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 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM

RAxML-NG was called at 13-Jul-2021 16:33:11 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96NS5/2_msa/Q96NS5_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96NS5/3_mltree/Q96NS5 --seed 2 --threads 9 --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 (9 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96NS5/2_msa/Q96NS5_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 1055 sites

WARNING: Sequences tr_G3QMX5_G3QMX5_GORGO_9595 and tr_H2NAT9_H2NAT9_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3QMX5_G3QMX5_GORGO_9595 and tr_H2Q1Y0_H2Q1Y0_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3QMX5_G3QMX5_GORGO_9595 and sp_Q12955_ANK3_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3QUG4_G3QUG4_GORGO_9595 and tr_H2PMV9_H2PMV9_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3QUG4_G3QUG4_GORGO_9595 and sp_Q9Y574_ASB4_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3SG36_G3SG36_GORGO_9595 and tr_K7DU15_K7DU15_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3SG36_G3SG36_GORGO_9595 and sp_Q8IWZ3_ANKH1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_F6XSE4_F6XSE4_CANLF_9615 and tr_F6W4W9_F6W4W9_HORSE_9796 are exactly identical!
WARNING: Sequences tr_F6XSE4_F6XSE4_CANLF_9615 and tr_A0A2U4AGJ9_A0A2U4AGJ9_TURTR_9739 are exactly identical!
WARNING: Sequences tr_F6XSE4_F6XSE4_CANLF_9615 and tr_A0A2U3ZD56_A0A2U3ZD56_ODORO_9708 are exactly identical!
WARNING: Sequences tr_F6XSE4_F6XSE4_CANLF_9615 and tr_A0A2U3XJ53_A0A2U3XJ53_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_F6XSE4_F6XSE4_CANLF_9615 and tr_A0A2Y9PPE1_A0A2Y9PPE1_DELLE_9749 are exactly identical!
WARNING: Sequences tr_F6XSE4_F6XSE4_CANLF_9615 and tr_A0A2Y9SX60_A0A2Y9SX60_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_F6XSE4_F6XSE4_CANLF_9615 and tr_A0A384B3D1_A0A384B3D1_BALAS_310752 are exactly identical!
WARNING: Sequences tr_W5Q8W7_W5Q8W7_SHEEP_9940 and tr_E1B719_E1B719_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_A0A158NYD8_A0A158NYD8_ATTCE_12957 and tr_A0A195AYV4_A0A195AYV4_9HYME_520822 are exactly identical!
WARNING: Sequences tr_F6ZH85_F6ZH85_MACMU_9544 and tr_A0A2K5Y5C2_A0A2K5Y5C2_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F7EBU2_F7EBU2_MACMU_9544 and tr_A0A2I3NH47_A0A2I3NH47_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_H0YTV7_H0YTV7_TAEGU_59729 and tr_U3K3W2_U3K3W2_FICAL_59894 are exactly identical!
WARNING: Sequences tr_B4MF25_B4MF25_DROVI_7244 and tr_D0Z7C6_D0Z7C6_DROVI_7244 are exactly identical!
WARNING: Sequences tr_G7PDE9_G7PDE9_MACFA_9541 and tr_A0A2K6CI25_A0A2K6CI25_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7PDE9_G7PDE9_MACFA_9541 and tr_A0A2K6ACH1_A0A2K6ACH1_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A0D9RKK3_A0A0D9RKK3_CHLSB_60711 and tr_A0A2K6CDT9_A0A2K6CDT9_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A0Q3PEH9_A0A0Q3PEH9_AMAAE_12930 and tr_A0A087R3L6_A0A087R3L6_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A2I0MH24_A0A2I0MH24_COLLI_8932 and tr_A0A1V4JV40_A0A1V4JV40_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A0V1D676_A0A0V1D676_TRIBR_45882 and tr_A0A0V0WNA2_A0A0V0WNA2_9BILA_92179 are exactly identical!
WARNING: Sequences tr_A0A0V1D676_A0A0V1D676_TRIBR_45882 and tr_A0A0V1LCQ3_A0A0V1LCQ3_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V0ZB57_A0A0V0ZB57_9BILA_990121 and tr_A0A0V0UDW4_A0A0V0UDW4_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A0V1P9M3_A0A0V1P9M3_9BILA_92180 and tr_A0A0V0UCC5_A0A0V0UCC5_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A2D0SPM5_A0A2D0SPM5_ICTPU_7998 and tr_A0A2D0SPN6_A0A2D0SPN6_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0SZG3_A0A2D0SZG3_ICTPU_7998 and tr_A0A2D0SZH1_A0A2D0SZH1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0SZG3_A0A2D0SZG3_ICTPU_7998 and tr_A0A2D0SZW2_A0A2D0SZW2_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0SZG3_A0A2D0SZG3_ICTPU_7998 and tr_A0A2D0SZW7_A0A2D0SZW7_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0SZG3_A0A2D0SZG3_ICTPU_7998 and tr_A0A2D0T0E7_A0A2D0T0E7_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0SZG3_A0A2D0SZG3_ICTPU_7998 and tr_A0A2D0T0F3_A0A2D0T0F3_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2Y9M5I2_A0A2Y9M5I2_DELLE_9749 and tr_A0A383Z7Q5_A0A383Z7Q5_BALAS_310752 are exactly identical!
WARNING: Duplicate sequences found: 36

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96NS5/3_mltree/Q96NS5.raxml.reduced.phy

Alignment comprises 1 partitions and 1055 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 1055 / 1055
Gaps: 40.37 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96NS5/3_mltree/Q96NS5.raxml.rba

Parallelization scheme autoconfig: 1 worker(s) x 9 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 / 118 / 9440
[00:00:00] Data distribution: max. searches per worker: 20

Starting ML tree search with 20 distinct starting trees

[00:00:00 -1316644.222641] Initial branch length optimization
[00:00:06 -1073188.842204] Model parameter optimization (eps = 10.000000)
[00:01:13 -1068884.655232] AUTODETECT spr round 1 (radius: 5)
[00:04:39 -743984.697668] AUTODETECT spr round 2 (radius: 10)
[00:08:17 -553258.912796] AUTODETECT spr round 3 (radius: 15)
[00:11:18 -475566.057471] AUTODETECT spr round 4 (radius: 20)
[00:13:44 -440787.981503] AUTODETECT spr round 5 (radius: 25)
[00:16:41 -428378.397168] SPR radius for FAST iterations: 25 (autodetect)
[00:16:41 -428378.397168] Model parameter optimization (eps = 3.000000)
[00:16:50 -428237.470058] FAST spr round 1 (radius: 25)
[00:19:29 -394311.890564] FAST spr round 2 (radius: 25)
[00:21:33 -392851.693203] FAST spr round 3 (radius: 25)
[00:23:20 -392727.627103] FAST spr round 4 (radius: 25)
[00:24:53 -392714.374286] FAST spr round 5 (radius: 25)
[00:26:20 -392707.043498] FAST spr round 6 (radius: 25)
[00:27:43 -392707.043220] Model parameter optimization (eps = 1.000000)
[00:28:05 -392085.489522] SLOW spr round 1 (radius: 5)
[00:30:07 -391996.090302] SLOW spr round 2 (radius: 5)
[00:32:05 -391979.170260] SLOW spr round 3 (radius: 5)
[00:33:58 -391973.362439] SLOW spr round 4 (radius: 5)
[00:35:47 -391973.361674] SLOW spr round 5 (radius: 10)
[00:37:41 -391965.994303] SLOW spr round 6 (radius: 5)
[00:39:56 -391958.899449] SLOW spr round 7 (radius: 5)
[00:41:55 -391955.349753] SLOW spr round 8 (radius: 5)
[00:43:49 -391951.871780] SLOW spr round 9 (radius: 5)
[00:45:41 -391946.248262] SLOW spr round 10 (radius: 5)
[00:47:30 -391945.980679] SLOW spr round 11 (radius: 5)
[00:49:18 -391945.979624] SLOW spr round 12 (radius: 10)
[00:51:10 -391945.979585] SLOW spr round 13 (radius: 15)
[00:54:49 -391944.105094] SLOW spr round 14 (radius: 5)
[00:57:06 -391943.988015] SLOW spr round 15 (radius: 5)
[00:59:07 -391943.986169] SLOW spr round 16 (radius: 10)
[01:01:07 -391943.986103] SLOW spr round 17 (radius: 15)
[01:04:36 -391942.302902] SLOW spr round 18 (radius: 5)
[01:06:53 -391942.301452] SLOW spr round 19 (radius: 10)
[01:09:11 -391942.301358] SLOW spr round 20 (radius: 15)
[01:12:31 -391942.301336] SLOW spr round 21 (radius: 20)
[01:18:03 -391942.301330] SLOW spr round 22 (radius: 25)
[01:25:19 -391942.301329] Model parameter optimization (eps = 0.100000)

[01:25:23] ML tree search #1, logLikelihood: -391942.201709

[01:25:23 -1328503.393208] Initial branch length optimization
[01:25:27 -1087235.804158] Model parameter optimization (eps = 10.000000)
[01:26:01 -1083012.796808] AUTODETECT spr round 1 (radius: 5)
[01:27:49 -764968.965414] AUTODETECT spr round 2 (radius: 10)
[01:29:43 -571223.855790] AUTODETECT spr round 3 (radius: 15)
[01:31:44 -493408.596820] AUTODETECT spr round 4 (radius: 20)
[01:34:00 -454474.096322] AUTODETECT spr round 5 (radius: 25)
[01:36:34 -439151.271168] SPR radius for FAST iterations: 25 (autodetect)
[01:36:34 -439151.271168] Model parameter optimization (eps = 3.000000)
[01:36:43 -439010.832582] FAST spr round 1 (radius: 25)
[01:39:24 -395276.675255] FAST spr round 2 (radius: 25)
[01:41:37 -392847.457850] FAST spr round 3 (radius: 25)
[01:43:28 -392746.084847] FAST spr round 4 (radius: 25)
[01:45:01 -392723.097711] FAST spr round 5 (radius: 25)
[01:46:27 -392722.010993] FAST spr round 6 (radius: 25)
[01:47:50 -392722.010752] Model parameter optimization (eps = 1.000000)
[01:48:10 -392095.429418] SLOW spr round 1 (radius: 5)
[01:50:12 -391983.829433] SLOW spr round 2 (radius: 5)
[01:52:11 -391967.852925] SLOW spr round 3 (radius: 5)
[01:54:03 -391960.758595] SLOW spr round 4 (radius: 5)
[01:55:52 -391960.757195] SLOW spr round 5 (radius: 10)
[01:57:48 -391955.089319] SLOW spr round 6 (radius: 5)
[02:00:02 -391951.788286] SLOW spr round 7 (radius: 5)
[02:02:01 -391951.785633] SLOW spr round 8 (radius: 10)
[02:04:00 -391951.784787] SLOW spr round 9 (radius: 15)
[02:07:23 -391945.978950] SLOW spr round 10 (radius: 5)
[02:09:40 -391945.978247] SLOW spr round 11 (radius: 10)
[02:11:58 -391945.978205] SLOW spr round 12 (radius: 15)
[02:15:12 -391945.978196] SLOW spr round 13 (radius: 20)
[02:20:11 -391945.978191] SLOW spr round 14 (radius: 25)
[02:26:44 -391945.978188] Model parameter optimization (eps = 0.100000)

[02:26:51] ML tree search #2, logLikelihood: -391945.615182

[02:26:51 -1320118.890964] Initial branch length optimization
[02:26:55 -1079020.676420] Model parameter optimization (eps = 10.000000)
[02:27:41 -1074588.147895] AUTODETECT spr round 1 (radius: 5)
[02:29:31 -750524.107352] AUTODETECT spr round 2 (radius: 10)
[02:31:22 -584762.277145] AUTODETECT spr round 3 (radius: 15)
[02:33:28 -483879.237940] AUTODETECT spr round 4 (radius: 20)
[02:35:52 -440968.140107] AUTODETECT spr round 5 (radius: 25)
[02:38:18 -433327.273596] SPR radius for FAST iterations: 25 (autodetect)
[02:38:18 -433327.273596] Model parameter optimization (eps = 3.000000)
[02:38:40 -432712.292198] FAST spr round 1 (radius: 25)
[02:41:16 -394262.042283] FAST spr round 2 (radius: 25)
[02:43:23 -392187.402381] FAST spr round 3 (radius: 25)
[02:45:07 -392110.993432] FAST spr round 4 (radius: 25)
[02:46:38 -392105.327656] FAST spr round 5 (radius: 25)
[02:48:02 -392105.326941] Model parameter optimization (eps = 1.000000)
[02:48:19 -392071.064562] SLOW spr round 1 (radius: 5)
[02:50:20 -391998.497602] SLOW spr round 2 (radius: 5)
[02:52:14 -391974.057106] SLOW spr round 3 (radius: 5)
[02:54:06 -391969.970863] SLOW spr round 4 (radius: 5)
[02:55:54 -391969.970142] SLOW spr round 5 (radius: 10)
[02:57:49 -391965.900254] SLOW spr round 6 (radius: 5)
[03:00:00 -391963.891949] SLOW spr round 7 (radius: 5)
[03:01:57 -391963.891930] SLOW spr round 8 (radius: 10)
[03:03:56 -391963.891929] SLOW spr round 9 (radius: 15)
[03:07:28 -391963.891929] SLOW spr round 10 (radius: 20)
[03:12:36 -391963.891929] SLOW spr round 11 (radius: 25)
[03:19:16 -391963.891929] Model parameter optimization (eps = 0.100000)

[03:19:21] ML tree search #3, logLikelihood: -391963.880125

[03:19:21 -1329103.652641] Initial branch length optimization
[03:19:25 -1088161.722640] Model parameter optimization (eps = 10.000000)
[03:19:52 -1084039.956117] AUTODETECT spr round 1 (radius: 5)
[03:21:40 -753967.265921] AUTODETECT spr round 2 (radius: 10)
[03:23:31 -574603.766699] AUTODETECT spr round 3 (radius: 15)
[03:25:33 -488428.444679] AUTODETECT spr round 4 (radius: 20)
[03:27:58 -448855.757285] AUTODETECT spr round 5 (radius: 25)
[03:30:55 -435066.287898] SPR radius for FAST iterations: 25 (autodetect)
[03:30:55 -435066.287898] Model parameter optimization (eps = 3.000000)
[03:31:22 -434514.990486] FAST spr round 1 (radius: 25)
[03:34:05 -394026.837729] FAST spr round 2 (radius: 25)
[03:36:13 -392274.805713] FAST spr round 3 (radius: 25)
[03:38:00 -392101.966424] FAST spr round 4 (radius: 25)
[03:39:36 -392076.626506] FAST spr round 5 (radius: 25)
[03:41:04 -392072.036552] FAST spr round 6 (radius: 25)
[03:42:29 -392070.336360] FAST spr round 7 (radius: 25)
[03:43:52 -392070.336351] Model parameter optimization (eps = 1.000000)
[03:44:05 -392060.536476] SLOW spr round 1 (radius: 5)
[03:45:59 -391982.714486] SLOW spr round 2 (radius: 5)
[03:47:51 -391976.809433] SLOW spr round 3 (radius: 5)
[03:49:39 -391976.808688] SLOW spr round 4 (radius: 10)
[03:51:34 -391974.694679] SLOW spr round 5 (radius: 5)
[03:53:47 -391974.188555] SLOW spr round 6 (radius: 5)
[03:55:46 -391973.757865] SLOW spr round 7 (radius: 5)
[03:57:37 -391973.756159] SLOW spr round 8 (radius: 10)
[03:59:40 -391960.700518] SLOW spr round 9 (radius: 5)
[04:01:57 -391952.588350] SLOW spr round 10 (radius: 5)
[04:03:58 -391949.808056] SLOW spr round 11 (radius: 5)
[04:05:50 -391948.786849] SLOW spr round 12 (radius: 5)
[04:07:39 -391948.785057] SLOW spr round 13 (radius: 10)
[04:09:34 -391948.784554] SLOW spr round 14 (radius: 15)
[04:13:19 -391948.293876] SLOW spr round 15 (radius: 5)
[04:15:37 -391945.355884] SLOW spr round 16 (radius: 5)
[04:17:38 -391945.355276] SLOW spr round 17 (radius: 10)
[04:19:41 -391945.355212] SLOW spr round 18 (radius: 15)
[04:23:16 -391945.355197] SLOW spr round 19 (radius: 20)
[04:28:31 -391945.355193] SLOW spr round 20 (radius: 25)
[04:35:25 -391945.355192] Model parameter optimization (eps = 0.100000)

[04:35:31] ML tree search #4, logLikelihood: -391945.251834

[04:35:31 -1327085.708121] Initial branch length optimization
[04:35:36 -1085693.908705] Model parameter optimization (eps = 10.000000)
[04:36:07 -1081215.824984] AUTODETECT spr round 1 (radius: 5)
[04:37:56 -760938.891936] AUTODETECT spr round 2 (radius: 10)
[04:39:47 -573852.270684] AUTODETECT spr round 3 (radius: 15)
[04:41:44 -483948.659930] AUTODETECT spr round 4 (radius: 20)
[04:43:52 -455747.446618] AUTODETECT spr round 5 (radius: 25)
[04:46:27 -437406.635410] SPR radius for FAST iterations: 25 (autodetect)
[04:46:27 -437406.635410] Model parameter optimization (eps = 3.000000)
[04:46:51 -436607.734777] FAST spr round 1 (radius: 25)
[04:49:37 -393853.851827] FAST spr round 2 (radius: 25)
[04:51:40 -392319.831078] FAST spr round 3 (radius: 25)
[04:53:24 -392156.770483] FAST spr round 4 (radius: 25)
[04:54:57 -392137.116915] FAST spr round 5 (radius: 25)
[04:56:25 -392121.586687] FAST spr round 6 (radius: 25)
[04:57:49 -392117.950081] FAST spr round 7 (radius: 25)
[04:59:12 -392116.431845] FAST spr round 8 (radius: 25)
[05:00:34 -392116.431720] Model parameter optimization (eps = 1.000000)
[05:00:40 -392113.780739] SLOW spr round 1 (radius: 5)
[05:02:34 -392041.283805] SLOW spr round 2 (radius: 5)
[05:04:27 -392039.588628] SLOW spr round 3 (radius: 5)
[05:06:18 -392039.588335] SLOW spr round 4 (radius: 10)
[05:08:16 -392038.308282] SLOW spr round 5 (radius: 5)
[05:10:33 -392026.503898] SLOW spr round 6 (radius: 5)
[05:12:34 -392026.503797] SLOW spr round 7 (radius: 10)
[05:14:37 -392026.503797] SLOW spr round 8 (radius: 15)
[05:18:19 -392025.050639] SLOW spr round 9 (radius: 5)
[05:20:44 -392018.078862] SLOW spr round 10 (radius: 5)
[05:23:07 -392016.331157] SLOW spr round 11 (radius: 5)
[05:25:20 -392016.328235] SLOW spr round 12 (radius: 10)
[05:27:37 -392016.327354] SLOW spr round 13 (radius: 15)
[05:31:52 -392016.327077] SLOW spr round 14 (radius: 20)
[05:37:57 -392016.326989] SLOW spr round 15 (radius: 25)
[05:46:10 -392016.326962] Model parameter optimization (eps = 0.100000)

[05:46:15] ML tree search #5, logLikelihood: -392016.302740

[05:46:15 -1317714.454466] Initial branch length optimization
[05:46:20 -1078044.131839] Model parameter optimization (eps = 10.000000)
[05:46:53 -1073731.563940] AUTODETECT spr round 1 (radius: 5)
[05:48:58 -747673.124816] AUTODETECT spr round 2 (radius: 10)
[05:51:08 -573143.389436] AUTODETECT spr round 3 (radius: 15)
[05:53:27 -483733.813888] AUTODETECT spr round 4 (radius: 20)
[05:56:00 -452333.408719] AUTODETECT spr round 5 (radius: 25)
[05:59:06 -433343.775123] SPR radius for FAST iterations: 25 (autodetect)
[05:59:06 -433343.775123] Model parameter optimization (eps = 3.000000)
[05:59:30 -432668.040619] FAST spr round 1 (radius: 25)
[06:02:46 -394255.618257] FAST spr round 2 (radius: 25)
[06:05:18 -392355.012190] FAST spr round 3 (radius: 25)
[06:07:29 -392087.345350] FAST spr round 4 (radius: 25)
[06:09:14 -392069.338108] FAST spr round 5 (radius: 25)
[06:10:51 -392069.336900] Model parameter optimization (eps = 1.000000)
[06:11:06 -392059.040111] SLOW spr round 1 (radius: 5)
[06:13:26 -391966.921035] SLOW spr round 2 (radius: 5)
[06:15:42 -391957.291338] SLOW spr round 3 (radius: 5)
[06:17:51 -391956.453402] SLOW spr round 4 (radius: 5)
[06:19:58 -391955.831370] SLOW spr round 5 (radius: 5)
[06:22:05 -391951.696198] SLOW spr round 6 (radius: 5)
[06:24:11 -391951.695894] SLOW spr round 7 (radius: 10)
[06:26:31 -391950.568737] SLOW spr round 8 (radius: 5)
[06:29:10 -391948.204653] SLOW spr round 9 (radius: 5)
[06:31:31 -391948.204463] SLOW spr round 10 (radius: 10)
[06:33:54 -391948.204393] SLOW spr round 11 (radius: 15)
[06:38:11 -391944.269557] SLOW spr round 12 (radius: 5)
[06:40:54 -391944.266342] SLOW spr round 13 (radius: 10)
[06:43:39 -391944.266186] SLOW spr round 14 (radius: 15)
[06:47:40 -391944.266170] SLOW spr round 15 (radius: 20)
[06:53:48 -391944.266165] SLOW spr round 16 (radius: 25)
[07:01:46 -391944.266162] Model parameter optimization (eps = 0.100000)

[07:01:54] ML tree search #6, logLikelihood: -391943.883026

[07:01:55 -1326023.850400] Initial branch length optimization
[07:01:59 -1083372.332278] Model parameter optimization (eps = 10.000000)
[07:02:35 -1078827.143870] AUTODETECT spr round 1 (radius: 5)
[07:04:43 -744038.451398] AUTODETECT spr round 2 (radius: 10)
[07:06:54 -582485.201107] AUTODETECT spr round 3 (radius: 15)
[07:09:15 -484372.479023] AUTODETECT spr round 4 (radius: 20)
[07:11:59 -447552.391923] AUTODETECT spr round 5 (radius: 25)
[07:15:07 -438902.817841] SPR radius for FAST iterations: 25 (autodetect)
[07:15:07 -438902.817841] Model parameter optimization (eps = 3.000000)
[07:15:34 -438010.815175] FAST spr round 1 (radius: 25)
[07:18:49 -394087.597962] FAST spr round 2 (radius: 25)
[07:21:24 -392291.813395] FAST spr round 3 (radius: 25)
[07:23:28 -392139.298325] FAST spr round 4 (radius: 25)
[07:25:22 -392123.776723] FAST spr round 5 (radius: 25)
[07:27:03 -392121.530779] FAST spr round 6 (radius: 25)
[07:28:35 -392121.519401] Model parameter optimization (eps = 1.000000)
[07:28:52 -392067.981360] SLOW spr round 1 (radius: 5)
[07:30:54 -391979.959729] SLOW spr round 2 (radius: 5)
[07:32:53 -391965.322936] SLOW spr round 3 (radius: 5)
[07:34:46 -391957.991661] SLOW spr round 4 (radius: 5)
[07:36:53 -391957.990459] SLOW spr round 5 (radius: 10)
[07:39:35 -391951.720480] SLOW spr round 6 (radius: 5)
[07:42:26 -391951.045139] SLOW spr round 7 (radius: 5)
[07:45:16 -391949.688088] SLOW spr round 8 (radius: 5)
[07:47:53 -391949.687470] SLOW spr round 9 (radius: 10)
[07:50:36 -391949.687434] SLOW spr round 10 (radius: 15)
[07:55:29 -391949.687430] SLOW spr round 11 (radius: 20)
[08:02:39 -391949.687428] SLOW spr round 12 (radius: 25)
[08:12:20 -391949.687427] Model parameter optimization (eps = 0.100000)

[08:12:31] ML tree search #7, logLikelihood: -391949.583329

[08:12:32 -1321884.074941] Initial branch length optimization
[08:12:36 -1083526.964693] Model parameter optimization (eps = 10.000000)
[08:13:24 -1079318.993462] AUTODETECT spr round 1 (radius: 5)
[08:15:56 -749616.008839] AUTODETECT spr round 2 (radius: 10)
[08:18:31 -588514.230706] AUTODETECT spr round 3 (radius: 15)
[08:21:27 -490186.492784] AUTODETECT spr round 4 (radius: 20)
[08:24:46 -439658.899375] AUTODETECT spr round 5 (radius: 25)
[08:28:28 -430391.088664] SPR radius for FAST iterations: 25 (autodetect)
[08:28:28 -430391.088664] Model parameter optimization (eps = 3.000000)
[08:29:05 -429798.820877] FAST spr round 1 (radius: 25)
[08:32:46 -394597.745404] FAST spr round 2 (radius: 25)
[08:35:42 -392241.811568] FAST spr round 3 (radius: 25)
[08:38:15 -392099.227630] FAST spr round 4 (radius: 25)
[08:40:25 -392044.081319] FAST spr round 5 (radius: 25)
[08:42:26 -392042.314655] FAST spr round 6 (radius: 25)
[08:44:31 -392042.314613] Model parameter optimization (eps = 1.000000)
[08:44:48 -392026.413870] SLOW spr round 1 (radius: 5)
[08:47:33 -391932.463693] SLOW spr round 2 (radius: 5)
[08:50:14 -391921.550496] SLOW spr round 3 (radius: 5)
[08:52:47 -391921.549551] SLOW spr round 4 (radius: 10)
[08:55:26 -391918.398269] SLOW spr round 5 (radius: 5)
[08:58:33 -391914.206564] SLOW spr round 6 (radius: 5)
[09:01:17 -391914.206304] SLOW spr round 7 (radius: 10)
[09:04:07 -391914.206298] SLOW spr round 8 (radius: 15)
[09:08:59 -391914.206297] SLOW spr round 9 (radius: 20)
[09:15:54 -391914.206297] SLOW spr round 10 (radius: 25)
[09:24:55 -391914.206297] Model parameter optimization (eps = 0.100000)

[09:25:09] ML tree search #8, logLikelihood: -391913.497698

[09:25:09 -1322291.313157] Initial branch length optimization
[09:25:14 -1076569.801470] Model parameter optimization (eps = 10.000000)
[09:26:19 -1072417.244738] AUTODETECT spr round 1 (radius: 5)
[09:28:44 -749830.204824] AUTODETECT spr round 2 (radius: 10)
[09:31:23 -591551.622730] AUTODETECT spr round 3 (radius: 15)
[09:34:24 -480952.958511] AUTODETECT spr round 4 (radius: 20)
[09:37:41 -443642.128478] AUTODETECT spr round 5 (radius: 25)
[09:41:11 -439009.072617] SPR radius for FAST iterations: 25 (autodetect)
[09:41:11 -439009.072617] Model parameter optimization (eps = 3.000000)
[09:41:26 -438862.519345] FAST spr round 1 (radius: 25)
[09:45:21 -394788.467978] FAST spr round 2 (radius: 25)
[09:48:19 -392803.139014] FAST spr round 3 (radius: 25)
[09:50:59 -392682.992829] FAST spr round 4 (radius: 25)
[09:53:16 -392661.420249] FAST spr round 5 (radius: 25)
[09:55:23 -392655.641415] FAST spr round 6 (radius: 25)
[09:57:31 -392651.985570] FAST spr round 7 (radius: 25)
[09:59:34 -392651.984852] Model parameter optimization (eps = 1.000000)
[10:00:05 -392059.457134] SLOW spr round 1 (radius: 5)
[10:02:56 -391965.960634] SLOW spr round 2 (radius: 5)
[10:05:38 -391953.730272] SLOW spr round 3 (radius: 5)
[10:08:19 -391952.980245] SLOW spr round 4 (radius: 5)
[10:10:58 -391952.980070] SLOW spr round 5 (radius: 10)
[10:13:45 -391939.262475] SLOW spr round 6 (radius: 5)
[10:17:02 -391934.478929] SLOW spr round 7 (radius: 5)
[10:19:38 -391932.787949] SLOW spr round 8 (radius: 5)
[10:22:21 -391932.787337] SLOW spr round 9 (radius: 10)
[10:25:03 -391932.787330] SLOW spr round 10 (radius: 15)
[10:29:50 -391932.787329] SLOW spr round 11 (radius: 20)
[10:36:30 -391932.787329] SLOW spr round 12 (radius: 25)
[10:45:06 -391932.787328] Model parameter optimization (eps = 0.100000)

[10:45:12] ML tree search #9, logLikelihood: -391932.727066

[10:45:12 -1332379.269352] Initial branch length optimization
[10:45:17 -1083852.593306] Model parameter optimization (eps = 10.000000)
[10:46:07 -1079252.339891] AUTODETECT spr round 1 (radius: 5)
[10:48:47 -754059.665428] AUTODETECT spr round 2 (radius: 10)
[10:51:26 -557551.288341] AUTODETECT spr round 3 (radius: 15)
[10:54:32 -465989.107630] AUTODETECT spr round 4 (radius: 20)
[10:57:51 -440854.178493] AUTODETECT spr round 5 (radius: 25)
[11:01:32 -435886.562051] SPR radius for FAST iterations: 25 (autodetect)
[11:01:32 -435886.562051] Model parameter optimization (eps = 3.000000)
[11:02:04 -435090.771965] FAST spr round 1 (radius: 25)
[11:05:55 -393993.483007] FAST spr round 2 (radius: 25)
[11:09:00 -392244.451177] FAST spr round 3 (radius: 25)
[11:11:26 -392123.977493] FAST spr round 4 (radius: 25)
[11:13:32 -392101.459858] FAST spr round 5 (radius: 25)
[11:15:44 -392090.426514] FAST spr round 6 (radius: 25)
[11:17:50 -392086.148183] FAST spr round 7 (radius: 25)
[11:19:54 -392086.146735] Model parameter optimization (eps = 1.000000)
[11:20:19 -392069.081114] SLOW spr round 1 (radius: 5)
[11:23:11 -391975.258209] SLOW spr round 2 (radius: 5)
[11:25:56 -391973.436384] SLOW spr round 3 (radius: 5)
[11:28:33 -391973.435894] SLOW spr round 4 (radius: 10)
[11:31:20 -391973.435392] SLOW spr round 5 (radius: 15)
[11:36:07 -391973.435391] SLOW spr round 6 (radius: 20)
[11:42:59 -391973.435390] SLOW spr round 7 (radius: 25)
[11:51:48 -391973.435390] Model parameter optimization (eps = 0.100000)

[11:51:54] ML tree search #10, logLikelihood: -391973.417115

[11:51:54 -1310008.025204] Initial branch length optimization
[11:51:59 -1070667.140190] Model parameter optimization (eps = 10.000000)
[11:52:37 -1066392.549248] AUTODETECT spr round 1 (radius: 5)
[11:55:01 -753307.133769] AUTODETECT spr round 2 (radius: 10)
[11:57:35 -567928.587637] AUTODETECT spr round 3 (radius: 15)
[12:00:22 -484926.692800] AUTODETECT spr round 4 (radius: 20)
[12:03:25 -445738.068194] AUTODETECT spr round 5 (radius: 25)
[12:06:56 -432238.227857] SPR radius for FAST iterations: 25 (autodetect)
[12:06:56 -432238.227857] Model parameter optimization (eps = 3.000000)
[12:07:10 -432125.379909] FAST spr round 1 (radius: 25)
[12:10:53 -395315.784049] FAST spr round 2 (radius: 25)
[12:13:45 -392781.642616] FAST spr round 3 (radius: 25)
[12:16:08 -392638.493960] FAST spr round 4 (radius: 25)
[12:18:12 -392628.187857] FAST spr round 5 (radius: 25)
[12:20:04 -392621.890395] FAST spr round 6 (radius: 25)
[12:21:59 -392621.888991] Model parameter optimization (eps = 1.000000)
[12:22:27 -392100.180736] SLOW spr round 1 (radius: 5)
[12:25:03 -391959.935441] SLOW spr round 2 (radius: 5)
[12:27:34 -391956.937431] SLOW spr round 3 (radius: 5)
[12:29:59 -391948.033447] SLOW spr round 4 (radius: 5)
[12:32:20 -391948.033431] SLOW spr round 5 (radius: 10)
[12:34:48 -391946.376482] SLOW spr round 6 (radius: 5)
[12:37:44 -391943.612439] SLOW spr round 7 (radius: 5)
[12:40:16 -391943.611088] SLOW spr round 8 (radius: 10)
[12:42:52 -391943.611018] SLOW spr round 9 (radius: 15)
[12:47:16 -391943.611014] SLOW spr round 10 (radius: 20)
[12:53:30 -391943.611012] SLOW spr round 11 (radius: 25)
[13:01:32 -391943.611010] Model parameter optimization (eps = 0.100000)

[13:01:44] ML tree search #11, logLikelihood: -391943.049846

[13:01:44 -1326299.099790] Initial branch length optimization
[13:01:49 -1081662.689658] Model parameter optimization (eps = 10.000000)
[13:02:20 -1077597.498145] AUTODETECT spr round 1 (radius: 5)
[13:04:45 -749032.300650] AUTODETECT spr round 2 (radius: 10)
[13:07:08 -587320.920826] AUTODETECT spr round 3 (radius: 15)
[13:09:55 -506600.362144] AUTODETECT spr round 4 (radius: 20)
[13:12:51 -457508.060535] AUTODETECT spr round 5 (radius: 25)
[13:16:21 -434837.763590] SPR radius for FAST iterations: 25 (autodetect)
[13:16:21 -434837.763590] Model parameter optimization (eps = 3.000000)
[13:16:48 -434078.535261] FAST spr round 1 (radius: 25)
[13:20:29 -393938.981725] FAST spr round 2 (radius: 25)
[13:23:04 -392210.812399] FAST spr round 3 (radius: 25)
[13:25:31 -392103.853196] FAST spr round 4 (radius: 25)
[13:27:44 -392084.391645] FAST spr round 5 (radius: 25)
[13:29:56 -392080.916979] FAST spr round 6 (radius: 25)
[13:32:02 -392080.915739] Model parameter optimization (eps = 1.000000)
[13:32:19 -392063.038112] SLOW spr round 1 (radius: 5)
[13:35:07 -391963.092338] SLOW spr round 2 (radius: 5)
[13:37:45 -391956.847546] SLOW spr round 3 (radius: 5)
[13:40:18 -391956.168723] SLOW spr round 4 (radius: 5)
[13:42:44 -391956.167426] SLOW spr round 5 (radius: 10)
[13:45:23 -391943.001432] SLOW spr round 6 (radius: 5)
[13:48:05 -391942.347279] SLOW spr round 7 (radius: 5)
[13:50:46 -391941.872259] SLOW spr round 8 (radius: 5)
[13:53:16 -391941.870829] SLOW spr round 9 (radius: 10)
[13:55:49 -391940.803572] SLOW spr round 10 (radius: 5)
[13:58:44 -391940.803150] SLOW spr round 11 (radius: 10)
[14:01:41 -391940.803145] SLOW spr round 12 (radius: 15)
[14:06:06 -391940.803142] SLOW spr round 13 (radius: 20)
[14:12:46 -391940.803138] SLOW spr round 14 (radius: 25)
[14:21:17 -391940.803134] Model parameter optimization (eps = 0.100000)

[14:21:23] ML tree search #12, logLikelihood: -391940.756257

[14:21:23 -1326653.091973] Initial branch length optimization
[14:21:28 -1082687.545418] Model parameter optimization (eps = 10.000000)
[14:22:12 -1078321.809135] AUTODETECT spr round 1 (radius: 5)
[14:24:43 -738278.899676] AUTODETECT spr round 2 (radius: 10)
[14:27:17 -568883.225023] AUTODETECT spr round 3 (radius: 15)
[14:30:14 -470781.390523] AUTODETECT spr round 4 (radius: 20)
[14:33:34 -436522.384463] AUTODETECT spr round 5 (radius: 25)
[14:37:05 -428409.252801] SPR radius for FAST iterations: 25 (autodetect)
[14:37:05 -428409.252801] Model parameter optimization (eps = 3.000000)
[14:37:37 -427559.735294] FAST spr round 1 (radius: 25)
[14:40:59 -393831.775757] FAST spr round 2 (radius: 25)
[14:43:39 -392196.719168] FAST spr round 3 (radius: 25)
[14:46:06 -392063.874528] FAST spr round 4 (radius: 25)
[14:48:21 -392048.036259] FAST spr round 5 (radius: 25)
[14:50:27 -392047.531639] FAST spr round 6 (radius: 25)
[14:52:23 -392047.529404] Model parameter optimization (eps = 1.000000)
[14:52:42 -392032.196900] SLOW spr round 1 (radius: 5)
[14:55:24 -391953.014047] SLOW spr round 2 (radius: 5)
[14:58:01 -391939.117384] SLOW spr round 3 (radius: 5)
[15:00:39 -391930.325649] SLOW spr round 4 (radius: 5)
[15:03:10 -391925.047939] SLOW spr round 5 (radius: 5)
[15:05:41 -391925.046505] SLOW spr round 6 (radius: 10)
[15:08:17 -391925.046447] SLOW spr round 7 (radius: 15)
[15:12:58 -391925.046444] SLOW spr round 8 (radius: 20)
[15:19:12 -391925.046444] SLOW spr round 9 (radius: 25)
[15:27:28 -391925.046444] Model parameter optimization (eps = 0.100000)

[15:27:33] ML tree search #13, logLikelihood: -391925.026950

[15:27:34 -1327774.581037] Initial branch length optimization
[15:27:39 -1080394.069715] Model parameter optimization (eps = 10.000000)
[15:28:17 -1076061.218307] AUTODETECT spr round 1 (radius: 5)
[15:30:50 -766594.880661] AUTODETECT spr round 2 (radius: 10)
[15:33:25 -589805.014540] AUTODETECT spr round 3 (radius: 15)
[15:36:10 -499355.849317] AUTODETECT spr round 4 (radius: 20)
[15:39:28 -449880.491463] AUTODETECT spr round 5 (radius: 25)
[15:43:48 -443920.523244] SPR radius for FAST iterations: 25 (autodetect)
[15:43:48 -443920.523244] Model parameter optimization (eps = 3.000000)
[15:44:17 -443228.886558] FAST spr round 1 (radius: 25)
[15:48:04 -394594.818968] FAST spr round 2 (radius: 25)
[15:51:03 -392309.722490] FAST spr round 3 (radius: 25)
[15:53:35 -392138.156211] FAST spr round 4 (radius: 25)
[15:55:50 -392103.295281] FAST spr round 5 (radius: 25)
[15:58:01 -392096.034554] FAST spr round 6 (radius: 25)
[16:00:00 -392096.033657] Model parameter optimization (eps = 1.000000)
[16:00:09 -392094.279893] SLOW spr round 1 (radius: 5)
[16:02:57 -392004.336032] SLOW spr round 2 (radius: 5)
[16:05:34 -391992.414844] SLOW spr round 3 (radius: 5)
[16:08:10 -391988.789082] SLOW spr round 4 (radius: 5)
[16:10:41 -391988.788384] SLOW spr round 5 (radius: 10)
[16:13:21 -391983.618111] SLOW spr round 6 (radius: 5)
[16:16:24 -391982.143217] SLOW spr round 7 (radius: 5)
[16:19:07 -391982.142830] SLOW spr round 8 (radius: 10)
[16:21:53 -391982.142813] SLOW spr round 9 (radius: 15)
[16:26:17 -391982.142812] SLOW spr round 10 (radius: 20)
[16:32:54 -391982.142812] SLOW spr round 11 (radius: 25)
[16:41:36 -391982.142812] Model parameter optimization (eps = 0.100000)

[16:42:14] ML tree search #14, logLikelihood: -391942.082397

[16:42:14 -1321858.960715] Initial branch length optimization
[16:42:22 -1082874.492948] Model parameter optimization (eps = 10.000000)
[16:43:38 -1078642.717924] AUTODETECT spr round 1 (radius: 5)
[16:48:19 -740756.999758] AUTODETECT spr round 2 (radius: 10)
[16:53:02 -593668.516115] AUTODETECT spr round 3 (radius: 15)
[16:56:05 -474385.572685] AUTODETECT spr round 4 (radius: 20)
[16:59:30 -441241.972953] AUTODETECT spr round 5 (radius: 25)
[17:03:17 -433224.689421] SPR radius for FAST iterations: 25 (autodetect)
[17:03:17 -433224.689421] Model parameter optimization (eps = 3.000000)
[17:03:46 -432399.773627] FAST spr round 1 (radius: 25)
[17:07:31 -393848.699417] FAST spr round 2 (radius: 25)
[17:10:28 -392197.144081] FAST spr round 3 (radius: 25)
[17:13:03 -392108.199134] FAST spr round 4 (radius: 25)
[17:15:12 -392088.492453] FAST spr round 5 (radius: 25)
[17:17:02 -392087.365808] FAST spr round 6 (radius: 25)
[17:19:11 -392078.927849] FAST spr round 7 (radius: 25)
[17:21:08 -392078.927527] Model parameter optimization (eps = 1.000000)
[17:21:25 -392073.089139] SLOW spr round 1 (radius: 5)
[17:24:07 -391988.323966] SLOW spr round 2 (radius: 5)
[17:26:41 -391982.829974] SLOW spr round 3 (radius: 5)
[17:29:10 -391982.518769] SLOW spr round 4 (radius: 5)
[17:31:36 -391982.518077] SLOW spr round 5 (radius: 10)
[17:34:11 -391969.474572] SLOW spr round 6 (radius: 5)
[17:37:09 -391967.546894] SLOW spr round 7 (radius: 5)
[17:39:48 -391967.546434] SLOW spr round 8 (radius: 10)
[17:42:32 -391967.546402] SLOW spr round 9 (radius: 15)
[17:47:10 -391967.546395] SLOW spr round 10 (radius: 20)
[17:54:07 -391967.546391] SLOW spr round 11 (radius: 25)
[18:02:59 -391967.546389] Model parameter optimization (eps = 0.100000)

[18:03:04] ML tree search #15, logLikelihood: -391967.477758

[18:03:05 -1340155.072795] Initial branch length optimization
[18:03:09 -1105569.046845] Model parameter optimization (eps = 10.000000)
[18:03:52 -1100759.614189] AUTODETECT spr round 1 (radius: 5)
[18:06:08 -732682.603549] AUTODETECT spr round 2 (radius: 10)
[18:08:48 -550185.032869] AUTODETECT spr round 3 (radius: 15)
[18:11:35 -476212.135723] AUTODETECT spr round 4 (radius: 20)
[18:14:47 -447987.153936] AUTODETECT spr round 5 (radius: 25)
[18:18:12 -441729.078544] SPR radius for FAST iterations: 25 (autodetect)
[18:18:12 -441729.078544] Model parameter optimization (eps = 3.000000)
[18:18:48 -441084.113827] FAST spr round 1 (radius: 25)
[18:22:31 -397896.525176] FAST spr round 2 (radius: 25)
[18:25:26 -392587.795781] FAST spr round 3 (radius: 25)
[18:27:55 -392123.857229] FAST spr round 4 (radius: 25)
[18:30:07 -392093.776605] FAST spr round 5 (radius: 25)
[18:32:04 -392079.840150] FAST spr round 6 (radius: 25)
[18:34:04 -392077.477942] FAST spr round 7 (radius: 25)
[18:35:56 -392077.476337] Model parameter optimization (eps = 1.000000)
[18:36:12 -392065.390813] SLOW spr round 1 (radius: 5)
[18:38:57 -391966.607011] SLOW spr round 2 (radius: 5)
[18:41:30 -391957.050210] SLOW spr round 3 (radius: 5)
[18:44:03 -391954.837010] SLOW spr round 4 (radius: 5)
[18:46:29 -391954.836900] SLOW spr round 5 (radius: 10)
[18:49:05 -391953.328210] SLOW spr round 6 (radius: 5)
[18:52:02 -391952.068461] SLOW spr round 7 (radius: 5)
[18:54:44 -391952.068172] SLOW spr round 8 (radius: 10)
[18:57:25 -391952.068154] SLOW spr round 9 (radius: 15)
[19:01:57 -391952.068153] SLOW spr round 10 (radius: 20)
[19:08:35 -391952.068153] SLOW spr round 11 (radius: 25)
[19:17:16 -391952.068153] Model parameter optimization (eps = 0.100000)

[19:17:22] ML tree search #16, logLikelihood: -391952.029996

[19:17:22 -1325841.024907] Initial branch length optimization
[19:17:27 -1086594.290395] Model parameter optimization (eps = 10.000000)
[19:18:06 -1082302.980564] AUTODETECT spr round 1 (radius: 5)
[19:20:33 -742793.678922] AUTODETECT spr round 2 (radius: 10)
[19:23:13 -553598.579815] AUTODETECT spr round 3 (radius: 15)
[19:26:07 -462906.721672] AUTODETECT spr round 4 (radius: 20)
[19:29:30 -431177.374430] AUTODETECT spr round 5 (radius: 25)
[19:33:30 -424656.107369] SPR radius for FAST iterations: 25 (autodetect)
[19:33:30 -424656.107369] Model parameter optimization (eps = 3.000000)
[19:34:06 -424041.123987] FAST spr round 1 (radius: 25)
[19:37:39 -393116.938802] FAST spr round 2 (radius: 25)
[19:40:30 -392143.002042] FAST spr round 3 (radius: 25)
[19:43:06 -392079.923164] FAST spr round 4 (radius: 25)
[19:45:22 -392073.469480] FAST spr round 5 (radius: 25)
[19:47:30 -392073.469457] Model parameter optimization (eps = 1.000000)
[19:47:55 -392064.479186] SLOW spr round 1 (radius: 5)
[19:50:32 -391950.922729] SLOW spr round 2 (radius: 5)
[19:53:17 -391945.354790] SLOW spr round 3 (radius: 5)
[19:55:58 -391945.353944] SLOW spr round 4 (radius: 10)
[19:58:42 -391945.353903] SLOW spr round 5 (radius: 15)
[20:03:34 -391945.353896] SLOW spr round 6 (radius: 20)
[20:10:20 -391945.353892] SLOW spr round 7 (radius: 25)
[20:18:56 -391945.353890] Model parameter optimization (eps = 0.100000)

[20:19:03] ML tree search #17, logLikelihood: -391945.300427

[20:19:03 -1329973.754987] Initial branch length optimization
[20:19:08 -1082129.162491] Model parameter optimization (eps = 10.000000)
[20:19:51 -1077705.245298] AUTODETECT spr round 1 (radius: 5)
[20:22:26 -749464.295577] AUTODETECT spr round 2 (radius: 10)
[20:25:03 -580951.128108] AUTODETECT spr round 3 (radius: 15)
[20:27:58 -495971.252491] AUTODETECT spr round 4 (radius: 20)
[20:31:14 -460059.398002] AUTODETECT spr round 5 (radius: 25)
[20:35:07 -443877.904502] SPR radius for FAST iterations: 25 (autodetect)
[20:35:07 -443877.904502] Model parameter optimization (eps = 3.000000)
[20:35:43 -443082.892826] FAST spr round 1 (radius: 25)
[20:39:39 -395961.778751] FAST spr round 2 (radius: 25)
[20:42:37 -392394.354046] FAST spr round 3 (radius: 25)
[20:44:54 -392161.169423] FAST spr round 4 (radius: 25)
[20:47:14 -392118.570989] FAST spr round 5 (radius: 25)
[20:49:19 -392114.763345] FAST spr round 6 (radius: 25)
[20:51:14 -392114.763267] Model parameter optimization (eps = 1.000000)
[20:51:45 -392062.968531] SLOW spr round 1 (radius: 5)
[20:54:31 -391999.633419] SLOW spr round 2 (radius: 5)
[20:57:11 -391980.472159] SLOW spr round 3 (radius: 5)
[20:59:45 -391979.042968] SLOW spr round 4 (radius: 5)
[21:02:09 -391979.041272] SLOW spr round 5 (radius: 10)
[21:04:49 -391977.962382] SLOW spr round 6 (radius: 5)
[21:07:48 -391977.180929] SLOW spr round 7 (radius: 5)
[21:10:34 -391976.675660] SLOW spr round 8 (radius: 5)
[21:13:07 -391976.675226] SLOW spr round 9 (radius: 10)
[21:15:48 -391958.440687] SLOW spr round 10 (radius: 5)
[21:18:54 -391944.434345] SLOW spr round 11 (radius: 5)
[21:21:34 -391944.434186] SLOW spr round 12 (radius: 10)
[21:24:20 -391939.067096] SLOW spr round 13 (radius: 5)
[21:27:20 -391928.585744] SLOW spr round 14 (radius: 5)
[21:30:02 -391928.585071] SLOW spr round 15 (radius: 10)
[21:32:46 -391928.585050] SLOW spr round 16 (radius: 15)
[21:37:28 -391928.585050] SLOW spr round 17 (radius: 20)
[21:43:54 -391928.585050] SLOW spr round 18 (radius: 25)
[21:52:30 -391928.585050] Model parameter optimization (eps = 0.100000)

[21:52:40] ML tree search #18, logLikelihood: -391928.445491

[21:52:40 -1323917.357409] Initial branch length optimization
[21:52:45 -1081317.098886] Model parameter optimization (eps = 10.000000)
[21:53:29 -1076932.249917] AUTODETECT spr round 1 (radius: 5)
[21:55:58 -743856.812384] AUTODETECT spr round 2 (radius: 10)
[21:58:31 -594536.901128] AUTODETECT spr round 3 (radius: 15)
[22:01:15 -502939.291554] AUTODETECT spr round 4 (radius: 20)
[22:04:23 -444330.422559] AUTODETECT spr round 5 (radius: 25)
[22:07:47 -435158.527794] SPR radius for FAST iterations: 25 (autodetect)
[22:07:47 -435158.527794] Model parameter optimization (eps = 3.000000)
[22:08:25 -434245.587530] FAST spr round 1 (radius: 25)
[22:12:08 -393649.453306] FAST spr round 2 (radius: 25)
[22:14:57 -392216.155972] FAST spr round 3 (radius: 25)
[22:17:16 -392093.667168] FAST spr round 4 (radius: 25)
[22:19:16 -392081.947122] FAST spr round 5 (radius: 25)
[22:21:12 -392080.057470] FAST spr round 6 (radius: 25)
[22:22:59 -392080.057425] Model parameter optimization (eps = 1.000000)
[22:23:21 -392014.328227] SLOW spr round 1 (radius: 5)
[22:26:07 -391940.638687] SLOW spr round 2 (radius: 5)
[22:28:33 -391928.527426] SLOW spr round 3 (radius: 5)
[22:31:02 -391928.510106] SLOW spr round 4 (radius: 10)
[22:33:18 -391925.475763] SLOW spr round 5 (radius: 5)
[22:36:11 -391925.230358] SLOW spr round 6 (radius: 5)
[22:38:45 -391925.229008] SLOW spr round 7 (radius: 10)
[22:41:23 -391925.228946] SLOW spr round 8 (radius: 15)
[22:45:56 -391925.228942] SLOW spr round 9 (radius: 20)
[22:52:47 -391925.228942] SLOW spr round 10 (radius: 25)
[23:01:48 -391925.228942] Model parameter optimization (eps = 0.100000)

[23:02:08] ML tree search #19, logLikelihood: -391924.230824

[23:02:08 -1322610.951265] Initial branch length optimization
[23:02:13 -1078442.299386] Model parameter optimization (eps = 10.000000)
[23:03:11 -1074388.331374] AUTODETECT spr round 1 (radius: 5)
[23:05:43 -765237.317593] AUTODETECT spr round 2 (radius: 10)
[23:08:24 -588344.948204] AUTODETECT spr round 3 (radius: 15)
[23:11:20 -488843.151697] AUTODETECT spr round 4 (radius: 20)
[23:14:55 -441163.705647] AUTODETECT spr round 5 (radius: 25)
[23:18:38 -432949.511926] SPR radius for FAST iterations: 25 (autodetect)
[23:18:38 -432949.511926] Model parameter optimization (eps = 3.000000)
[23:18:52 -432832.894819] FAST spr round 1 (radius: 25)
[23:22:49 -394366.294213] FAST spr round 2 (radius: 25)
[23:25:38 -392739.393997] FAST spr round 3 (radius: 25)
[23:28:13 -392637.855234] FAST spr round 4 (radius: 25)
[23:30:28 -392616.246479] FAST spr round 5 (radius: 25)
[23:32:29 -392616.244890] Model parameter optimization (eps = 1.000000)
[23:32:59 -392077.321800] SLOW spr round 1 (radius: 5)
[23:35:45 -391962.511387] SLOW spr round 2 (radius: 5)
[23:38:25 -391951.241583] SLOW spr round 3 (radius: 5)
[23:41:02 -391951.240929] SLOW spr round 4 (radius: 10)
[23:43:45 -391941.727105] SLOW spr round 5 (radius: 5)
[23:46:55 -391935.257419] SLOW spr round 6 (radius: 5)
[23:49:41 -391935.256357] SLOW spr round 7 (radius: 10)
[23:52:31 -391932.972005] SLOW spr round 8 (radius: 5)
[23:55:29 -391932.971238] SLOW spr round 9 (radius: 10)
[23:58:20 -391932.971208] SLOW spr round 10 (radius: 15)
[24:02:44 -391932.971206] SLOW spr round 11 (radius: 20)
[24:09:32 -391932.971204] SLOW spr round 12 (radius: 25)
[24:18:19 -391932.971203] Model parameter optimization (eps = 0.100000)

[24:18:33] ML tree search #20, logLikelihood: -391932.397046


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.096506,0.422332) (0.087187,0.434076) (0.455920,0.883030) (0.360386,1.439581) 
   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: -391913.497698

AIC score: 787836.995397 / AICc score: 8831896.995397 / BIC score: 797784.393969
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=1055).
         This might lead to overfitting and compromise tree inference results!


Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96NS5/3_mltree/Q96NS5.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96NS5/3_mltree/Q96NS5.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96NS5/3_mltree/Q96NS5.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96NS5/3_mltree/Q96NS5.raxml.log

Analysis started: 13-Jul-2021 16:33:11 / finished: 14-Jul-2021 16:51:45

Elapsed time: 87513.414 seconds

Consumed energy: 7272.609 Wh (= 36 km in an electric car, or 182 km with an e-scooter!)