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 03-Jul-2021 06:28:18 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5VZ89/2_msa/Q5VZ89_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5VZ89/3_mltree/Q5VZ89 --seed 2 --threads 8 --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 (8 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5VZ89/2_msa/Q5VZ89_trimmed_msa.fasta
[00:00:00] Loaded alignment with 677 taxa and 2254 sites

WARNING: Sequences tr_B6Q251_B6Q251_TALMQ_441960 and tr_A0A093W3Z2_A0A093W3Z2_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_B2W140_B2W140_PYRTR_426418 and tr_A0A2W1F7K2_A0A2W1F7K2_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_G2YYK7_G2YYK7_BOTF4_999810 and tr_M7TZ10_M7TZ10_BOTF1_1290391 are exactly identical!
WARNING: Duplicate sequences found: 3

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/Q5VZ89/3_mltree/Q5VZ89.raxml.reduced.phy

Alignment comprises 1 partitions and 2254 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 2254 / 2254
Gaps: 46.58 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5VZ89/3_mltree/Q5VZ89.raxml.rba

Parallelization scheme autoconfig: 1 worker(s) x 8 thread(s)

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

[00:00:00] Generating 20 random starting tree(s) with 677 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 282 / 22560
[00:00:00] Data distribution: max. searches per worker: 20

Starting ML tree search with 20 distinct starting trees

[00:00:00 -1601837.070372] Initial branch length optimization
[00:00:07 -1298819.437146] Model parameter optimization (eps = 10.000000)
[00:01:46 -1294310.571070] AUTODETECT spr round 1 (radius: 5)
[00:03:41 -924930.085214] AUTODETECT spr round 2 (radius: 10)
[00:05:49 -675768.308130] AUTODETECT spr round 3 (radius: 15)
[00:08:16 -538473.362697] AUTODETECT spr round 4 (radius: 20)
[00:11:17 -523277.538026] AUTODETECT spr round 5 (radius: 25)
[00:14:44 -509203.362154] SPR radius for FAST iterations: 25 (autodetect)
[00:14:44 -509203.362154] Model parameter optimization (eps = 3.000000)
[00:15:27 -506951.651906] FAST spr round 1 (radius: 25)
[00:18:33 -461340.592441] FAST spr round 2 (radius: 25)
[00:20:54 -459944.779789] FAST spr round 3 (radius: 25)
[00:22:45 -459887.889016] FAST spr round 4 (radius: 25)
[00:24:18 -459856.464211] FAST spr round 5 (radius: 25)
[00:25:43 -459850.823549] FAST spr round 6 (radius: 25)
[00:27:02 -459834.011684] FAST spr round 7 (radius: 25)
[00:28:20 -459833.996471] Model parameter optimization (eps = 1.000000)
[00:28:36 -459824.924415] SLOW spr round 1 (radius: 5)
[00:30:53 -459748.147575] SLOW spr round 2 (radius: 5)
[00:32:56 -459744.736027] SLOW spr round 3 (radius: 5)
[00:34:56 -459744.707066] SLOW spr round 4 (radius: 10)
[00:37:14 -459744.706031] SLOW spr round 5 (radius: 15)
[00:42:14 -459740.800225] SLOW spr round 6 (radius: 5)
[00:45:07 -459740.710802] SLOW spr round 7 (radius: 10)
[00:48:05 -459740.710754] SLOW spr round 8 (radius: 15)
[00:52:36 -459740.710707] SLOW spr round 9 (radius: 20)
[00:59:21 -459740.710660] SLOW spr round 10 (radius: 25)
[01:06:04 -459740.710614] Model parameter optimization (eps = 0.100000)

[01:06:13] ML tree search #1, logLikelihood: -459740.506844

[01:06:13 -1624485.664410] Initial branch length optimization
[01:06:20 -1321724.315669] Model parameter optimization (eps = 10.000000)
[01:07:45 -1316798.159913] AUTODETECT spr round 1 (radius: 5)
[01:09:21 -909110.242267] AUTODETECT spr round 2 (radius: 10)
[01:11:12 -680951.112066] AUTODETECT spr round 3 (radius: 15)
[01:13:05 -589009.096864] AUTODETECT spr round 4 (radius: 20)
[01:15:33 -536478.096899] AUTODETECT spr round 5 (radius: 25)
[01:18:59 -524801.053209] SPR radius for FAST iterations: 25 (autodetect)
[01:18:59 -524801.053209] Model parameter optimization (eps = 3.000000)
[01:19:41 -522179.807533] FAST spr round 1 (radius: 25)
[01:22:24 -461496.816351] FAST spr round 2 (radius: 25)
[01:24:23 -459936.072643] FAST spr round 3 (radius: 25)
[01:26:02 -459865.712387] FAST spr round 4 (radius: 25)
[01:27:30 -459844.295468] FAST spr round 5 (radius: 25)
[01:28:49 -459838.008381] FAST spr round 6 (radius: 25)
[01:30:02 -459838.002958] Model parameter optimization (eps = 1.000000)
[01:30:16 -459832.161052] SLOW spr round 1 (radius: 5)
[01:32:23 -459776.786541] SLOW spr round 2 (radius: 5)
[01:34:20 -459767.869152] SLOW spr round 3 (radius: 5)
[01:36:12 -459767.867023] SLOW spr round 4 (radius: 10)
[01:38:22 -459766.119118] SLOW spr round 5 (radius: 5)
[01:40:57 -459762.046354] SLOW spr round 6 (radius: 5)
[01:43:08 -459762.044451] SLOW spr round 7 (radius: 10)
[01:45:27 -459760.963593] SLOW spr round 8 (radius: 5)
[01:48:01 -459753.149304] SLOW spr round 9 (radius: 5)
[01:50:11 -459753.148849] SLOW spr round 10 (radius: 10)
[01:52:28 -459753.148569] SLOW spr round 11 (radius: 15)
[01:57:04 -459752.326359] SLOW spr round 12 (radius: 5)
[01:59:45 -459752.204299] SLOW spr round 13 (radius: 5)
[02:02:01 -459752.204242] SLOW spr round 14 (radius: 10)
[02:04:22 -459752.204206] SLOW spr round 15 (radius: 15)
[02:08:53 -459752.204178] SLOW spr round 16 (radius: 20)
[02:15:44 -459748.884963] SLOW spr round 17 (radius: 5)
[02:18:31 -459748.837467] SLOW spr round 18 (radius: 10)
[02:21:27 -459748.834479] SLOW spr round 19 (radius: 15)
[02:25:44 -459748.833317] SLOW spr round 20 (radius: 20)
[02:32:36 -459748.832857] SLOW spr round 21 (radius: 25)
[02:40:12 -459748.832667] Model parameter optimization (eps = 0.100000)

[02:40:17] ML tree search #2, logLikelihood: -459748.772191

[02:40:17 -1618997.373133] Initial branch length optimization
[02:40:24 -1321973.449635] Model parameter optimization (eps = 10.000000)
[02:41:49 -1317414.526022] AUTODETECT spr round 1 (radius: 5)
[02:43:38 -921696.688854] AUTODETECT spr round 2 (radius: 10)
[02:45:39 -689243.268156] AUTODETECT spr round 3 (radius: 15)
[02:47:59 -541664.970052] AUTODETECT spr round 4 (radius: 20)
[02:50:51 -524142.385364] AUTODETECT spr round 5 (radius: 25)
[02:54:15 -520641.795120] SPR radius for FAST iterations: 25 (autodetect)
[02:54:15 -520641.795120] Model parameter optimization (eps = 3.000000)
[02:54:58 -518558.513200] FAST spr round 1 (radius: 25)
[02:57:54 -462097.380276] FAST spr round 2 (radius: 25)
[02:59:54 -459971.795799] FAST spr round 3 (radius: 25)
[03:01:38 -459863.275841] FAST spr round 4 (radius: 25)
[03:02:57 -459863.215732] Model parameter optimization (eps = 1.000000)
[03:03:17 -459845.376375] SLOW spr round 1 (radius: 5)
[03:05:23 -459771.193297] SLOW spr round 2 (radius: 5)
[03:07:24 -459757.392009] SLOW spr round 3 (radius: 5)
[03:09:18 -459756.685049] SLOW spr round 4 (radius: 5)
[03:11:10 -459756.681141] SLOW spr round 5 (radius: 10)
[03:13:22 -459752.367110] SLOW spr round 6 (radius: 5)
[03:16:01 -459747.451428] SLOW spr round 7 (radius: 5)
[03:18:11 -459747.448203] SLOW spr round 8 (radius: 10)
[03:20:28 -459745.636956] SLOW spr round 9 (radius: 5)
[03:23:02 -459737.398044] SLOW spr round 10 (radius: 5)
[03:25:11 -459737.397912] SLOW spr round 11 (radius: 10)
[03:27:26 -459737.397867] SLOW spr round 12 (radius: 15)
[03:31:56 -459736.597724] SLOW spr round 13 (radius: 5)
[03:34:37 -459736.475954] SLOW spr round 14 (radius: 5)
[03:36:52 -459736.475931] SLOW spr round 15 (radius: 10)
[03:39:10 -459736.475914] SLOW spr round 16 (radius: 15)
[03:43:37 -459736.475899] SLOW spr round 17 (radius: 20)
[03:50:14 -459733.238433] SLOW spr round 18 (radius: 5)
[03:53:00 -459733.189690] SLOW spr round 19 (radius: 10)
[03:55:50 -459733.186562] SLOW spr round 20 (radius: 15)
[04:00:03 -459733.185341] SLOW spr round 21 (radius: 20)
[04:06:41 -459733.184860] SLOW spr round 22 (radius: 25)
[04:14:13 -459733.184665] Model parameter optimization (eps = 0.100000)

[04:14:19] ML tree search #3, logLikelihood: -459733.088766

[04:14:19 -1595545.163948] Initial branch length optimization
[04:14:26 -1301222.732319] Model parameter optimization (eps = 10.000000)
[04:15:57 -1296563.170930] AUTODETECT spr round 1 (radius: 5)
[04:17:40 -906866.066707] AUTODETECT spr round 2 (radius: 10)
[04:19:40 -639113.204074] AUTODETECT spr round 3 (radius: 15)
[04:21:58 -527752.636568] AUTODETECT spr round 4 (radius: 20)
[04:24:39 -518518.976740] AUTODETECT spr round 5 (radius: 25)
[04:27:32 -517347.186960] SPR radius for FAST iterations: 25 (autodetect)
[04:27:32 -517347.186960] Model parameter optimization (eps = 3.000000)
[04:28:17 -515588.338855] FAST spr round 1 (radius: 25)
[04:31:10 -462334.746143] FAST spr round 2 (radius: 25)
[04:33:20 -459996.195105] FAST spr round 3 (radius: 25)
[04:35:09 -459841.997365] FAST spr round 4 (radius: 25)
[04:36:30 -459835.614685] FAST spr round 5 (radius: 25)
[04:37:45 -459835.614240] Model parameter optimization (eps = 1.000000)
[04:38:01 -459830.070046] SLOW spr round 1 (radius: 5)
[04:40:02 -459757.898439] SLOW spr round 2 (radius: 5)
[04:42:01 -459742.334472] SLOW spr round 3 (radius: 5)
[04:43:53 -459742.333902] SLOW spr round 4 (radius: 10)
[04:45:59 -459742.184061] SLOW spr round 5 (radius: 5)
[04:48:32 -459742.180579] SLOW spr round 6 (radius: 10)
[04:51:03 -459742.179789] SLOW spr round 7 (radius: 15)
[04:55:21 -459740.081082] SLOW spr round 8 (radius: 5)
[04:58:03 -459739.989735] SLOW spr round 9 (radius: 10)
[05:00:47 -459737.930320] SLOW spr round 10 (radius: 5)
[05:03:20 -459727.411228] SLOW spr round 11 (radius: 5)
[05:05:28 -459727.406853] SLOW spr round 12 (radius: 10)
[05:07:44 -459727.405614] SLOW spr round 13 (radius: 15)
[05:12:20 -459727.405141] SLOW spr round 14 (radius: 20)
[05:19:09 -459727.404935] SLOW spr round 15 (radius: 25)
[05:26:55 -459727.404829] Model parameter optimization (eps = 0.100000)

[05:27:04] ML tree search #4, logLikelihood: -459727.273788

[05:27:04 -1611936.540573] Initial branch length optimization
[05:27:11 -1317683.008646] Model parameter optimization (eps = 10.000000)
[05:28:54 -1312960.051084] AUTODETECT spr round 1 (radius: 5)
[05:30:41 -943640.720545] AUTODETECT spr round 2 (radius: 10)
[05:32:42 -668835.384002] AUTODETECT spr round 3 (radius: 15)
[05:34:56 -562094.237232] AUTODETECT spr round 4 (radius: 20)
[05:37:38 -516290.042228] AUTODETECT spr round 5 (radius: 25)
[05:41:00 -513927.563444] SPR radius for FAST iterations: 25 (autodetect)
[05:41:00 -513927.563444] Model parameter optimization (eps = 3.000000)
[05:41:44 -511718.466212] FAST spr round 1 (radius: 25)
[05:44:30 -461629.229456] FAST spr round 2 (radius: 25)
[05:46:48 -459963.696695] FAST spr round 3 (radius: 25)
[05:48:44 -459890.048664] FAST spr round 4 (radius: 25)
[05:50:14 -459868.949455] FAST spr round 5 (radius: 25)
[05:51:36 -459866.330223] FAST spr round 6 (radius: 25)
[05:52:56 -459864.180503] FAST spr round 7 (radius: 25)
[05:54:14 -459864.179322] Model parameter optimization (eps = 1.000000)
[05:54:35 -459852.687171] SLOW spr round 1 (radius: 5)
[05:56:52 -459741.983168] SLOW spr round 2 (radius: 5)
[05:58:58 -459734.140222] SLOW spr round 3 (radius: 5)
[06:00:42 -459733.262160] SLOW spr round 4 (radius: 5)
[06:02:25 -459733.259571] SLOW spr round 5 (radius: 10)
[06:04:25 -459731.970123] SLOW spr round 6 (radius: 5)
[06:06:49 -459730.491882] SLOW spr round 7 (radius: 5)
[06:08:56 -459730.489985] SLOW spr round 8 (radius: 10)
[06:11:21 -459728.606574] SLOW spr round 9 (radius: 5)
[06:14:05 -459728.587213] SLOW spr round 10 (radius: 10)
[06:16:49 -459728.585301] SLOW spr round 11 (radius: 15)
[06:21:27 -459727.768531] SLOW spr round 12 (radius: 5)
[06:24:23 -459727.645719] SLOW spr round 13 (radius: 5)
[06:26:50 -459727.645627] SLOW spr round 14 (radius: 10)
[06:29:22 -459727.645570] SLOW spr round 15 (radius: 15)
[06:34:06 -459727.645526] SLOW spr round 16 (radius: 20)
[06:41:08 -459727.645487] SLOW spr round 17 (radius: 25)
[06:49:18 -459727.645450] Model parameter optimization (eps = 0.100000)

[06:49:26] ML tree search #5, logLikelihood: -459727.556798

[06:49:27 -1621993.739078] Initial branch length optimization
[06:49:40 -1324280.485474] Model parameter optimization (eps = 10.000000)
[06:51:09 -1319764.591308] AUTODETECT spr round 1 (radius: 5)
[06:53:03 -908709.305508] AUTODETECT spr round 2 (radius: 10)
[06:55:16 -636670.793823] AUTODETECT spr round 3 (radius: 15)
[06:57:30 -541852.327191] AUTODETECT spr round 4 (radius: 20)
[07:00:04 -515271.224446] AUTODETECT spr round 5 (radius: 25)
[07:03:48 -513204.987811] SPR radius for FAST iterations: 25 (autodetect)
[07:03:48 -513204.987811] Model parameter optimization (eps = 3.000000)
[07:04:36 -510842.136881] FAST spr round 1 (radius: 25)
[07:07:51 -461508.471478] FAST spr round 2 (radius: 25)
[07:10:03 -459938.189980] FAST spr round 3 (radius: 25)
[07:11:45 -459881.083017] FAST spr round 4 (radius: 25)
[07:13:14 -459878.829166] FAST spr round 5 (radius: 25)
[07:14:35 -459878.786459] Model parameter optimization (eps = 1.000000)
[07:14:56 -459855.078481] SLOW spr round 1 (radius: 5)
[07:17:13 -459753.367830] SLOW spr round 2 (radius: 5)
[07:19:18 -459749.783697] SLOW spr round 3 (radius: 5)
[07:21:20 -459749.779247] SLOW spr round 4 (radius: 10)
[07:23:41 -459749.042791] SLOW spr round 5 (radius: 5)
[07:26:30 -459748.984392] SLOW spr round 6 (radius: 10)
[07:29:20 -459748.983178] SLOW spr round 7 (radius: 15)
[07:33:29 -459745.495952] SLOW spr round 8 (radius: 5)
[07:36:22 -459745.453751] SLOW spr round 9 (radius: 10)
[07:39:21 -459745.453440] SLOW spr round 10 (radius: 15)
[07:43:54 -459745.453284] SLOW spr round 11 (radius: 20)
[07:51:03 -459745.453190] SLOW spr round 12 (radius: 25)
[07:59:06 -459745.453121] Model parameter optimization (eps = 0.100000)

[07:59:21] ML tree search #6, logLikelihood: -459744.916551

[07:59:21 -1603973.127193] Initial branch length optimization
[07:59:29 -1303225.735307] Model parameter optimization (eps = 10.000000)
[08:01:00 -1298465.806649] AUTODETECT spr round 1 (radius: 5)
[08:02:53 -939132.312409] AUTODETECT spr round 2 (radius: 10)
[08:05:09 -659353.202039] AUTODETECT spr round 3 (radius: 15)
[08:07:41 -567578.323275] AUTODETECT spr round 4 (radius: 20)
[08:10:35 -531081.969880] AUTODETECT spr round 5 (radius: 25)
[08:13:39 -525556.387055] SPR radius for FAST iterations: 25 (autodetect)
[08:13:39 -525556.387055] Model parameter optimization (eps = 3.000000)
[08:14:21 -523290.429629] FAST spr round 1 (radius: 25)
[08:17:24 -462275.419969] FAST spr round 2 (radius: 25)
[08:19:31 -459934.641136] FAST spr round 3 (radius: 25)
[08:21:17 -459854.527831] FAST spr round 4 (radius: 25)
[08:22:42 -459841.259128] FAST spr round 5 (radius: 25)
[08:23:58 -459841.258493] Model parameter optimization (eps = 1.000000)
[08:24:11 -459831.237893] SLOW spr round 1 (radius: 5)
[08:26:18 -459750.876286] SLOW spr round 2 (radius: 5)
[08:28:15 -459747.393282] SLOW spr round 3 (radius: 5)
[08:30:07 -459747.374475] SLOW spr round 4 (radius: 10)
[08:32:21 -459746.279681] SLOW spr round 5 (radius: 5)
[08:34:56 -459746.275750] SLOW spr round 6 (radius: 10)
[08:37:37 -459746.065294] SLOW spr round 7 (radius: 5)
[08:40:07 -459745.993272] SLOW spr round 8 (radius: 10)
[08:42:43 -459745.992522] SLOW spr round 9 (radius: 15)
[08:47:11 -459742.884801] SLOW spr round 10 (radius: 5)
[08:49:55 -459742.800231] SLOW spr round 11 (radius: 10)
[08:52:47 -459742.141397] SLOW spr round 12 (radius: 5)
[08:55:18 -459737.510982] SLOW spr round 13 (radius: 5)
[08:57:30 -459733.042898] SLOW spr round 14 (radius: 5)
[08:59:31 -459733.042119] SLOW spr round 15 (radius: 10)
[09:01:45 -459733.041976] SLOW spr round 16 (radius: 15)
[09:06:18 -459733.041911] SLOW spr round 17 (radius: 20)
[09:12:44 -459733.041872] SLOW spr round 18 (radius: 25)
[09:20:08 -459733.041841] Model parameter optimization (eps = 0.100000)

[09:20:13] ML tree search #7, logLikelihood: -459732.991267

[09:20:13 -1607269.427584] Initial branch length optimization
[09:20:20 -1304746.137957] Model parameter optimization (eps = 10.000000)
[09:21:41 -1300125.532577] AUTODETECT spr round 1 (radius: 5)
[09:23:27 -930485.236360] AUTODETECT spr round 2 (radius: 10)
[09:25:23 -710521.271655] AUTODETECT spr round 3 (radius: 15)
[09:27:39 -563151.074905] AUTODETECT spr round 4 (radius: 20)
[09:30:20 -518903.378374] AUTODETECT spr round 5 (radius: 25)
[09:33:50 -517099.680756] SPR radius for FAST iterations: 25 (autodetect)
[09:33:50 -517099.680756] Model parameter optimization (eps = 3.000000)
[09:34:35 -515229.108557] FAST spr round 1 (radius: 25)
[09:37:34 -461714.261864] FAST spr round 2 (radius: 25)
[09:39:47 -459992.444830] FAST spr round 3 (radius: 25)
[09:41:31 -459806.127247] FAST spr round 4 (radius: 25)
[09:42:52 -459802.290367] FAST spr round 5 (radius: 25)
[09:44:07 -459802.290288] Model parameter optimization (eps = 1.000000)
[09:44:24 -459790.220119] SLOW spr round 1 (radius: 5)
[09:46:22 -459735.192754] SLOW spr round 2 (radius: 5)
[09:48:16 -459726.707907] SLOW spr round 3 (radius: 5)
[09:50:09 -459726.706727] SLOW spr round 4 (radius: 10)
[09:52:18 -459726.304435] SLOW spr round 5 (radius: 5)
[09:54:54 -459725.313541] SLOW spr round 6 (radius: 5)
[09:57:06 -459725.312891] SLOW spr round 7 (radius: 10)
[09:59:23 -459725.259783] SLOW spr round 8 (radius: 15)
[10:04:01 -459724.427894] SLOW spr round 9 (radius: 5)
[10:06:43 -459724.298361] SLOW spr round 10 (radius: 5)
[10:09:00 -459724.298065] SLOW spr round 11 (radius: 10)
[10:11:21 -459724.297922] SLOW spr round 12 (radius: 15)
[10:15:58 -459724.297838] SLOW spr round 13 (radius: 20)
[10:22:44 -459721.172496] SLOW spr round 14 (radius: 5)
[10:25:32 -459721.124882] SLOW spr round 15 (radius: 10)
[10:28:28 -459721.121758] SLOW spr round 16 (radius: 15)
[10:32:48 -459721.120509] SLOW spr round 17 (radius: 20)
[10:39:32 -459721.119994] SLOW spr round 18 (radius: 25)
[10:47:07 -459721.119764] Model parameter optimization (eps = 0.100000)

[10:47:18] ML tree search #8, logLikelihood: -459720.957747

[10:47:18 -1613300.550246] Initial branch length optimization
[10:47:25 -1320316.399703] Model parameter optimization (eps = 10.000000)
[10:48:48 -1316003.594987] AUTODETECT spr round 1 (radius: 5)
[10:50:34 -903823.714460] AUTODETECT spr round 2 (radius: 10)
[10:52:34 -656372.966797] AUTODETECT spr round 3 (radius: 15)
[10:54:48 -534723.371302] AUTODETECT spr round 4 (radius: 20)
[10:57:37 -512446.545318] AUTODETECT spr round 5 (radius: 25)
[11:01:26 -510107.773095] SPR radius for FAST iterations: 25 (autodetect)
[11:01:26 -510107.773095] Model parameter optimization (eps = 3.000000)
[11:02:09 -508104.358653] FAST spr round 1 (radius: 25)
[11:05:10 -461717.712921] FAST spr round 2 (radius: 25)
[11:07:10 -459925.927856] FAST spr round 3 (radius: 25)
[11:08:53 -459873.608303] FAST spr round 4 (radius: 25)
[11:10:13 -459872.670720] FAST spr round 5 (radius: 25)
[11:11:27 -459872.563751] FAST spr round 6 (radius: 25)
[11:12:40 -459872.563665] Model parameter optimization (eps = 1.000000)
[11:12:58 -459867.896406] SLOW spr round 1 (radius: 5)
[11:14:54 -459748.728500] SLOW spr round 2 (radius: 5)
[11:16:49 -459743.592348] SLOW spr round 3 (radius: 5)
[11:18:41 -459743.590743] SLOW spr round 4 (radius: 10)
[11:20:50 -459743.589510] SLOW spr round 5 (radius: 15)
[11:25:41 -459741.219498] SLOW spr round 6 (radius: 5)
[11:28:21 -459741.153064] SLOW spr round 7 (radius: 10)
[11:31:08 -459741.152627] SLOW spr round 8 (radius: 15)
[11:35:34 -459741.152285] SLOW spr round 9 (radius: 20)
[11:42:29 -459741.151986] SLOW spr round 10 (radius: 25)
[11:50:30 -459741.151710] Model parameter optimization (eps = 0.100000)

[11:50:39] ML tree search #9, logLikelihood: -459740.971842

[11:50:39 -1622349.036121] Initial branch length optimization
[11:50:47 -1320814.007185] Model parameter optimization (eps = 10.000000)
[11:52:24 -1316134.035147] AUTODETECT spr round 1 (radius: 5)
[11:54:13 -913792.139925] AUTODETECT spr round 2 (radius: 10)
[11:56:11 -660249.485695] AUTODETECT spr round 3 (radius: 15)
[11:58:28 -550244.560429] AUTODETECT spr round 4 (radius: 20)
[12:01:37 -513589.892417] AUTODETECT spr round 5 (radius: 25)
[12:05:10 -512032.055752] SPR radius for FAST iterations: 25 (autodetect)
[12:05:10 -512032.055752] Model parameter optimization (eps = 3.000000)
[12:05:53 -509413.655575] FAST spr round 1 (radius: 25)
[12:08:44 -461089.645359] FAST spr round 2 (radius: 25)
[12:10:50 -459909.061829] FAST spr round 3 (radius: 25)
[12:12:35 -459843.250689] FAST spr round 4 (radius: 25)
[12:13:57 -459841.270165] FAST spr round 5 (radius: 25)
[12:15:13 -459841.257468] Model parameter optimization (eps = 1.000000)
[12:15:29 -459826.000429] SLOW spr round 1 (radius: 5)
[12:17:35 -459751.963916] SLOW spr round 2 (radius: 5)
[12:19:33 -459746.418148] SLOW spr round 3 (radius: 5)
[12:21:28 -459746.417769] SLOW spr round 4 (radius: 10)
[12:23:41 -459746.417652] SLOW spr round 5 (radius: 15)
[12:28:33 -459743.242040] SLOW spr round 6 (radius: 5)
[12:31:16 -459743.158429] SLOW spr round 7 (radius: 10)
[12:34:06 -459742.565684] SLOW spr round 8 (radius: 5)
[12:36:36 -459742.119756] SLOW spr round 9 (radius: 5)
[12:38:45 -459742.118868] SLOW spr round 10 (radius: 10)
[12:41:04 -459741.702256] SLOW spr round 11 (radius: 5)
[12:43:40 -459740.429475] SLOW spr round 12 (radius: 5)
[12:45:51 -459740.427704] SLOW spr round 13 (radius: 10)
[12:48:10 -459739.800935] SLOW spr round 14 (radius: 5)
[12:50:41 -459739.797687] SLOW spr round 15 (radius: 10)
[12:53:15 -459739.797011] SLOW spr round 16 (radius: 15)
[12:57:40 -459739.796827] SLOW spr round 17 (radius: 20)
[13:04:28 -459739.796752] SLOW spr round 18 (radius: 25)
[13:12:08 -459739.796700] Model parameter optimization (eps = 0.100000)

[13:12:20] ML tree search #10, logLikelihood: -459739.627845

[13:12:20 -1616469.493817] Initial branch length optimization
[13:12:28 -1308964.373123] Model parameter optimization (eps = 10.000000)
[13:13:59 -1304431.578200] AUTODETECT spr round 1 (radius: 5)
[13:15:45 -931531.886135] AUTODETECT spr round 2 (radius: 10)
[13:17:46 -672473.559728] AUTODETECT spr round 3 (radius: 15)
[13:20:00 -535945.481607] AUTODETECT spr round 4 (radius: 20)
[13:22:45 -511103.501883] AUTODETECT spr round 5 (radius: 25)
[13:26:27 -507179.387299] SPR radius for FAST iterations: 25 (autodetect)
[13:26:27 -507179.387299] Model parameter optimization (eps = 3.000000)
[13:27:08 -505103.259953] FAST spr round 1 (radius: 25)
[13:30:10 -461491.204190] FAST spr round 2 (radius: 25)
[13:32:27 -460012.903972] FAST spr round 3 (radius: 25)
[13:34:13 -459859.329711] FAST spr round 4 (radius: 25)
[13:35:37 -459836.319714] FAST spr round 5 (radius: 25)
[13:36:52 -459836.314906] Model parameter optimization (eps = 1.000000)
[13:37:08 -459824.751858] SLOW spr round 1 (radius: 5)
[13:39:08 -459747.818640] SLOW spr round 2 (radius: 5)
[13:41:03 -459745.552607] SLOW spr round 3 (radius: 5)
[13:42:56 -459745.550853] SLOW spr round 4 (radius: 10)
[13:45:10 -459743.779778] SLOW spr round 5 (radius: 5)
[13:47:44 -459743.777092] SLOW spr round 6 (radius: 10)
[13:50:24 -459742.791680] SLOW spr round 7 (radius: 5)
[13:52:54 -459742.296620] SLOW spr round 8 (radius: 5)
[13:55:02 -459742.295227] SLOW spr round 9 (radius: 10)
[13:57:21 -459742.294877] SLOW spr round 10 (radius: 15)
[14:01:54 -459742.294753] SLOW spr round 11 (radius: 20)
[14:08:20 -459739.084439] SLOW spr round 12 (radius: 5)
[14:11:08 -459739.036433] SLOW spr round 13 (radius: 10)
[14:14:05 -459739.033282] SLOW spr round 14 (radius: 15)
[14:18:22 -459739.032022] SLOW spr round 15 (radius: 20)
[14:24:49 -459739.031502] SLOW spr round 16 (radius: 25)
[14:32:11 -459739.031270] Model parameter optimization (eps = 0.100000)

[14:32:18] ML tree search #11, logLikelihood: -459738.952532

[14:32:19 -1615744.186860] Initial branch length optimization
[14:32:25 -1309587.573908] Model parameter optimization (eps = 10.000000)
[14:33:43 -1304748.994129] AUTODETECT spr round 1 (radius: 5)
[14:35:31 -927468.902998] AUTODETECT spr round 2 (radius: 10)
[14:37:31 -677023.166102] AUTODETECT spr round 3 (radius: 15)
[14:39:49 -557148.649788] AUTODETECT spr round 4 (radius: 20)
[14:42:26 -524180.413807] AUTODETECT spr round 5 (radius: 25)
[14:45:43 -516657.185624] SPR radius for FAST iterations: 25 (autodetect)
[14:45:43 -516657.185624] Model parameter optimization (eps = 3.000000)
[14:46:26 -514533.933107] FAST spr round 1 (radius: 25)
[14:49:29 -462690.000102] FAST spr round 2 (radius: 25)
[14:51:26 -459996.829341] FAST spr round 3 (radius: 25)
[14:53:14 -459842.425771] FAST spr round 4 (radius: 25)
[14:54:42 -459825.149712] FAST spr round 5 (radius: 25)
[14:55:57 -459825.074900] Model parameter optimization (eps = 1.000000)
[14:56:17 -459819.008657] SLOW spr round 1 (radius: 5)
[14:58:22 -459736.809298] SLOW spr round 2 (radius: 5)
[15:00:15 -459736.236146] SLOW spr round 3 (radius: 5)
[15:02:07 -459736.235773] SLOW spr round 4 (radius: 10)
[15:04:18 -459736.235660] SLOW spr round 5 (radius: 15)
[15:08:55 -459736.235579] SLOW spr round 6 (radius: 20)
[15:15:41 -459736.235513] SLOW spr round 7 (radius: 25)
[15:23:20 -459736.235457] Model parameter optimization (eps = 0.100000)

[15:23:25] ML tree search #12, logLikelihood: -459736.168627

[15:23:25 -1603779.587340] Initial branch length optimization
[15:23:32 -1306228.560306] Model parameter optimization (eps = 10.000000)
[15:24:29 -1301247.678695] AUTODETECT spr round 1 (radius: 5)
[15:26:16 -921179.424560] AUTODETECT spr round 2 (radius: 10)
[15:28:14 -697958.866129] AUTODETECT spr round 3 (radius: 15)
[15:30:29 -565797.213234] AUTODETECT spr round 4 (radius: 20)
[15:33:00 -531734.271537] AUTODETECT spr round 5 (radius: 25)
[15:36:43 -522211.991331] SPR radius for FAST iterations: 25 (autodetect)
[15:36:43 -522211.991331] Model parameter optimization (eps = 3.000000)
[15:37:32 -520336.091315] FAST spr round 1 (radius: 25)
[15:40:26 -462119.053691] FAST spr round 2 (radius: 25)
[15:42:36 -459970.121080] FAST spr round 3 (radius: 25)
[15:44:22 -459837.816921] FAST spr round 4 (radius: 25)
[15:45:44 -459835.854084] FAST spr round 5 (radius: 25)
[15:47:04 -459831.372272] FAST spr round 6 (radius: 25)
[15:48:17 -459831.369564] Model parameter optimization (eps = 1.000000)
[15:48:38 -459804.817402] SLOW spr round 1 (radius: 5)
[15:50:43 -459747.399408] SLOW spr round 2 (radius: 5)
[15:52:38 -459742.994487] SLOW spr round 3 (radius: 5)
[15:54:30 -459742.993641] SLOW spr round 4 (radius: 10)
[15:56:43 -459742.503236] SLOW spr round 5 (radius: 5)
[15:59:21 -459741.270223] SLOW spr round 6 (radius: 5)
[16:01:36 -459740.488084] SLOW spr round 7 (radius: 5)
[16:03:38 -459740.484505] SLOW spr round 8 (radius: 10)
[16:05:50 -459738.990612] SLOW spr round 9 (radius: 5)
[16:08:25 -459738.984390] SLOW spr round 10 (radius: 10)
[16:10:58 -459738.983256] SLOW spr round 11 (radius: 15)
[16:15:26 -459738.178654] SLOW spr round 12 (radius: 5)
[16:18:09 -459738.056692] SLOW spr round 13 (radius: 5)
[16:20:26 -459738.056637] SLOW spr round 14 (radius: 10)
[16:22:46 -459738.056603] SLOW spr round 15 (radius: 15)
[16:27:19 -459738.056577] SLOW spr round 16 (radius: 20)
[16:34:07 -459734.923388] SLOW spr round 17 (radius: 5)
[16:36:56 -459734.875587] SLOW spr round 18 (radius: 10)
[16:39:51 -459734.872474] SLOW spr round 19 (radius: 15)
[16:44:11 -459734.871246] SLOW spr round 20 (radius: 20)
[16:51:01 -459734.870755] SLOW spr round 21 (radius: 25)
[16:58:46 -459734.870551] Model parameter optimization (eps = 0.100000)

[16:58:54] ML tree search #13, logLikelihood: -459734.696257

[16:58:54 -1614198.199311] Initial branch length optimization
[16:59:01 -1315554.013050] Model parameter optimization (eps = 10.000000)
[17:00:36 -1310878.377376] AUTODETECT spr round 1 (radius: 5)
[17:02:23 -936065.328759] AUTODETECT spr round 2 (radius: 10)
[17:04:24 -681440.585282] AUTODETECT spr round 3 (radius: 15)
[17:06:41 -570893.458359] AUTODETECT spr round 4 (radius: 20)
[17:09:28 -535701.759380] AUTODETECT spr round 5 (radius: 25)
[17:12:52 -526004.987728] SPR radius for FAST iterations: 25 (autodetect)
[17:12:52 -526004.987728] Model parameter optimization (eps = 3.000000)
[17:13:36 -523288.824710] FAST spr round 1 (radius: 25)
[17:16:16 -462067.353095] FAST spr round 2 (radius: 25)
[17:18:16 -460024.516918] FAST spr round 3 (radius: 25)
[17:20:02 -459906.949026] FAST spr round 4 (radius: 25)
[17:21:25 -459898.905200] FAST spr round 5 (radius: 25)
[17:22:40 -459898.733664] FAST spr round 6 (radius: 25)
[17:23:55 -459896.440257] FAST spr round 7 (radius: 25)
[17:25:07 -459896.426504] Model parameter optimization (eps = 1.000000)
[17:25:22 -459888.744760] SLOW spr round 1 (radius: 5)
[17:27:15 -459748.324667] SLOW spr round 2 (radius: 5)
[17:29:01 -459742.756128] SLOW spr round 3 (radius: 5)
[17:30:44 -459742.753913] SLOW spr round 4 (radius: 10)
[17:32:46 -459741.572706] SLOW spr round 5 (radius: 5)
[17:35:06 -459741.567972] SLOW spr round 6 (radius: 10)
[17:37:30 -459741.567140] SLOW spr round 7 (radius: 15)
[17:41:27 -459739.321970] SLOW spr round 8 (radius: 5)
[17:43:56 -459739.271240] SLOW spr round 9 (radius: 10)
[17:46:32 -459739.267964] SLOW spr round 10 (radius: 15)
[17:50:52 -459739.266653] SLOW spr round 11 (radius: 20)
[17:57:35 -459739.266110] SLOW spr round 12 (radius: 25)
[18:05:07 -459739.265869] Model parameter optimization (eps = 0.100000)

[18:05:13] ML tree search #14, logLikelihood: -459739.186720

[18:05:13 -1599165.695972] Initial branch length optimization
[18:05:22 -1292670.011181] Model parameter optimization (eps = 10.000000)
[18:06:43 -1288219.188600] AUTODETECT spr round 1 (radius: 5)
[18:08:31 -901726.082361] AUTODETECT spr round 2 (radius: 10)
[18:10:28 -680620.918256] AUTODETECT spr round 3 (radius: 15)
[18:12:47 -541449.149254] AUTODETECT spr round 4 (radius: 20)
[18:15:41 -513123.185406] AUTODETECT spr round 5 (radius: 25)
[18:19:06 -511447.433600] SPR radius for FAST iterations: 25 (autodetect)
[18:19:06 -511447.433600] Model parameter optimization (eps = 3.000000)
[18:19:48 -509181.202910] FAST spr round 1 (radius: 25)
[18:22:43 -461192.824374] FAST spr round 2 (radius: 25)
[18:24:51 -459910.171837] FAST spr round 3 (radius: 25)
[18:26:39 -459838.867505] FAST spr round 4 (radius: 25)
[18:28:10 -459829.119707] FAST spr round 5 (radius: 25)
[18:29:29 -459823.303553] FAST spr round 6 (radius: 25)
[18:30:43 -459823.303328] Model parameter optimization (eps = 1.000000)
[18:30:57 -459811.109664] SLOW spr round 1 (radius: 5)
[18:33:02 -459732.960933] SLOW spr round 2 (radius: 5)
[18:35:01 -459726.386659] SLOW spr round 3 (radius: 5)
[18:36:55 -459726.328625] SLOW spr round 4 (radius: 10)
[18:39:05 -459725.287295] SLOW spr round 5 (radius: 5)
[18:41:40 -459725.280357] SLOW spr round 6 (radius: 10)
[18:44:15 -459725.278377] SLOW spr round 7 (radius: 15)
[18:48:26 -459724.464676] SLOW spr round 8 (radius: 5)
[18:51:10 -459724.340649] SLOW spr round 9 (radius: 5)
[18:53:28 -459724.340143] SLOW spr round 10 (radius: 10)
[18:55:48 -459724.339796] SLOW spr round 11 (radius: 15)
[19:00:06 -459724.339514] SLOW spr round 12 (radius: 20)
[19:06:33 -459724.339262] SLOW spr round 13 (radius: 25)
[19:13:50 -459724.339025] Model parameter optimization (eps = 0.100000)

[19:13:58] ML tree search #15, logLikelihood: -459724.175442

[19:13:58 -1598783.807111] Initial branch length optimization
[19:14:06 -1300414.197913] Model parameter optimization (eps = 10.000000)
[19:15:42 -1295898.122513] AUTODETECT spr round 1 (radius: 5)
[19:17:27 -915699.688336] AUTODETECT spr round 2 (radius: 10)
[19:19:26 -662153.460939] AUTODETECT spr round 3 (radius: 15)
[19:21:49 -526689.300790] AUTODETECT spr round 4 (radius: 20)
[19:24:33 -512009.468032] AUTODETECT spr round 5 (radius: 25)
[19:28:02 -508890.318039] SPR radius for FAST iterations: 25 (autodetect)
[19:28:02 -508890.318039] Model parameter optimization (eps = 3.000000)
[19:28:56 -506910.076422] FAST spr round 1 (radius: 25)
[19:31:43 -461852.449355] FAST spr round 2 (radius: 25)
[19:33:47 -459953.573035] FAST spr round 3 (radius: 25)
[19:35:35 -459868.522250] FAST spr round 4 (radius: 25)
[19:36:58 -459866.286617] FAST spr round 5 (radius: 25)
[19:38:16 -459866.226539] Model parameter optimization (eps = 1.000000)
[19:38:31 -459854.736040] SLOW spr round 1 (radius: 5)
[19:40:34 -459760.566812] SLOW spr round 2 (radius: 5)
[19:42:30 -459753.497500] SLOW spr round 3 (radius: 5)
[19:44:24 -459753.496892] SLOW spr round 4 (radius: 10)
[19:46:39 -459753.074401] SLOW spr round 5 (radius: 5)
[19:49:17 -459747.380695] SLOW spr round 6 (radius: 5)
[19:51:29 -459746.719563] SLOW spr round 7 (radius: 5)
[19:53:31 -459746.717738] SLOW spr round 8 (radius: 10)
[19:55:44 -459746.716754] SLOW spr round 9 (radius: 15)
[20:00:23 -459744.787645] SLOW spr round 10 (radius: 5)
[20:03:07 -459741.970659] SLOW spr round 11 (radius: 5)
[20:05:23 -459741.970440] SLOW spr round 12 (radius: 10)
[20:07:33 -459741.970322] SLOW spr round 13 (radius: 15)
[20:11:37 -459741.970243] SLOW spr round 14 (radius: 20)
[20:17:35 -459741.970180] SLOW spr round 15 (radius: 25)
[20:24:24 -459741.970124] Model parameter optimization (eps = 0.100000)

[20:24:32] ML tree search #16, logLikelihood: -459741.804681

[20:24:32 -1627020.230985] Initial branch length optimization
[20:24:40 -1320504.107861] Model parameter optimization (eps = 10.000000)
[20:26:15 -1315821.736856] AUTODETECT spr round 1 (radius: 5)
[20:28:13 -951104.988195] AUTODETECT spr round 2 (radius: 10)
[20:30:16 -703705.090303] AUTODETECT spr round 3 (radius: 15)
[20:32:29 -564312.961560] AUTODETECT spr round 4 (radius: 20)
[20:35:06 -517136.573275] AUTODETECT spr round 5 (radius: 25)
[20:38:04 -507887.031931] SPR radius for FAST iterations: 25 (autodetect)
[20:38:04 -507887.031931] Model parameter optimization (eps = 3.000000)
[20:38:47 -505656.701271] FAST spr round 1 (radius: 25)
[20:41:36 -461274.637182] FAST spr round 2 (radius: 25)
[20:43:38 -459999.769068] FAST spr round 3 (radius: 25)
[20:45:22 -459879.164004] FAST spr round 4 (radius: 25)
[20:46:43 -459876.096704] FAST spr round 5 (radius: 25)
[20:48:00 -459874.190484] FAST spr round 6 (radius: 25)
[20:49:13 -459874.188706] Model parameter optimization (eps = 1.000000)
[20:49:34 -459855.602768] SLOW spr round 1 (radius: 5)
[20:51:33 -459757.463649] SLOW spr round 2 (radius: 5)
[20:53:33 -459747.636343] SLOW spr round 3 (radius: 5)
[20:55:27 -459747.633993] SLOW spr round 4 (radius: 10)
[20:57:38 -459743.862597] SLOW spr round 5 (radius: 5)
[21:00:15 -459743.427307] SLOW spr round 6 (radius: 5)
[21:02:28 -459743.425758] SLOW spr round 7 (radius: 10)
[21:04:46 -459743.425218] SLOW spr round 8 (radius: 15)
[21:09:14 -459742.610078] SLOW spr round 9 (radius: 5)
[21:11:58 -459742.487216] SLOW spr round 10 (radius: 5)
[21:14:15 -459742.486748] SLOW spr round 11 (radius: 10)
[21:16:35 -459742.486424] SLOW spr round 12 (radius: 15)
[21:21:01 -459742.486154] SLOW spr round 13 (radius: 20)
[21:27:42 -459739.448587] SLOW spr round 14 (radius: 5)
[21:30:30 -459739.401510] SLOW spr round 15 (radius: 10)
[21:33:24 -459739.398379] SLOW spr round 16 (radius: 15)
[21:37:36 -459739.397033] SLOW spr round 17 (radius: 20)
[21:44:18 -459739.396372] SLOW spr round 18 (radius: 25)
[21:51:44 -459739.395973] Model parameter optimization (eps = 0.100000)

[21:51:50] ML tree search #17, logLikelihood: -459739.373346

[21:51:50 -1612244.684953] Initial branch length optimization
[21:51:58 -1314230.912249] Model parameter optimization (eps = 10.000000)
[21:53:27 -1309727.723483] AUTODETECT spr round 1 (radius: 5)
[21:55:13 -926558.006906] AUTODETECT spr round 2 (radius: 10)
[21:57:16 -639466.666004] AUTODETECT spr round 3 (radius: 15)
[21:59:30 -529068.596535] AUTODETECT spr round 4 (radius: 20)
[22:02:12 -511829.232149] AUTODETECT spr round 5 (radius: 25)
[22:05:38 -510838.781338] SPR radius for FAST iterations: 25 (autodetect)
[22:05:38 -510838.781338] Model parameter optimization (eps = 3.000000)
[22:06:26 -508593.892211] FAST spr round 1 (radius: 25)
[22:09:18 -461834.407801] FAST spr round 2 (radius: 25)
[22:11:25 -460061.473081] FAST spr round 3 (radius: 25)
[22:13:10 -459916.035475] FAST spr round 4 (radius: 25)
[22:14:34 -459896.668177] FAST spr round 5 (radius: 25)
[22:15:52 -459890.745990] FAST spr round 6 (radius: 25)
[22:17:05 -459890.745864] Model parameter optimization (eps = 1.000000)
[22:17:28 -459882.044182] SLOW spr round 1 (radius: 5)
[22:19:31 -459750.808072] SLOW spr round 2 (radius: 5)
[22:21:32 -459737.418971] SLOW spr round 3 (radius: 5)
[22:23:25 -459737.418144] SLOW spr round 4 (radius: 10)
[22:25:34 -459734.937457] SLOW spr round 5 (radius: 5)
[22:28:08 -459734.932582] SLOW spr round 6 (radius: 10)
[22:30:40 -459734.931829] SLOW spr round 7 (radius: 15)
[22:34:56 -459734.121392] SLOW spr round 8 (radius: 5)
[22:37:38 -459733.999489] SLOW spr round 9 (radius: 5)
[22:39:55 -459733.999413] SLOW spr round 10 (radius: 10)
[22:42:13 -459733.999357] SLOW spr round 11 (radius: 15)
[22:46:25 -459733.999309] SLOW spr round 12 (radius: 20)
[22:52:50 -459731.006434] SLOW spr round 13 (radius: 5)
[22:55:37 -459730.959324] SLOW spr round 14 (radius: 10)
[22:58:30 -459730.956303] SLOW spr round 15 (radius: 15)
[23:02:40 -459730.955108] SLOW spr round 16 (radius: 20)
[23:09:13 -459730.954619] SLOW spr round 17 (radius: 25)
[23:16:41 -459730.954404] Model parameter optimization (eps = 0.100000)

[23:16:54] ML tree search #18, logLikelihood: -459730.607937

[23:16:55 -1629186.077392] Initial branch length optimization
[23:17:02 -1322810.238983] Model parameter optimization (eps = 10.000000)
[23:18:27 -1318182.954525] AUTODETECT spr round 1 (radius: 5)
[23:20:16 -896445.002401] AUTODETECT spr round 2 (radius: 10)
[23:22:15 -698980.069955] AUTODETECT spr round 3 (radius: 15)
[23:24:26 -592562.079555] AUTODETECT spr round 4 (radius: 20)
[23:27:10 -511853.896189] AUTODETECT spr round 5 (radius: 25)
[23:30:38 -508947.495678] SPR radius for FAST iterations: 25 (autodetect)
[23:30:38 -508947.495678] Model parameter optimization (eps = 3.000000)
[23:31:21 -506602.466171] FAST spr round 1 (radius: 25)
[23:34:21 -461939.296382] FAST spr round 2 (radius: 25)
[23:36:20 -459994.116197] FAST spr round 3 (radius: 25)
[23:38:02 -459854.805481] FAST spr round 4 (radius: 25)
[23:39:23 -459844.274999] FAST spr round 5 (radius: 25)
[23:40:39 -459844.274086] Model parameter optimization (eps = 1.000000)
[23:40:55 -459835.073863] SLOW spr round 1 (radius: 5)
[23:42:56 -459748.110839] SLOW spr round 2 (radius: 5)
[23:44:50 -459747.935312] SLOW spr round 3 (radius: 5)
[23:46:42 -459747.921286] SLOW spr round 4 (radius: 10)
[23:48:56 -459744.941387] SLOW spr round 5 (radius: 5)
[23:51:33 -459741.681016] SLOW spr round 6 (radius: 5)
[23:53:44 -459741.678639] SLOW spr round 7 (radius: 10)
[23:56:02 -459741.678042] SLOW spr round 8 (radius: 15)
[24:00:38 -459737.793315] SLOW spr round 9 (radius: 5)
[24:03:20 -459737.703798] SLOW spr round 10 (radius: 10)
[24:06:07 -459737.703469] SLOW spr round 11 (radius: 15)
[24:10:26 -459737.703210] SLOW spr round 12 (radius: 20)
[24:16:51 -459737.702982] SLOW spr round 13 (radius: 25)
[24:23:39 -459737.702762] Model parameter optimization (eps = 0.100000)

[24:23:48] ML tree search #19, logLikelihood: -459737.575731

[24:23:48 -1603602.061035] Initial branch length optimization
[24:23:55 -1301691.783203] Model parameter optimization (eps = 10.000000)
[24:24:58 -1296945.608134] AUTODETECT spr round 1 (radius: 5)
[24:26:35 -914581.927988] AUTODETECT spr round 2 (radius: 10)
[24:28:24 -686789.834886] AUTODETECT spr round 3 (radius: 15)
[24:30:21 -591783.444187] AUTODETECT spr round 4 (radius: 20)
[24:32:47 -536388.035003] AUTODETECT spr round 5 (radius: 25)
[24:35:12 -527661.925302] SPR radius for FAST iterations: 25 (autodetect)
[24:35:12 -527661.925302] Model parameter optimization (eps = 3.000000)
[24:35:51 -525343.402512] FAST spr round 1 (radius: 25)
[24:38:30 -462225.145025] FAST spr round 2 (radius: 25)
[24:40:44 -460063.028060] FAST spr round 3 (radius: 25)
[24:42:46 -459917.264337] FAST spr round 4 (radius: 25)
[24:44:22 -459910.142781] FAST spr round 5 (radius: 25)
[24:45:48 -459910.141598] Model parameter optimization (eps = 1.000000)
[24:46:12 -459892.737203] SLOW spr round 1 (radius: 5)
[24:48:25 -459760.305662] SLOW spr round 2 (radius: 5)
[24:50:31 -459750.906160] SLOW spr round 3 (radius: 5)
[24:52:37 -459750.904421] SLOW spr round 4 (radius: 10)
[24:55:03 -459748.994258] SLOW spr round 5 (radius: 5)
[24:57:54 -459748.954092] SLOW spr round 6 (radius: 10)
[25:00:49 -459748.953484] SLOW spr round 7 (radius: 15)
[25:05:32 -459748.132089] SLOW spr round 8 (radius: 5)
[25:08:33 -459748.008952] SLOW spr round 9 (radius: 5)
[25:11:05 -459748.008480] SLOW spr round 10 (radius: 10)
[25:13:44 -459748.008154] SLOW spr round 11 (radius: 15)
[25:18:37 -459748.007884] SLOW spr round 12 (radius: 20)
[25:25:44 -459748.007637] SLOW spr round 13 (radius: 25)
[25:33:46 -459746.608184] SLOW spr round 14 (radius: 5)
[25:36:57 -459745.138331] SLOW spr round 15 (radius: 5)
[25:39:36 -459742.295499] SLOW spr round 16 (radius: 5)
[25:41:56 -459742.244375] SLOW spr round 17 (radius: 10)
[25:44:24 -459742.244145] SLOW spr round 18 (radius: 15)
[25:49:16 -459742.243914] SLOW spr round 19 (radius: 20)
[25:56:10 -459742.243683] SLOW spr round 20 (radius: 25)
[26:04:05 -459742.243453] Model parameter optimization (eps = 0.100000)

[26:04:21] ML tree search #20, logLikelihood: -459741.967076


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.157254,0.525131) (0.084261,0.559075) (0.377060,0.660021) (0.381425,1.629274) 
   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: -459720.957747

AIC score: 922155.915494 / AICc score: 926269.321744 / BIC score: 929918.582014
Free parameters (model + branch lengths): 1357

WARNING: Best ML tree contains 20 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5VZ89/3_mltree/Q5VZ89.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5VZ89/3_mltree/Q5VZ89.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5VZ89/3_mltree/Q5VZ89.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5VZ89/3_mltree/Q5VZ89.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5VZ89/3_mltree/Q5VZ89.raxml.log

Analysis started: 03-Jul-2021 06:28:18 / finished: 04-Jul-2021 08:32:39

Elapsed time: 93861.187 seconds

Consumed energy: 8160.778 Wh (= 41 km in an electric car, or 204 km with an e-scooter!)