:43 -273208.360183] AUTODETECT spr round 5 (radius: 25)
[04:11:21 -261358.828885] SPR radius for FAST iterations: 25 (autodetect)
[04:11:21 -261358.828885] Model parameter optimization (eps = 3.000000)
[04:11:36 -261242.926675] FAST spr round 1 (radius: 25)
[04:13:41 -223743.438050] FAST spr round 2 (radius: 25)
[04:15:19 -222135.488690] FAST spr round 3 (radius: 25)
[04:16:46 -221978.414747] FAST spr round 4 (radius: 25)
[04:18:08 -221950.800613] FAST spr round 5 (radius: 25)
[04:19:26 -221945.931470] FAST spr round 6 (radius: 25)
[04:20:42 -221945.930520] Model parameter optimization (eps = 1.000000)
[04:20:59 -221928.646930] SLOW spr round 1 (radius: 5)
[04:22:40 -221855.552822] SLOW spr round 2 (radius: 5)
[04:24:18 -221847.915584] SLOW spr round 3 (radius: 5)
[04:25:52 -221847.913893] SLOW spr round 4 (radius: 10)
[04:27:32 -221839.245534] SLOW spr round 5 (radius: 5)
[04:29:24 -221838.816948] SLOW spr round 6 (radius: 5)
[04:31:06 -221838.815615] SLOW spr round 7 (radius: 10)
[04:32:51 -221838.815238] SLOW spr round 8 (radius: 15)
[04:35:35 -221837.402019] SLOW spr round 9 (radius: 5)
[04:37:31 -221835.389471] SLOW spr round 10 (radius: 5)
[04:39:15 -221835.387673] SLOW spr round 11 (radius: 10)
[04:41:01 -221835.387517] SLOW spr round 12 (radius: 15)
[04:43:43 -221835.387410] SLOW spr round 13 (radius: 20)
[04:47:36 -221835.387304] SLOW spr round 14 (radius: 25)
[04:51:55 -221835.387196] Model parameter optimization (eps = 0.100000)

[04:52:02] ML tree search #6, logLikelihood: -221835.222947

[04:52:02 -689545.583522] Initial branch length optimization
[04:52:04 -580855.004502] Model parameter optimization (eps = 10.000000)
[04:52:38 -576869.534026] AUTODETECT spr round 1 (radius: 5)
[04:54:06 -452047.582289] AUTODETECT spr round 2 (radius: 10)
[04:55:45 -353674.069458] AUTODETECT spr round 3 (radius: 15)
[04:57:31 -303379.843855] AUTODETECT spr round 4 (radius: 20)
[04:59:53 -266224.379180] AUTODETECT spr round 5 (radius: 25)
[05:02:45 -256927.877384] SPR radius for FAST iterations: 25 (autodetect)
[05:02:45 -256927.877384] Model parameter optimization (eps = 3.000000)
[05:02:59 -256818.283876] FAST spr round 1 (radius: 25)
[05:05:02 -223102.797924] FAST spr round 2 (radius: 25)
[05:06:36 -222072.345694] FAST spr round 3 (radius: 25)
[05:08:04 -221991.677489] FAST spr round 4 (radius: 25)
[05:09:23 -221975.104175] FAST spr round 5 (radius: 25)
[05:10:39 -221975.103004] Model parameter optimization (eps = 1.000000)
[05:10:50 -221964.302901] SLOW spr round 1 (radius: 5)
[05:12:29 -221916.201829] SLOW spr round 2 (radius: 5)
[05:14:04 -221912.969392] SLOW spr round 3 (radius: 5)
[05:15:37 -221912.119195] SLOW spr round 4 (radius: 5)
[05:17:09 -221912.107457] SLOW spr round 5 (radius: 10)
[05:18:49 -221909.354651] SLOW spr round 6 (radius: 5)
[05:20:39 -221905.616355] SLOW spr round 7 (radius: 5)
[05:22:19 -221905.614683] SLOW spr round 8 (radius: 10)
[05:24:03 -221905.614240] SLOW spr round 9 (radius: 15)
[05:26:57 -221905.614118] SLOW spr round 10 (radius: 20)
[05:31:24 -221905.614001] SLOW spr round 11 (radius: 25)
[05:36:19 -221905.613883] Model parameter optimization (eps = 0.100000)

[05:36:24] ML tree search #7, logLikelihood: -221905.490064

[05:36:25 -684407.828601] Initial branch length optimization
[05:36:28 -577648.828945] Model parameter optimization (eps = 10.000000)
[05:37:02 -573989.345106] AUTODETECT spr round 1 (radius: 5)
[05:38:32 -457483.256683] AUTODETECT spr round 2 (radius: 10)
[05:40:11 -357766.147706] AUTODETECT spr round 3 (radius: 15)
[05:42:03 -285119.336299] AUTODETECT spr round 4 (radius: 20)
[05:44:15 -264752.397880] AUTODETECT spr round 5 (radius: 25)
[05:46:50 -261506.246451] SPR radius for FAST iterations: 25 (autodetect)
[05:46:50 -261506.246451] Model parameter optimization (eps = 3.000000)
[05:47:03 -261417.442494] FAST spr round 1 (radius: 25)
[05:49:07 -224663.209905] FAST spr round 2 (radius: 25)
[05:50:48 -222267.985008] FAST spr round 3 (radius: 25)
[05:52:16 -221994.599224] FAST spr round 4 (radius: 25)
[05:53:39 -221960.626790] FAST spr round 5 (radius: 25)
[05:54:56 -221957.395571] FAST spr round 6 (radius: 25)
[05:56:11 -221957.394934] Model parameter optimization (eps = 1.000000)
[05:56:22 -221948.298569] SLOW spr round 1 (radius: 5)
[05:58:04 -221888.305291] SLOW spr round 2 (radius: 5)
[05:59:41 -221880.139995] SLOW spr round 3 (radius: 5)
[06:01:14 -221879.604455] SLOW spr round 4 (radius: 5)
[06:02:47 -221879.603711] SLOW spr round 5 (radius: 10)
[06:04:28 -221872.098284] SLOW spr round 6 (radius: 5)
[06:06:20 -221861.321424] SLOW spr round 7 (radius: 5)
[06:08:00 -221861.321276] SLOW spr round 8 (radius: 10)
[06:09:45 -221861.321151] SLOW spr round 9 (radius: 15)
[06:12:32 -221861.321024] SLOW spr round 10 (radius: 20)
[06:16:38 -221861.320896] SLOW spr round 11 (radius: 25)
[06:21:20 -221861.320767] Model parameter optimization (eps = 0.100000)

[06:21:26] ML tree search #8, logLikelihood: -221861.233036

[06:21:26 -689138.937160] Initial branch length optimization
[06:21:30 -579003.287701] Model parameter optimization (eps = 10.000000)
[06:22:06 -575334.906904] AUTODETECT spr round 1 (radius: 5)
[06:23:35 -449445.446214] AUTODETECT spr round 2 (radius: 10)
[06:25:16 -353954.707039] AUTODETECT spr round 3 (radius: 15)
[06:27:01 -304879.205506] AUTODETECT spr round 4 (radius: 20)
[06:29:17 -269194.218002] AUTODETECT spr round 5 (radius: 25)
[06:31:56 -260448.057685] SPR radius for FAST iterations: 25 (autodetect)
[06:31:56 -260448.057685] Model parameter optimization (eps = 3.000000)
[06:32:17 -260334.938914] FAST spr round 1 (radius: 25)
[06:34:24 -224029.667645] FAST spr round 2 (radius: 25)
[06:36:06 -222050.887138] FAST spr round 3 (radius: 25)
[06:37:35 -221962.886568] FAST spr round 4 (radius: 25)
[06:38:56 -221942.815330] FAST spr round 5 (radius: 25)
[06:40:16 -221923.141828] FAST spr round 6 (radius: 25)
[06:41:32 -221921.339523] FAST spr round 7 (radius: 25)
[06:42:46 -221920.084011] FAST spr round 8 (radius: 25)
[06:43:59 -221920.083851] Model parameter optimization (eps = 1.000000)
[06:44:11 -221910.695710] SLOW spr round 1 (radius: 5)
[06:45:52 -221864.094706] SLOW spr round 2 (radius: 5)
[06:47:28 -221857.342732] SLOW spr round 3 (radius: 5)
[06:49:00 -221853.200401] SLOW spr round 4 (radius: 5)
[06:50:32 -221853.200035] SLOW spr round 5 (radius: 10)
[06:52:11 -221852.454190] SLOW spr round 6 (radius: 5)
[06:54:01 -221852.453689] SLOW spr round 7 (radius: 10)
[06:55:55 -221852.453522] SLOW spr round 8 (radius: 15)
[06:58:33 -221852.453381] SLOW spr round 9 (radius: 20)
[07:02:27 -221852.453241] SLOW spr round 10 (radius: 25)
[07:06:46 -221852.453099] Model parameter optimization (eps = 0.100000)

[07:06:54] ML tree search #9, logLikelihood: -221852.199101

[07:06:54 -683029.704502] Initial branch length optimization
[07:06:56 -576947.927386] Model parameter optimization (eps = 10.000000)
[07:07:31 -573440.968360] AUTODETECT spr round 1 (radius: 5)
[07:08:59 -453525.502415] AUTODETECT spr round 2 (radius: 10)
[07:10:39 -355428.761587] AUTODETECT spr round 3 (radius: 15)
[07:12:27 -296725.494361] AUTODETECT spr round 4 (radius: 20)
[07:14:42 -263916.168570] AUTODETECT spr round 5 (radius: 25)
[07:17:07 -262033.492630] SPR radius for FAST iterations: 25 (autodetect)
[07:17:07 -262033.492630] Model parameter optimization (eps = 3.000000)
[07:17:22 -261935.670413] FAST spr round 1 (radius: 25)
[07:19:25 -223151.396935] FAST spr round 2 (radius: 25)
[07:21:04 -222124.764567] FAST spr round 3 (radius: 25)
[07:22:34 -221961.543476] FAST spr round 4 (radius: 25)
[07:23:54 -221943.113402] FAST spr round 5 (radius: 25)
[07:25:10 -221943.111336] Model parameter optimization (eps = 1.000000)
[07:25:23 -221933.328394] SLOW spr round 1 (radius: 5)
[07:27:05 -221870.732554] SLOW spr round 2 (radius: 5)
[07:28:42 -221862.165497] SLOW spr round 3 (radius: 5)
[07:30:16 -221856.691891] SLOW spr round 4 (radius: 5)
[07:31:48 -221856.691702] SLOW spr round 5 (radius: 10)
[07:33:28 -221854.339449] SLOW spr round 6 (radius: 5)
[07:35:20 -221849.899540] SLOW spr round 7 (radius: 5)
[07:37:00 -221849.899268] SLOW spr round 8 (radius: 10)
[07:38:44 -221849.899136] SLOW spr round 9 (radius: 15)
[07:41:29 -221849.899037] SLOW spr round 10 (radius: 20)
[07:45:35 -221849.898945] SLOW spr round 11 (radius: 25)
[07:50:00 -221849.898855] Model parameter optimization (eps = 0.100000)

[07:50:04] ML tree search #10, logLikelihood: -221849.802371

[07:50:04 -688436.347365] Initial branch length optimization
[07:50:07 -578459.510502] Model parameter optimization (eps = 10.000000)
[07:50:45 -574580.371741] AUTODETECT spr round 1 (radius: 5)
[07:52:14 -457845.668699] AUTODETECT spr round 2 (radius: 10)
[07:53:54 -348221.418261] AUTODETECT spr round 3 (radius: 15)
[07:55:41 -298560.989411] AUTODETECT spr round 4 (radius: 20)
[07:57:48 -265729.876419] AUTODETECT spr round 5 (radius: 25)
[08:00:16 -257131.562455] SPR radius for FAST iterations: 25 (autodetect)
[08:00:16 -257131.562455] Model parameter optimization (eps = 3.000000)
[08:00:30 -256995.328335] FAST spr round 1 (radius: 25)
[08:02:38 -223257.830764] FAST spr round 2 (radius: 25)
[08:04:18 -222095.690052] FAST spr round 3 (radius: 25)
[08:05:49 -221990.431587] FAST spr round 4 (radius: 25)
[08:07:11 -221969.893581] FAST spr round 5 (radius: 25)
[08:08:29 -221964.020907] FAST spr round 6 (radius: 25)
[08:09:45 -221960.642974] FAST spr round 7 (radius: 25)
[08:10:59 -221960.642137] Model parameter optimization (eps = 1.000000)
[08:11:05 -221960.183629] SLOW spr round 1 (radius: 5)
[08:12:45 -221897.895791] SLOW spr round 2 (radius: 5)
[08:14:20 -221890.110517] SLOW spr round 3 (radius: 5)
[08:15:55 -221888.046856] SLOW spr round 4 (radius: 5)
[08:17:27 -221888.046753] SLOW spr round 5 (radius: 10)
[08:19:07 -221887.984956] SLOW spr round 6 (radius: 15)
[08:22:05 -221887.984749] SLOW spr round 7 (radius: 20)
[08:26:23 -221887.984740] SLOW spr round 8 (radius: 25)
[08:31:23 -221887.984739] Model parameter optimization (eps = 0.100000)

[08:31:29] ML tree search #11, logLikelihood: -221887.848317

[08:31:29 -688287.492786] Initial branch length optimization
[08:31:31 -579143.703689] Model parameter optimization (eps = 10.000000)
[08:32:07 -575308.291037] AUTODETECT spr round 1 (radius: 5)
[08:33:35 -448283.885477] AUTODETECT spr round 2 (radius: 10)
[08:35:15 -346541.808684] AUTODETECT spr round 3 (radius: 15)
[08:37:05 -289084.037844] AUTODETECT spr round 4 (radius: 20)
[08:39:29 -258471.361185] AUTODETECT spr round 5 (radius: 25)
[08:42:04 -250908.399627] SPR radius for FAST iterations: 25 (autodetect)
[08:42:04 -250908.399627] Model parameter optimization (eps = 3.000000)
[08:42:19 -250807.318058] FAST spr round 1 (radius: 25)
[08:44:23 -223054.523972] FAST spr round 2 (radius: 25)
[08:46:00 -222058.729244] FAST spr round 3 (radius: 25)
[08:47:27 -221983.918112] FAST spr round 4 (radius: 25)
[08:48:46 -221974.020841] FAST spr round 5 (radius: 25)
[08:50:03 -221972.063689] FAST spr round 6 (radius: 25)
[08:51:18 -221972.062271] Model parameter optimization (eps = 1.000000)
[08:51:28 -221961.752274] SLOW spr round 1 (radius: 5)
[08:53:09 -221901.319747] SLOW spr round 2 (radius: 5)
[08:54:46 -221892.587511] SLOW spr round 3 (radius: 5)
[08:56:19 -221891.532744] SLOW spr round 4 (radius: 5)
[08:57:52 -221886.457156] SLOW spr round 5 (radius: 5)
[08:59:24 -221886.456370] SLOW spr round 6 (radius: 10)
[09:01:04 -221879.303210] SLOW spr round 7 (radius: 5)
[09:02:55 -221875.489578] SLOW spr round 8 (radius: 5)
[09:04:36 -221873.694318] SLOW spr round 9 (radius: 5)
[09:06:11 -221873.694166] SLOW spr round 10 (radius: 10)
[09:07:51 -221872.418959] SLOW spr round 11 (radius: 5)
[09:09:42 -221866.027439] SLOW spr round 12 (radius: 5)
[09:11:22 -221866.024736] SLOW spr round 13 (radius: 10)
[09:13:04 -221866.024044] SLOW spr round 14 (radius: 15)
[09:15:43 -221860.034345] SLOW spr round 15 (radius: 5)
[09:17:41 -221846.494013] SLOW spr round 16 (radius: 5)
[09:19:26 -221844.400914] SLOW spr round 17 (radius: 5)
[09:21:02 -221844.400773] SLOW spr round 18 (radius: 10)
[09:22:44 -221840.109290] SLOW spr round 19 (radius: 5)
[09:24:34 -221839.562098] SLOW spr round 20 (radius: 5)
[09:26:14 -221839.561839] SLOW spr round 21 (radius: 10)
[09:27:57 -221839.561832] SLOW spr round 22 (radius: 15)
[09:30:36 -221839.561830] SLOW spr round 23 (radius: 20)
[09:34:23 -221839.561828] SLOW spr round 24 (radius: 25)
[09:38:46 -221839.561825] Model parameter optimization (eps = 0.100000)

[09:38:53] ML tree search #12, logLikelihood: -221839.443349

[09:38:53 -686134.682894] Initial branch length optimization
[09:38:56 -580969.786180] Model parameter optimization (eps = 10.000000)
[09:39:29 -577246.145532] AUTODETECT spr round 1 (radius: 5)
[09:40:59 -449937.459331] AUTODETECT spr round 2 (radius: 10)
[09:42:37 -345707.785527] AUTODETECT spr round 3 (radius: 15)
[09:44:23 -300243.020612] AUTODETECT spr round 4 (radius: 20)
[09:46:28 -277972.672175] AUTODETECT spr round 5 (radius: 25)
[09:48:50 -264977.180692] SPR radius for FAST iterations: 25 (autodetect)
[09:48:50 -264977.180692] Model parameter optimization (eps = 3.000000)
[09:48:55 -264971.429660] FAST spr round 1 (radius: 25)
[09:51:03 -223716.000326] FAST spr round 2 (radius: 25)
[09:52:44 -222192.593103] FAST spr round 3 (radius: 25)
[09:54:12 -222116.853614] FAST spr round 4 (radius: 25)
[09:55:34 -222102.697625] FAST spr round 5 (radius: 25)
[09:56:51 -222101.739858] FAST spr round 6 (radius: 25)
[09:58:06 -222101.727856] Model parameter optimization (eps = 1.000000)
[09:58:20 -221965.290921] SLOW spr round 1 (radius: 5)
[09:59:59 -221890.429612] SLOW spr round 2 (radius: 5)
[10:01:37 -221883.616983] SLOW spr round 3 (radius: 5)
[10:03:09 -221883.615967] SLOW spr round 4 (radius: 10)
[10:04:51 -221874.470675] SLOW spr round 5 (radius: 5)
[10:06:44 -221872.382544] SLOW spr round 6 (radius: 5)
[10:08:26 -221872.382247] SLOW spr round 7 (radius: 10)
[10:10:11 -221870.170263] SLOW spr round 8 (radius: 5)
[10:12:05 -221855.007116] SLOW spr round 9 (radius: 5)
[10:13:46 -221854.068237] SLOW spr round 10 (radius: 5)
[10:15:23 -221853.774664] SLOW spr round 11 (radius: 5)
[10:16:57 -221852.765213] SLOW spr round 12 (radius: 5)
[10:18:30 -221852.764768] SLOW spr round 13 (radius: 10)
[10:20:10 -221852.764610] SLOW spr round 14 (radius: 15)
[10:23:02 -221852.764472] SLOW spr round 15 (radius: 20)
[10:27:06 -221852.764335] SLOW spr round 16 (radius: 25)
[10:31:48 -221852.764197] Model parameter optimization (eps = 0.100000)

[10:31:57] ML tree search #13, logLikelihood: -221852.548298

[10:31:57 -691651.799776] Initial branch length optimization
[10:32:00 -582819.616903] Model parameter optimization (eps = 10.000000)
[10:32:33 -578944.588155] AUTODETECT spr round 1 (radius: 5)
[10:34:02 -463500.550591] AUTODETECT spr round 2 (radius: 10)
[10:35:44 -355945.306622] AUTODETECT spr round 3 (radius: 15)
[10:37:28 -303731.028020] AUTODETECT spr round 4 (radius: 20)
[10:39:41 -269956.040944] AUTODETECT spr round 5 (radius: 25)
[10:42:08 -264856.587155] SPR radius for FAST iterations: 25 (autodetect)
[10:42:08 -264856.587155] Model parameter optimization (eps = 3.000000)
[10:42:27 -264749.570400] FAST spr round 1 (radius: 25)
[10:44:30 -223461.705579] FAST spr round 2 (radius: 25)
[10:46:08 -222291.990259] FAST spr round 3 (radius: 25)
[10:47:37 -222019.764007] FAST spr round 4 (radius: 25)
[10:48:58 -222005.927044] FAST spr round 5 (radius: 25)
[10:50:15 -222005.926251] Model parameter optimization (eps = 1.000000)
[10:50:27 -221983.051466] SLOW spr round 1 (radius: 5)
[10:52:06 -221907.749320] SLOW spr round 2 (radius: 5)
[10:53:46 -221880.061758] SLOW spr round 3 (radius: 5)
[10:55:19 -221879.392921] SLOW spr round 4 (radius: 5)
[10:56:52 -221879.391478] SLOW spr round 5 (radius: 10)
[10:58:33 -221869.477194] SLOW spr round 6 (radius: 5)
[11:00:28 -221854.658704] SLOW spr round 7 (radius: 5)
[11:02:09 -221854.658399] SLOW spr round 8 (radius: 10)
[11:03:53 -221854.475491] SLOW spr round 9 (radius: 5)
[11:05:43 -221851.115531] SLOW spr round 10 (radius: 5)
[11:07:26 -221849.706762] SLOW spr round 11 (radius: 5)
[11:09:02 -221849.706142] SLOW spr round 12 (radius: 10)
[11:10:43 -221849.705953] SLOW spr round 13 (radius: 15)
[11:13:31 -221848.770545] SLOW spr round 14 (radius: 5)
[11:15:27 -221847.534016] SLOW spr round 15 (radius: 5)
[11:17:09 -221847.532635] SLOW spr round 16 (radius: 10)
[11:18:55 -221847.532318] SLOW spr round 17 (radius: 15)
[11:21:39 -221847.532216] SLOW spr round 18 (radius: 20)
[11:25:36 -221847.532182] SLOW spr round 19 (radius: 25)
[11:29:55 -221847.532170] Model parameter optimization (eps = 0.100000)

[11:29:59] ML tree search #14, logLikelihood: -221847.461610

[11:29:59 -689141.150199] Initial branch length optimization
[11:30:02 -580140.062818] Model parameter optimization (eps = 10.000000)
[11:30:32 -576174.424508] AUTODETECT spr round 1 (radius: 5)
[11:32:01 -456539.221483] AUTODETECT spr round 2 (radius: 10)
[11:33:41 -348918.537788] AUTODETECT spr round 3 (radius: 15)
[11:35:36 -282453.793579] AUTODETECT spr round 4 (radius: 20)
[11:37:48 -256886.930942] AUTODETECT spr round 5 (radius: 25)
[11:40:31 -252790.620618] SPR radius for FAST iterations: 25 (autodetect)
[11:40:31 -252790.620618] Model parameter optimization (eps = 3.000000)
[11:40:44 -252676.604236] FAST spr round 1 (radius: 25)
[11:42:47 -222958.701345] FAST spr round 2 (radius: 25)
[11:44:26 -222107.887506] FAST spr round 3 (radius: 25)
[11:45:56 -221978.896615] FAST spr round 4 (radius: 25)
[11:47:17 -221956.026919] FAST spr round 5 (radius: 25)
[11:48:34 -221956.026226] Model parameter optimization (eps = 1.000000)
[11:48:44 -221951.149879] SLOW spr round 1 (radius: 5)
[11:50:25 -221873.592886] SLOW spr round 2 (radius: 5)
[11:52:02 -221860.405289] SLOW spr round 3 (radius: 5)
[11:53:36 -221860.394008] SLOW spr round 4 (radius: 10)
[11:55:17 -221847.802042] SLOW spr round 5 (radius: 5)
[11:57:11 -221834.167734] SLOW spr round 6 (radius: 5)
[11:58:52 -221834.015387] SLOW spr round 7 (radius: 5)
[12:00:28 -221834.015254] SLOW spr round 8 (radius: 10)
[12:02:09 -221834.015134] SLOW spr round 9 (radius: 15)
[12:05:01 -221834.015013] SLOW spr round 10 (radius: 20)
[12:09:04 -221834.014891] SLOW spr round 11 (radius: 25)
[12:13:35 -221834.014767] Model parameter optimization (eps = 0.100000)

[12:13:44] ML tree search #15, logLikelihood: -221833.962851

[12:13:45 -688524.193792] Initial branch length optimization
[12:13:47 -581578.788647] Model parameter optimization (eps = 10.000000)
[12:14:17 -577645.313863] AUTODETECT spr round 1 (radius: 5)
[12:15:46 -459955.902958] AUTODETECT spr round 2 (radius: 10)
[12:17:28 -351564.714255] AUTODETECT spr round 3 (radius: 15)
[12:19:18 -281392.945843] AUTODETECT spr round 4 (radius: 20)
[12:21:38 -257968.021532] AUTODETECT spr round 5 (radius: 25)
[12:24:34 -254442.969784] SPR radius for FAST iterations: 25 (autodetect)
[12:24:34 -254442.969784] Model parameter optimization (eps = 3.000000)
[12:24:39 -254437.496971] FAST spr round 1 (radius: 25)
[12:26:44 -223715.480658] FAST spr round 2 (radius: 25)
[12:28:24 -222230.069929] FAST spr round 3 (radius: 25)
[12:29:55 -222100.575609] FAST spr round 4 (radius: 25)
[12:31:16 -222068.696942] FAST spr round 5 (radius: 25)
[12:32:33 -222066.404659] FAST spr round 6 (radius: 25)
[12:33:48 -222066.393076] Model parameter optimization (eps = 1.000000)
[12:34:01 -221938.647194] SLOW spr round 1 (radius: 5)
[12:35:43 -221864.067680] SLOW spr round 2 (radius: 5)
[12:37:20 -221857.887488] SLOW spr round 3 (radius: 5)
[12:38:54 -221852.448726] SLOW spr round 4 (radius: 5)
[12:40:26 -221852.448395] SLOW spr round 5 (radius: 10)
[12:42:07 -221852.448291] SLOW spr round 6 (radius: 15)
[12:44:59 -221852.448187] SLOW spr round 7 (radius: 20)
[12:49:08 -221852.448083] SLOW spr round 8 (radius: 25)
[12:53:47 -221852.447977] Model parameter optimization (eps = 0.100000)

[12:53:51] ML tree search #16, logLikelihood: -221852.406435

[12:53:51 -685584.204700] Initial branch length optimization
[12:53:53 -578948.701142] Model parameter optimization (eps = 10.000000)
[12:54:28 -574913.835581] AUTODETECT spr round 1 (radius: 5)
[12:55:58 -444382.940568] AUTODETECT spr round 2 (radius: 10)
[12:57:37 -358813.331492] AUTODETECT spr round 3 (radius: 15)
[12:59:24 -310676.639056] AUTODETECT spr round 4 (radius: 20)
[13:01:32 -268698.034472] AUTODETECT spr round 5 (radius: 25)
[13:04:00 -259523.358536] SPR radius for FAST iterations: 25 (autodetect)
[13:04:00 -259523.358536] Model parameter optimization (eps = 3.000000)
[13:04:13 -259402.018809] FAST spr round 1 (radius: 25)
[13:06:15 -223966.312999] FAST spr round 2 (radius: 25)
[13:07:55 -222083.838395] FAST spr round 3 (radius: 25)
[13:09:25 -221999.802844] FAST spr round 4 (radius: 25)
[13:10:47 -221977.602296] FAST spr round 5 (radius: 25)
[13:12:05 -221975.683665] FAST spr round 6 (radius: 25)
[13:13:21 -221974.217696] FAST spr round 7 (radius: 25)
[13:14:35 -221974.206360] Model parameter optimization (eps = 1.000000)
[13:14:48 -221962.011260] SLOW spr round 1 (radius: 5)
[13:16:28 -221903.465162] SLOW spr round 2 (radius: 5)
[13:18:03 -221897.016012] SLOW spr round 3 (radius: 5)
[13:19:38 -221876.038824] SLOW spr round 4 (radius: 5)
[13:21:12 -221871.360701] SLOW spr round 5 (radius: 5)
[13:22:44 -221870.221907] SLOW spr round 6 (radius: 5)
[13:24:17 -221868.636939] SLOW spr round 7 (radius: 5)
[13:25:49 -221868.636699] SLOW spr round 8 (radius: 10)
[13:27:29 -221867.520353] SLOW spr round 9 (radius: 5)
[13:29:21 -221863.788614] SLOW spr round 10 (radius: 5)
[13:31:01 -221863.788584] SLOW spr round 11 (radius: 10)
[13:32:46 -221863.788556] SLOW spr round 12 (radius: 15)
[13:35:37 -221860.294648] SLOW spr round 13 (radius: 5)
[13:37:33 -221860.047978] SLOW spr round 14 (radius: 5)
[13:39:17 -221860.045808] SLOW spr round 15 (radius: 10)
[13:41:03 -221860.045249] SLOW spr round 16 (radius: 15)
[13:43:51 -221860.045049] SLOW spr round 17 (radius: 20)
[13:47:58 -221860.044962] SLOW spr round 18 (radius: 25)
[13:52:27 -221860.044912] Model parameter optimization (eps = 0.100000)

[13:52:31] ML tree search #17, logLikelihood: -221859.994118

[13:52:31 -687482.084485] Initial branch length optimization
[13:52:34 -578009.742313] Model parameter optimization (eps = 10.000000)
[13:53:20 -574564.995086] AUTODETECT spr round 1 (radius: 5)
[13:54:50 -455864.203037] AUTODETECT spr round 2 (radius: 10)
[13:56:30 -360335.254743] AUTODETECT spr round 3 (radius: 15)
[13:58:25 -293289.869437] AUTODETECT spr round 4 (radius: 20)
[14:00:34 -268794.931023] AUTODETECT spr round 5 (radius: 25)
[14:02:57 -260054.831362] SPR radius for FAST iterations: 25 (autodetect)
[14:02:57 -260054.831362] Model parameter optimization (eps = 3.000000)
[14:03:11 -259982.328929] FAST spr round 1 (radius: 25)
[14:05:16 -225850.154223] FAST spr round 2 (radius: 25)
[14:07:01 -222800.218869] FAST spr round 3 (radius: 25)
[14:08:34 -222031.610195] FAST spr round 4 (radius: 25)
[14:10:02 -221960.312499] FAST spr round 5 (radius: 25)
[14:11:19 -221952.790756] FAST spr round 6 (radius: 25)
[14:12:34 -221952.790444] Model parameter optimization (eps = 1.000000)
[14:12:49 -221933.314642] SLOW spr round 1 (radius: 5)
[14:14:30 -221864.696145] SLOW spr round 2 (radius: 5)
[14:16:07 -221857.047597] SLOW spr round 3 (radius: 5)
[14:17:40 -221857.047307] SLOW spr round 4 (radius: 10)
[14:19:21 -221856.087393] SLOW spr round 5 (radius: 5)
[14:21:13 -221855.402228] SLOW spr round 6 (radius: 5)
[14:22:54 -221855.401939] SLOW spr round 7 (radius: 10)
[14:24:39 -221855.401795] SLOW spr round 8 (radius: 15)
[14:27:29 -221855.401662] SLOW spr round 9 (radius: 20)
[14:31:44 -221855.401527] SLOW spr round 10 (radius: 25)
[14:36:22 -221855.401391] Model parameter optimization (eps = 0.100000)

[14:36:32] ML tree search #18, logLikelihood: -221854.275251

[14:36:32 -687927.644819] Initial branch length optimization
[14:36:35 -579325.311184] Model parameter optimization (eps = 10.000000)
[14:37:13 -575491.893133] AUTODETECT spr round 1 (radius: 5)
[14:38:43 -452787.617500] AUTODETECT spr round 2 (radius: 10)
[14:40:26 -338268.615422] AUTODETECT spr round 3 (radius: 15)
[14:42:14 -285575.955747] AUTODETECT spr round 4 (radius: 20)
[14:44:25 -261781.932221] AUTODETECT spr round 5 (radius: 25)
[14:46:58 -259150.077748] SPR radius for FAST iterations: 25 (autodetect)
[14:46:58 -259150.077748] Model parameter optimization (eps = 3.000000)
[14:47:03 -259145.888210] FAST spr round 1 (radius: 25)
[14:49:08 -223298.539374] FAST spr round 2 (radius: 25)
[14:50:46 -222130.036996] FAST spr round 3 (radius: 25)
[14:52:15 -222075.633902] FAST spr round 4 (radius: 25)
[14:53:34 -222071.809003] FAST spr round 5 (radius: 25)
[14:54:50 -222071.808923] Model parameter optimization (eps = 1.000000)
[14:55:04 -221960.121476] SLOW spr round 1 (radius: 5)
[14:56:46 -221900.078769] SLOW spr round 2 (radius: 5)
[14:58:23 -221889.114699] SLOW spr round 3 (radius: 5)
[14:59:56 -221888.799737] SLOW spr round 4 (radius: 5)
[15:01:29 -221888.799550] SLOW spr round 5 (radius: 10)
[15:03:09 -221888.602518] SLOW spr round 6 (radius: 5)
[15:04:59 -221888.596890] SLOW spr round 7 (radius: 10)
[15:06:54 -221886.344379] SLOW spr round 8 (radius: 5)
[15:08:44 -221876.838847] SLOW spr round 9 (radius: 5)
[15:10:23 -221876.217111] SLOW spr round 10 (radius: 5)
[15:11:58 -221876.216690] SLOW spr round 11 (radius: 10)
[15:13:40 -221876.216562] SLOW spr round 12 (radius: 15)
[15:16:28 -221876.216446] SLOW spr round 13 (radius: 20)
[15:20:34 -221876.216333] SLOW spr round 14 (radius: 25)
[15:25:21 -221876.216219] Model parameter optimization (eps = 0.100000)

[15:25:27] ML tree search #19, logLikelihood: -221876.101877

[15:25:27 -693218.253859] Initial branch length optimization
[15:25:30 -581402.892025] Model parameter optimization (eps = 10.000000)
[15:26:10 -577454.571165] AUTODETECT spr round 1 (radius: 5)
[15:27:39 -461306.302212] AUTODETECT spr round 2 (radius: 10)
[15:29:19 -353209.366001] AUTODETECT spr round 3 (radius: 15)
[15:31:10 -300229.540280] AUTODETECT spr round 4 (radius: 20)
[15:33:21 -267718.886760] AUTODETECT spr round 5 (radius: 25)
[15:35:55 -256620.446922] SPR radius for FAST iterations: 25 (autodetect)
[15:35:55 -256620.446922] Model parameter optimization (eps = 3.000000)
[15:36:07 -256527.291523] FAST spr round 1 (radius: 25)
[15:38:12 -223154.033856] FAST spr round 2 (radius: 25)
[15:39:49 -222067.083170] FAST spr round 3 (radius: 25)
[15:41:18 -221957.762313] FAST spr round 4 (radius: 25)
[15:42:37 -221947.501058] FAST spr round 5 (radius: 25)
[15:43:52 -221947.489697] Model parameter optimization (eps = 1.000000)
[15:44:05 -221936.443564] SLOW spr round 1 (radius: 5)
[15:45:47 -221862.960947] SLOW spr round 2 (radius: 5)
[15:47:23 -221853.554112] SLOW spr round 3 (radius: 5)
[15:48:55 -221853.552616] SLOW spr round 4 (radius: 10)
[15:50:34 -221850.942537] SLOW spr round 5 (radius: 5)
[15:52:24 -221845.868088] SLOW spr round 6 (radius: 5)
[15:54:04 -221845.805585] SLOW spr round 7 (radius: 10)
[15:55:47 -221844.979205] SLOW spr round 8 (radius: 5)
[15:57:36 -221844.974519] SLOW spr round 9 (radius: 10)
[15:59:27 -221844.973069] SLOW spr round 10 (radius: 15)
[16:02:05 -221844.972580] SLOW spr round 11 (radius: 20)
[16:05:59 -221844.972415] SLOW spr round 12 (radius: 25)
[16:10:15 -221844.972357] Model parameter optimization (eps = 0.100000)

[16:10:26] ML tree search #20, logLikelihood: -221844.688400


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.169960,0.462623) (0.221548,0.513479) (0.311899,0.814714) (0.296593,1.866207) 
   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: -221833.962851

AIC score: 447437.925703 / AICc score: 7557657.925703 / BIC score: 455162.795725
Free parameters (model + branch lengths): 1885

WARNING: Number of free parameters (K=1885) is larger than alignment size (n=445).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 48 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P17735/3_mltree/P17735.raxml.bestTreeCollapsed
Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P17735/3_mltree/P17735.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P17735/3_mltree/P17735.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P17735/3_mltree/P17735.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P17735/3_mltree/P17735.raxml.log

Analysis started: 01-Jul-2021 14:36:29 / finished: 02-Jul-2021 06:46:55

Elapsed time: 58226.254 seconds