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 15:19:06 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9C0A0/2_msa/Q9C0A0_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9C0A0/3_mltree/Q9C0A0 --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/Q9C0A0/2_msa/Q9C0A0_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 1311 sites

WARNING: Sequences tr_G1Q7M7_G1Q7M7_MYOLU_59463 and tr_G1TVV6_G1TVV6_RABIT_9986 are exactly identical!
WARNING: Sequences tr_G1Q7M7_G1Q7M7_MYOLU_59463 and tr_F6ZU60_F6ZU60_MONDO_13616 are exactly identical!
WARNING: Sequences tr_G1Q7M7_G1Q7M7_MYOLU_59463 and tr_G3WDR2_G3WDR2_SARHA_9305 are exactly identical!
WARNING: Sequences tr_G1Q7M7_G1Q7M7_MYOLU_59463 and tr_G1MKK6_G1MKK6_AILME_9646 are exactly identical!
WARNING: Sequences tr_G1Q7M7_G1Q7M7_MYOLU_59463 and tr_A0A091ERN4_A0A091ERN4_CORBR_85066 are exactly identical!
WARNING: Sequences tr_G1Q7M7_G1Q7M7_MYOLU_59463 and tr_A0A091ILE4_A0A091ILE4_EGRGA_188379 are exactly identical!
WARNING: Sequences tr_G1Q7M7_G1Q7M7_MYOLU_59463 and tr_A0A093PPP6_A0A093PPP6_9PASS_328815 are exactly identical!
WARNING: Sequences tr_G1Q7M7_G1Q7M7_MYOLU_59463 and tr_A0A091V1C0_A0A091V1C0_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_G1Q7M7_G1Q7M7_MYOLU_59463 and tr_A0A087QHR8_A0A087QHR8_APTFO_9233 are exactly identical!
WARNING: Sequences tr_G1Q7M7_G1Q7M7_MYOLU_59463 and tr_A0A091GKP6_A0A091GKP6_9AVES_55661 are exactly identical!
WARNING: Sequences tr_G1Q7M7_G1Q7M7_MYOLU_59463 and tr_A0A091I750_A0A091I750_CALAN_9244 are exactly identical!
WARNING: Sequences tr_G1QBQ5_G1QBQ5_MYOLU_59463 and tr_G1U865_G1U865_RABIT_9986 are exactly identical!
WARNING: Sequences tr_G1QBQ5_G1QBQ5_MYOLU_59463 and tr_W5NTD8_W5NTD8_SHEEP_9940 are exactly identical!
WARNING: Sequences tr_G1QBQ5_G1QBQ5_MYOLU_59463 and tr_G1MMY5_G1MMY5_AILME_9646 are exactly identical!
WARNING: Sequences tr_G1QBQ5_G1QBQ5_MYOLU_59463 and tr_G3N0D3_G3N0D3_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_H2R9Q6_H2R9Q6_PANTR_9598 and sp_P78357_CNTP1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2R9Q6_H2R9Q6_PANTR_9598 and tr_A0A2R9A9Y5_A0A2R9A9Y5_PANPA_9597 are exactly identical!
WARNING: Sequences tr_W5NTB7_W5NTB7_SHEEP_9940 and tr_G3MWQ3_G3MWQ3_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_F7B7T3_F7B7T3_MACMU_9544 and tr_A0A2K6BQZ5_A0A2K6BQZ5_MACNE_9545 are exactly identical!
WARNING: Sequences tr_K7F0N1_K7F0N1_PELSI_13735 and tr_A0A093GUR3_A0A093GUR3_DRYPU_118200 are exactly identical!
WARNING: Sequences tr_A0A091UP89_A0A091UP89_NIPNI_128390 and tr_A0A087QTV9_A0A087QTV9_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091UP89_A0A091UP89_NIPNI_128390 and tr_A0A091FKH7_A0A091FKH7_9AVES_55661 are exactly identical!
WARNING: Sequences tr_A0A2D0R5G2_A0A2D0R5G2_ICTPU_7998 and tr_A0A2D0R5H4_A0A2D0R5H4_ICTPU_7998 are exactly identical!
WARNING: Duplicate sequences found: 23

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/Q9C0A0/3_mltree/Q9C0A0.raxml.reduced.phy

Alignment comprises 1 partitions and 1311 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 1311 / 1311
Gaps: 41.23 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9C0A0/3_mltree/Q9C0A0.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 1001 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 164 / 13120
[00:00:00] Data distribution: max. searches per worker: 20

Starting ML tree search with 20 distinct starting trees

[00:00:00 -1478623.310041] Initial branch length optimization
[00:00:09 -1233647.784229] Model parameter optimization (eps = 10.000000)
[00:01:55 -1228412.904490] AUTODETECT spr round 1 (radius: 5)
[00:04:45 -855927.166323] AUTODETECT spr round 2 (radius: 10)
[00:07:56 -643466.188327] AUTODETECT spr round 3 (radius: 15)
[00:11:23 -534998.316139] AUTODETECT spr round 4 (radius: 20)
[00:15:39 -512842.801538] AUTODETECT spr round 5 (radius: 25)
[00:20:56 -509145.369106] SPR radius for FAST iterations: 25 (autodetect)
[00:20:56 -509145.369106] Model parameter optimization (eps = 3.000000)
[00:21:38 -508059.502048] FAST spr round 1 (radius: 25)
[00:26:35 -458944.125520] FAST spr round 2 (radius: 25)
[00:30:02 -457389.443891] FAST spr round 3 (radius: 25)
[00:32:56 -457172.685964] FAST spr round 4 (radius: 25)
[00:35:29 -457142.818042] FAST spr round 5 (radius: 25)
[00:38:01 -457128.935850] FAST spr round 6 (radius: 25)
[00:40:16 -457127.136202] FAST spr round 7 (radius: 25)
[00:42:28 -457127.134916] Model parameter optimization (eps = 1.000000)
[00:42:49 -457116.702979] SLOW spr round 1 (radius: 5)
[00:45:51 -457018.035295] SLOW spr round 2 (radius: 5)
[00:48:47 -457009.820715] SLOW spr round 3 (radius: 5)
[00:51:46 -457005.382944] SLOW spr round 4 (radius: 5)
[00:54:42 -457005.353260] SLOW spr round 5 (radius: 10)
[00:57:49 -457002.608011] SLOW spr round 6 (radius: 5)
[01:01:29 -456996.780918] SLOW spr round 7 (radius: 5)
[01:04:45 -456996.778645] SLOW spr round 8 (radius: 10)
[01:08:03 -456995.926100] SLOW spr round 9 (radius: 5)
[01:11:35 -456995.922476] SLOW spr round 10 (radius: 10)
[01:15:08 -456995.921685] SLOW spr round 11 (radius: 15)
[01:20:09 -456995.921268] SLOW spr round 12 (radius: 20)
[01:27:32 -456995.921011] SLOW spr round 13 (radius: 25)
[01:38:39 -456995.920837] Model parameter optimization (eps = 0.100000)

[01:38:53] ML tree search #1, logLikelihood: -456995.838934

[01:38:53 -1476007.659104] Initial branch length optimization
[01:39:03 -1227915.744010] Model parameter optimization (eps = 10.000000)
[01:40:46 -1222530.540002] AUTODETECT spr round 1 (radius: 5)
[01:43:35 -880904.323603] AUTODETECT spr round 2 (radius: 10)
[01:46:45 -625406.234355] AUTODETECT spr round 3 (radius: 15)
[01:50:14 -536400.290276] AUTODETECT spr round 4 (radius: 20)
[01:54:04 -514181.462579] AUTODETECT spr round 5 (radius: 25)
[01:59:28 -501977.125925] SPR radius for FAST iterations: 25 (autodetect)
[01:59:28 -501977.125925] Model parameter optimization (eps = 3.000000)
[02:00:08 -500856.055776] FAST spr round 1 (radius: 25)
[02:04:46 -458643.388074] FAST spr round 2 (radius: 25)
[02:08:05 -457278.272854] FAST spr round 3 (radius: 25)
[02:10:51 -457147.733871] FAST spr round 4 (radius: 25)
[02:13:18 -457136.255232] FAST spr round 5 (radius: 25)
[02:15:38 -457120.270382] FAST spr round 6 (radius: 25)
[02:17:50 -457113.958541] FAST spr round 7 (radius: 25)
[02:20:00 -457113.834923] FAST spr round 8 (radius: 25)
[02:22:09 -457113.809956] Model parameter optimization (eps = 1.000000)
[02:22:31 -457107.204439] SLOW spr round 1 (radius: 5)
[02:25:25 -457006.639851] SLOW spr round 2 (radius: 5)
[02:28:22 -456993.666156] SLOW spr round 3 (radius: 5)
[02:31:15 -456993.212848] SLOW spr round 4 (radius: 5)
[02:34:07 -456993.208876] SLOW spr round 5 (radius: 10)
[02:37:07 -456993.207932] SLOW spr round 6 (radius: 15)
[02:42:17 -456993.093896] SLOW spr round 7 (radius: 5)
[02:45:53 -456993.072059] SLOW spr round 8 (radius: 10)
[02:49:34 -456993.071862] SLOW spr round 9 (radius: 15)
[02:54:26 -456993.071834] SLOW spr round 10 (radius: 20)
[03:02:15 -456993.071824] SLOW spr round 11 (radius: 25)
[03:13:54 -456993.071817] Model parameter optimization (eps = 0.100000)

[03:14:04] ML tree search #2, logLikelihood: -456993.021371

[03:14:04 -1484422.688652] Initial branch length optimization
[03:14:13 -1235390.400382] Model parameter optimization (eps = 10.000000)
[03:16:11 -1230371.924838] AUTODETECT spr round 1 (radius: 5)
[03:18:57 -873401.320062] AUTODETECT spr round 2 (radius: 10)
[03:22:07 -646392.536777] AUTODETECT spr round 3 (radius: 15)
[03:25:35 -556402.310097] AUTODETECT spr round 4 (radius: 20)
[03:29:23 -510895.389317] AUTODETECT spr round 5 (radius: 25)
[03:33:40 -506139.849493] SPR radius for FAST iterations: 25 (autodetect)
[03:33:40 -506139.849493] Model parameter optimization (eps = 3.000000)
[03:34:32 -504842.807166] FAST spr round 1 (radius: 25)
[03:39:07 -458490.566142] FAST spr round 2 (radius: 25)
[03:42:34 -457202.567886] FAST spr round 3 (radius: 25)
[03:45:33 -457127.424838] FAST spr round 4 (radius: 25)
[03:48:03 -457123.077583] FAST spr round 5 (radius: 25)
[03:50:23 -457118.505593] FAST spr round 6 (radius: 25)
[03:52:38 -457114.544160] FAST spr round 7 (radius: 25)
[03:54:49 -457114.522316] Model parameter optimization (eps = 1.000000)
[03:55:11 -457105.239481] SLOW spr round 1 (radius: 5)
[03:58:16 -457008.660089] SLOW spr round 2 (radius: 5)
[04:01:12 -457006.724833] SLOW spr round 3 (radius: 5)
[04:04:05 -457005.459134] SLOW spr round 4 (radius: 5)
[04:06:54 -457005.458076] SLOW spr round 5 (radius: 10)
[04:09:53 -457005.457631] SLOW spr round 6 (radius: 15)
[04:15:07 -457005.338635] SLOW spr round 7 (radius: 5)
[04:18:45 -457005.337876] SLOW spr round 8 (radius: 10)
[04:22:30 -457005.167130] SLOW spr round 9 (radius: 5)
[04:25:56 -457003.833768] SLOW spr round 10 (radius: 5)
[04:29:00 -457003.831951] SLOW spr round 11 (radius: 10)
[04:32:11 -457003.831732] SLOW spr round 12 (radius: 15)
[04:37:13 -457003.700452] SLOW spr round 13 (radius: 5)
[04:40:48 -457003.700258] SLOW spr round 14 (radius: 10)
[04:44:27 -457003.700089] SLOW spr round 15 (radius: 15)
[04:49:20 -457003.699937] SLOW spr round 16 (radius: 20)
[04:57:18 -457003.699794] SLOW spr round 17 (radius: 25)
[05:09:15 -457003.699658] Model parameter optimization (eps = 0.100000)

[05:09:34] ML tree search #3, logLikelihood: -457003.513198

[05:09:34 -1473340.185805] Initial branch length optimization
[05:09:44 -1230003.438544] Model parameter optimization (eps = 10.000000)
[05:11:37 -1224691.608420] AUTODETECT spr round 1 (radius: 5)
[05:14:30 -869491.168090] AUTODETECT spr round 2 (radius: 10)
[05:17:45 -631735.865755] AUTODETECT spr round 3 (radius: 15)
[05:21:15 -553692.800442] AUTODETECT spr round 4 (radius: 20)
[05:25:13 -518550.919770] AUTODETECT spr round 5 (radius: 25)
[05:29:32 -510933.698418] SPR radius for FAST iterations: 25 (autodetect)
[05:29:32 -510933.698418] Model parameter optimization (eps = 3.000000)
[05:30:11 -509815.525347] FAST spr round 1 (radius: 25)
[05:34:47 -460170.574364] FAST spr round 2 (radius: 25)
[05:38:25 -457359.401615] FAST spr round 3 (radius: 25)
[05:41:32 -457129.215299] FAST spr round 4 (radius: 25)
[05:44:09 -457103.774028] FAST spr round 5 (radius: 25)
[05:46:27 -457103.769817] Model parameter optimization (eps = 1.000000)
[05:46:47 -457094.645198] SLOW spr round 1 (radius: 5)
[05:49:55 -456994.281436] SLOW spr round 2 (radius: 5)
[05:52:52 -456984.021233] SLOW spr round 3 (radius: 5)
[05:55:47 -456980.835904] SLOW spr round 4 (radius: 5)
[05:58:37 -456980.808729] SLOW spr round 5 (radius: 10)
[06:01:40 -456980.808535] SLOW spr round 6 (radius: 15)
[06:06:55 -456980.808342] SLOW spr round 7 (radius: 20)
[06:14:26 -456980.808150] SLOW spr round 8 (radius: 25)
[06:25:48 -456980.807956] Model parameter optimization (eps = 0.100000)

[06:25:55] ML tree search #4, logLikelihood: -456980.753204

[06:25:55 -1477714.475416] Initial branch length optimization
[06:26:05 -1235342.702787] Model parameter optimization (eps = 10.000000)
[06:27:38 -1230309.046016] AUTODETECT spr round 1 (radius: 5)
[06:30:20 -861869.212935] AUTODETECT spr round 2 (radius: 10)
[06:33:22 -648740.080016] AUTODETECT spr round 3 (radius: 15)
[06:36:48 -556371.165537] AUTODETECT spr round 4 (radius: 20)
[06:40:33 -521243.327133] AUTODETECT spr round 5 (radius: 25)
[06:44:46 -518216.232976] SPR radius for FAST iterations: 25 (autodetect)
[06:44:46 -518216.232976] Model parameter optimization (eps = 3.000000)
[06:45:33 -516952.262472] FAST spr round 1 (radius: 25)
[06:50:03 -459810.250454] FAST spr round 2 (radius: 25)
[06:53:24 -457287.236537] FAST spr round 3 (radius: 25)
[06:56:15 -457143.091421] FAST spr round 4 (radius: 25)
[06:58:44 -457125.760240] FAST spr round 5 (radius: 25)
[07:01:01 -457125.758838] Model parameter optimization (eps = 1.000000)
[07:01:16 -457120.549380] SLOW spr round 1 (radius: 5)
[07:04:17 -457024.530450] SLOW spr round 2 (radius: 5)
[07:07:17 -457015.823027] SLOW spr round 3 (radius: 5)
[07:10:09 -457014.281838] SLOW spr round 4 (radius: 5)
[07:12:59 -457014.281137] SLOW spr round 5 (radius: 10)
[07:15:59 -457014.280692] SLOW spr round 6 (radius: 15)
[07:21:12 -457014.280320] SLOW spr round 7 (radius: 20)
[07:28:35 -457014.279994] SLOW spr round 8 (radius: 25)
[07:40:00 -457014.279696] Model parameter optimization (eps = 0.100000)

[07:40:14] ML tree search #5, logLikelihood: -457013.899433

[07:40:14 -1465030.061136] Initial branch length optimization
[07:40:24 -1226785.471074] Model parameter optimization (eps = 10.000000)
[07:41:42 -1221553.643366] AUTODETECT spr round 1 (radius: 5)
[07:44:27 -863895.146117] AUTODETECT spr round 2 (radius: 10)
[07:47:40 -640806.424245] AUTODETECT spr round 3 (radius: 15)
[07:51:07 -545059.734487] AUTODETECT spr round 4 (radius: 20)
[07:55:14 -506215.301328] AUTODETECT spr round 5 (radius: 25)
[08:00:13 -504182.993486] SPR radius for FAST iterations: 25 (autodetect)
[08:00:13 -504182.993486] Model parameter optimization (eps = 3.000000)
[08:00:51 -503020.660752] FAST spr round 1 (radius: 25)
[08:05:06 -458708.299384] FAST spr round 2 (radius: 25)
[08:08:33 -457236.354560] FAST spr round 3 (radius: 25)
[08:11:24 -457156.757315] FAST spr round 4 (radius: 25)
[08:13:56 -457143.207059] FAST spr round 5 (radius: 25)
[08:16:12 -457139.577908] FAST spr round 6 (radius: 25)
[08:18:24 -457135.976460] FAST spr round 7 (radius: 25)
[08:20:32 -457135.970830] Model parameter optimization (eps = 1.000000)
[08:20:50 -457127.492738] SLOW spr round 1 (radius: 5)
[08:23:40 -457025.871532] SLOW spr round 2 (radius: 5)
[08:26:34 -457012.818292] SLOW spr round 3 (radius: 5)
[08:29:27 -457008.375257] SLOW spr round 4 (radius: 5)
[08:32:14 -457008.374290] SLOW spr round 5 (radius: 10)
[08:35:18 -457005.812030] SLOW spr round 6 (radius: 5)
[08:38:42 -457004.681374] SLOW spr round 7 (radius: 5)
[08:41:45 -457004.674507] SLOW spr round 8 (radius: 10)
[08:44:55 -457004.594056] SLOW spr round 9 (radius: 15)
[08:49:57 -457004.592336] SLOW spr round 10 (radius: 20)
[08:57:38 -457004.251590] SLOW spr round 11 (radius: 5)
[09:01:18 -457004.249890] SLOW spr round 12 (radius: 10)
[09:04:57 -457004.249538] SLOW spr round 13 (radius: 15)
[09:09:02 -457004.249367] SLOW spr round 14 (radius: 20)
[09:15:38 -457003.914490] SLOW spr round 15 (radius: 5)
[09:18:42 -457003.913745] SLOW spr round 16 (radius: 10)
[09:21:56 -457003.913600] SLOW spr round 17 (radius: 15)
[09:26:01 -457003.759228] SLOW spr round 18 (radius: 5)
[09:28:59 -457003.759193] SLOW spr round 19 (radius: 10)
[09:32:04 -457003.759171] SLOW spr round 20 (radius: 15)
[09:36:08 -457003.759157] SLOW spr round 21 (radius: 20)
[09:42:42 -457003.759148] SLOW spr round 22 (radius: 25)
[09:52:37 -457003.759142] Model parameter optimization (eps = 0.100000)

[09:52:50] ML tree search #6, logLikelihood: -457002.558631

[09:52:51 -1474753.255451] Initial branch length optimization
[09:52:58 -1231709.403958] Model parameter optimization (eps = 10.000000)
[09:54:11 -1226354.446682] AUTODETECT spr round 1 (radius: 5)
[09:56:26 -883355.145972] AUTODETECT spr round 2 (radius: 10)
[09:59:00 -641541.904727] AUTODETECT spr round 3 (radius: 15)
[10:01:45 -541565.368417] AUTODETECT spr round 4 (radius: 20)
[10:04:59 -508806.489630] AUTODETECT spr round 5 (radius: 25)
[10:09:00 -503940.274932] SPR radius for FAST iterations: 25 (autodetect)
[10:09:00 -503940.274932] Model parameter optimization (eps = 3.000000)
[10:09:23 -502898.135252] FAST spr round 1 (radius: 25)
[10:13:21 -459951.888772] FAST spr round 2 (radius: 25)
[10:16:13 -457431.632544] FAST spr round 3 (radius: 25)
[10:18:34 -457223.963539] FAST spr round 4 (radius: 25)
[10:20:37 -457134.129613] FAST spr round 5 (radius: 25)
[10:22:30 -457125.128463] FAST spr round 6 (radius: 25)
[10:24:20 -457125.125977] Model parameter optimization (eps = 1.000000)
[10:24:37 -457117.439985] SLOW spr round 1 (radius: 5)
[10:27:14 -457010.525991] SLOW spr round 2 (radius: 5)
[10:30:14 -456988.607476] SLOW spr round 3 (radius: 5)
[10:33:09 -456988.131105] SLOW spr round 4 (radius: 5)
[10:36:02 -456988.130857] SLOW spr round 5 (radius: 10)
[10:39:08 -456986.900838] SLOW spr round 6 (radius: 5)
[10:42:36 -456986.894266] SLOW spr round 7 (radius: 10)
[10:46:09 -456986.893040] SLOW spr round 8 (radius: 15)
[10:51:17 -456986.578308] SLOW spr round 9 (radius: 5)
[10:54:56 -456986.577559] SLOW spr round 10 (radius: 10)
[10:58:40 -456986.577344] SLOW spr round 11 (radius: 15)
[11:03:43 -456986.577326] SLOW spr round 12 (radius: 20)
[11:11:37 -456983.978436] SLOW spr round 13 (radius: 5)
[11:15:19 -456983.976256] SLOW spr round 14 (radius: 10)
[11:19:12 -456983.975229] SLOW spr round 15 (radius: 15)
[11:24:11 -456983.974754] SLOW spr round 16 (radius: 20)
[11:32:00 -456983.974537] SLOW spr round 17 (radius: 25)
[11:43:56 -456983.920745] Model parameter optimization (eps = 0.100000)

[11:44:12] ML tree search #7, logLikelihood: -456982.582755

[11:44:12 -1473471.813249] Initial branch length optimization
[11:44:20 -1232777.014949] Model parameter optimization (eps = 10.000000)
[11:45:43 -1227563.448218] AUTODETECT spr round 1 (radius: 5)
[11:48:28 -865619.088841] AUTODETECT spr round 2 (radius: 10)
[11:51:40 -650127.928529] AUTODETECT spr round 3 (radius: 15)
[11:55:02 -551904.644921] AUTODETECT spr round 4 (radius: 20)
[11:58:53 -518953.155227] AUTODETECT spr round 5 (radius: 25)
[12:03:35 -513584.820789] SPR radius for FAST iterations: 25 (autodetect)
[12:03:35 -513584.820789] Model parameter optimization (eps = 3.000000)
[12:04:15 -512437.961090] FAST spr round 1 (radius: 25)
[12:08:46 -459310.767585] FAST spr round 2 (radius: 25)
[12:12:23 -457289.441245] FAST spr round 3 (radius: 25)
[12:15:28 -457161.914427] FAST spr round 4 (radius: 25)
[12:18:10 -457141.761381] FAST spr round 5 (radius: 25)
[12:20:44 -457129.625153] FAST spr round 6 (radius: 25)
[12:23:04 -457124.771112] FAST spr round 7 (radius: 25)
[12:25:18 -457124.247397] FAST spr round 8 (radius: 25)
[12:27:31 -457124.246578] Model parameter optimization (eps = 1.000000)
[12:27:55 -457101.198620] SLOW spr round 1 (radius: 5)
[12:30:58 -457013.181229] SLOW spr round 2 (radius: 5)
[12:34:00 -457002.936660] SLOW spr round 3 (radius: 5)
[12:37:04 -456996.637432] SLOW spr round 4 (radius: 5)
[12:39:59 -456996.506917] SLOW spr round 5 (radius: 5)
[12:42:52 -456996.506057] SLOW spr round 6 (radius: 10)
[12:45:55 -456996.505692] SLOW spr round 7 (radius: 15)
[12:51:06 -456995.256039] SLOW spr round 8 (radius: 5)
[12:54:42 -456995.254529] SLOW spr round 9 (radius: 10)
[12:58:19 -456995.253880] SLOW spr round 10 (radius: 15)
[13:03:11 -456995.253560] SLOW spr round 11 (radius: 20)
[13:10:31 -456995.253390] SLOW spr round 12 (radius: 25)
[13:21:22 -456995.126323] SLOW spr round 13 (radius: 5)
[13:25:08 -456995.115247] SLOW spr round 14 (radius: 10)
[13:29:02 -456995.112076] SLOW spr round 15 (radius: 15)
[13:33:52 -456995.110456] SLOW spr round 16 (radius: 20)
[13:41:20 -456995.109625] SLOW spr round 17 (radius: 25)
[13:52:18 -456995.109193] Model parameter optimization (eps = 0.100000)

[13:52:38] ML tree search #8, logLikelihood: -456994.790749

[13:52:38 -1472254.481954] Initial branch length optimization
[13:52:47 -1232186.299706] Model parameter optimization (eps = 10.000000)
[13:54:34 -1226753.886640] AUTODETECT spr round 1 (radius: 5)
[13:57:23 -881364.337997] AUTODETECT spr round 2 (radius: 10)
[14:00:32 -636017.213659] AUTODETECT spr round 3 (radius: 15)
[14:03:56 -538685.372232] AUTODETECT spr round 4 (radius: 20)
[14:07:51 -514571.043579] AUTODETECT spr round 5 (radius: 25)
[14:12:32 -508059.466315] SPR radius for FAST iterations: 25 (autodetect)
[14:12:32 -508059.466315] Model parameter optimization (eps = 3.000000)
[14:13:20 -506945.379069] FAST spr round 1 (radius: 25)
[14:17:57 -460148.628073] FAST spr round 2 (radius: 25)
[14:21:26 -457537.302210] FAST spr round 3 (radius: 25)
[14:24:25 -457119.492415] FAST spr round 4 (radius: 25)
[14:26:53 -457109.579704] FAST spr round 5 (radius: 25)
[14:29:07 -457109.579238] Model parameter optimization (eps = 1.000000)
[14:29:31 -457103.015367] SLOW spr round 1 (radius: 5)
[14:32:44 -457012.682223] SLOW spr round 2 (radius: 5)
[14:35:44 -457004.251890] SLOW spr round 3 (radius: 5)
[14:38:37 -457004.236908] SLOW spr round 4 (radius: 10)
[14:41:42 -457001.864603] SLOW spr round 5 (radius: 5)
[14:45:13 -457001.556502] SLOW spr round 6 (radius: 5)
[14:48:21 -457001.554643] SLOW spr round 7 (radius: 10)
[14:51:34 -457000.987807] SLOW spr round 8 (radius: 5)
[14:54:57 -457000.986113] SLOW spr round 9 (radius: 10)
[14:58:25 -457000.985228] SLOW spr round 10 (radius: 15)
[15:03:32 -457000.505101] SLOW spr round 11 (radius: 5)
[15:07:08 -457000.504006] SLOW spr round 12 (radius: 10)
[15:10:51 -457000.503380] SLOW spr round 13 (radius: 15)
[15:15:56 -457000.502873] SLOW spr round 14 (radius: 20)
[15:24:09 -457000.502373] SLOW spr round 15 (radius: 25)
[15:36:33 -457000.383170] SLOW spr round 16 (radius: 5)
[15:40:20 -457000.363912] SLOW spr round 17 (radius: 10)
[15:44:20 -457000.363214] SLOW spr round 18 (radius: 15)
[15:49:21 -457000.362618] SLOW spr round 19 (radius: 20)
[15:57:30 -457000.362074] SLOW spr round 20 (radius: 25)
[16:09:50 -457000.361556] Model parameter optimization (eps = 0.100000)

[16:09:58] ML tree search #9, logLikelihood: -457000.288225

[16:09:58 -1472257.321439] Initial branch length optimization
[16:10:07 -1225817.033501] Model parameter optimization (eps = 10.000000)
[16:11:37 -1220620.281305] AUTODETECT spr round 1 (radius: 5)
[16:14:23 -881220.280586] AUTODETECT spr round 2 (radius: 10)
[16:17:28 -674823.630555] AUTODETECT spr round 3 (radius: 15)
[16:20:50 -576691.369561] AUTODETECT spr round 4 (radius: 20)
[16:25:03 -518603.141192] AUTODETECT spr round 5 (radius: 25)
[16:29:55 -508418.934975] SPR radius for FAST iterations: 25 (autodetect)
[16:29:55 -508418.934975] Model parameter optimization (eps = 3.000000)
[16:30:33 -507325.009560] FAST spr round 1 (radius: 25)
[16:34:54 -459172.557393] FAST spr round 2 (radius: 25)
[16:38:27 -457345.041418] FAST spr round 3 (radius: 25)
[16:41:20 -457169.840640] FAST spr round 4 (radius: 25)
[16:43:55 -457150.912285] FAST spr round 5 (radius: 25)
[16:46:15 -457148.785000] FAST spr round 6 (radius: 25)
[16:48:32 -457147.958504] FAST spr round 7 (radius: 25)
[16:50:44 -457147.956265] Model parameter optimization (eps = 1.000000)
[16:51:08 -457135.468039] SLOW spr round 1 (radius: 5)
[16:54:02 -457058.819184] SLOW spr round 2 (radius: 5)
[16:56:56 -457036.813235] SLOW spr round 3 (radius: 5)
[16:59:46 -457036.105466] SLOW spr round 4 (radius: 5)
[17:02:31 -457036.104906] SLOW spr round 5 (radius: 10)
[17:05:32 -457031.211992] SLOW spr round 6 (radius: 5)
[17:08:54 -457019.365163] SLOW spr round 7 (radius: 5)
[17:11:57 -457015.535199] SLOW spr round 8 (radius: 5)
[17:14:47 -457015.532497] SLOW spr round 9 (radius: 10)
[17:17:46 -457015.532215] SLOW spr round 10 (radius: 15)
[17:22:26 -457015.532133] SLOW spr round 11 (radius: 20)
[17:29:17 -457015.532098] SLOW spr round 12 (radius: 25)
[17:39:25 -457015.532076] Model parameter optimization (eps = 0.100000)

[17:39:40] ML tree search #10, logLikelihood: -457015.402671

[17:39:40 -1471344.657380] Initial branch length optimization
[17:39:49 -1232301.485183] Model parameter optimization (eps = 10.000000)
[17:41:20 -1226794.834347] AUTODETECT spr round 1 (radius: 5)
[17:44:00 -885649.792033] AUTODETECT spr round 2 (radius: 10)
[17:47:01 -631817.581498] AUTODETECT spr round 3 (radius: 15)
[17:50:12 -548217.411535] AUTODETECT spr round 4 (radius: 20)
[17:53:48 -505911.787026] AUTODETECT spr round 5 (radius: 25)
[17:58:21 -504154.137643] SPR radius for FAST iterations: 25 (autodetect)
[17:58:21 -504154.137643] Model parameter optimization (eps = 3.000000)
[17:59:17 -503053.909727] FAST spr round 1 (radius: 25)
[18:03:31 -458465.271196] FAST spr round 2 (radius: 25)
[18:06:50 -457238.665539] FAST spr round 3 (radius: 25)
[18:09:36 -457143.465238] FAST spr round 4 (radius: 25)
[18:12:02 -457134.729413] FAST spr round 5 (radius: 25)
[18:14:19 -457129.847717] FAST spr round 6 (radius: 25)
[18:16:33 -457126.902856] FAST spr round 7 (radius: 25)
[18:18:44 -457125.656768] FAST spr round 8 (radius: 25)
[18:20:52 -457125.655850] Model parameter optimization (eps = 1.000000)
[18:21:13 -457118.264519] SLOW spr round 1 (radius: 5)
[18:24:03 -457023.058793] SLOW spr round 2 (radius: 5)
[18:26:53 -457021.487707] SLOW spr round 3 (radius: 5)
[18:29:41 -457021.486621] SLOW spr round 4 (radius: 10)
[18:32:44 -457019.660011] SLOW spr round 5 (radius: 5)
[18:36:05 -457019.643317] SLOW spr round 6 (radius: 10)
[18:39:30 -457019.643280] SLOW spr round 7 (radius: 15)
[18:44:16 -457017.921358] SLOW spr round 8 (radius: 5)
[18:47:48 -457014.844017] SLOW spr round 9 (radius: 5)
[18:50:59 -457014.841875] SLOW spr round 10 (radius: 10)
[18:54:25 -457014.840823] SLOW spr round 11 (radius: 15)
[18:59:34 -457014.783932] SLOW spr round 12 (radius: 20)
[19:07:25 -457014.783683] SLOW spr round 13 (radius: 25)
[19:19:21 -457014.783560] Model parameter optimization (eps = 0.100000)

[19:19:34] ML tree search #11, logLikelihood: -457014.628421

[19:19:34 -1486568.921159] Initial branch length optimization
[19:19:43 -1238599.331617] Model parameter optimization (eps = 10.000000)
[19:21:20 -1233645.158065] AUTODETECT spr round 1 (radius: 5)
[19:24:05 -876239.316169] AUTODETECT spr round 2 (radius: 10)
[19:27:15 -654159.982789] AUTODETECT spr round 3 (radius: 15)
[19:30:50 -543217.507683] AUTODETECT spr round 4 (radius: 20)
[19:34:49 -513048.356918] AUTODETECT spr round 5 (radius: 25)
[19:39:21 -506284.987804] SPR radius for FAST iterations: 25 (autodetect)
[19:39:21 -506284.987804] Model parameter optimization (eps = 3.000000)
[19:40:01 -505044.771455] FAST spr round 1 (radius: 25)
[19:44:22 -458681.776080] FAST spr round 2 (radius: 25)
[19:47:43 -457247.533656] FAST spr round 3 (radius: 25)
[19:50:35 -457175.313090] FAST spr round 4 (radius: 25)
[19:53:06 -457163.884294] FAST spr round 5 (radius: 25)
[19:55:23 -457163.872642] Model parameter optimization (eps = 1.000000)
[19:55:41 -457153.898821] SLOW spr round 1 (radius: 5)
[19:58:37 -457032.542077] SLOW spr round 2 (radius: 5)
[20:01:36 -457025.081671] SLOW spr round 3 (radius: 5)
[20:04:33 -457024.430465] SLOW spr round 4 (radius: 5)
[20:07:27 -457024.429565] SLOW spr round 5 (radius: 10)
[20:10:33 -457024.429078] SLOW spr round 6 (radius: 15)
[20:15:46 -457024.222319] SLOW spr round 7 (radius: 5)
[20:19:27 -457024.220910] SLOW spr round 8 (radius: 10)
[20:23:10 -457024.220213] SLOW spr round 9 (radius: 15)
[20:28:05 -457024.219659] SLOW spr round 10 (radius: 20)
[20:35:44 -457024.219176] SLOW spr round 11 (radius: 25)
[20:47:13 -457024.218731] Model parameter optimization (eps = 0.100000)

[20:47:20] ML tree search #12, logLikelihood: -457024.175952

[20:47:20 -1475610.133038] Initial branch length optimization
[20:47:29 -1231743.250935] Model parameter optimization (eps = 10.000000)
[20:49:17 -1226301.306045] AUTODETECT spr round 1 (radius: 5)
[20:52:10 -865298.350787] AUTODETECT spr round 2 (radius: 10)
[20:55:25 -635856.759473] AUTODETECT spr round 3 (radius: 15)
[20:58:56 -535477.631151] AUTODETECT spr round 4 (radius: 20)
[21:03:13 -511963.395099] AUTODETECT spr round 5 (radius: 25)
[21:08:13 -508516.019189] SPR radius for FAST iterations: 25 (autodetect)
[21:08:13 -508516.019189] Model parameter optimization (eps = 3.000000)
[21:08:52 -507368.936433] FAST spr round 1 (radius: 25)
[21:13:51 -458822.210631] FAST spr round 2 (radius: 25)
[21:17:35 -457171.048540] FAST spr round 3 (radius: 25)
[21:20:27 -457127.702097] FAST spr round 4 (radius: 25)
[21:22:55 -457123.541364] FAST spr round 5 (radius: 25)
[21:25:14 -457123.540632] Model parameter optimization (eps = 1.000000)
[21:25:27 -457117.617907] SLOW spr round 1 (radius: 5)
[21:28:30 -457008.489781] SLOW spr round 2 (radius: 5)
[21:31:34 -456987.451152] SLOW spr round 3 (radius: 5)
[21:34:29 -456987.449771] SLOW spr round 4 (radius: 10)
[21:37:40 -456983.878976] SLOW spr round 5 (radius: 5)
[21:41:18 -456978.307399] SLOW spr round 6 (radius: 5)
[21:44:29 -456978.289788] SLOW spr round 7 (radius: 10)
[21:47:46 -456977.439788] SLOW spr round 8 (radius: 5)
[21:51:13 -456977.438202] SLOW spr round 9 (radius: 10)
[21:54:43 -456977.437504] SLOW spr round 10 (radius: 15)
[21:59:49 -456973.494311] SLOW spr round 11 (radius: 5)
[22:03:28 -456973.038217] SLOW spr round 12 (radius: 5)
[22:06:42 -456973.037961] SLOW spr round 13 (radius: 10)
[22:10:02 -456973.037728] SLOW spr round 14 (radius: 15)
[22:15:17 -456973.037499] SLOW spr round 15 (radius: 20)
[22:23:18 -456973.037271] SLOW spr round 16 (radius: 25)
[22:35:23 -456973.037043] Model parameter optimization (eps = 0.100000)

[22:35:40] ML tree search #13, logLikelihood: -456972.736126

[22:35:40 -1470834.751105] Initial branch length optimization
[22:35:50 -1232607.681701] Model parameter optimization (eps = 10.000000)
[22:37:11 -1227409.178369] AUTODETECT spr round 1 (radius: 5)
[22:39:59 -861540.499569] AUTODETECT spr round 2 (radius: 10)
[22:43:15 -630797.194840] AUTODETECT spr round 3 (radius: 15)
[22:46:46 -554948.832313] AUTODETECT spr round 4 (radius: 20)
[22:51:00 -531908.718558] AUTODETECT spr round 5 (radius: 25)
[22:56:16 -510450.147390] SPR radius for FAST iterations: 25 (autodetect)
[22:56:16 -510450.147390] Model parameter optimization (eps = 3.000000)
[22:56:56 -509367.480631] FAST spr round 1 (radius: 25)
[23:01:50 -459843.245110] FAST spr round 2 (radius: 25)
[23:05:44 -457343.744962] FAST spr round 3 (radius: 25)
[23:08:51 -457166.293316] FAST spr round 4 (radius: 25)
[23:11:25 -457162.559654] FAST spr round 5 (radius: 25)
[23:13:48 -457162.558301] Model parameter optimization (eps = 1.000000)
[23:14:10 -457156.471069] SLOW spr round 1 (radius: 5)
[23:17:24 -457038.416501] SLOW spr round 2 (radius: 5)
[23:20:28 -457024.822515] SLOW spr round 3 (radius: 5)
[23:23:32 -457024.094388] SLOW spr round 4 (radius: 5)
[23:26:32 -457024.088542] SLOW spr round 5 (radius: 10)
[23:29:42 -457021.869908] SLOW spr round 6 (radius: 5)
[23:33:12 -457021.868808] SLOW spr round 7 (radius: 10)
[23:36:48 -457021.868376] SLOW spr round 8 (radius: 15)
[23:42:00 -457021.867316] SLOW spr round 9 (radius: 20)
[23:50:01 -457021.867133] SLOW spr round 10 (radius: 25)
[24:02:16 -457021.713948] SLOW spr round 11 (radius: 5)
[24:06:07 -457021.713149] SLOW spr round 12 (radius: 10)
[24:10:12 -457021.712846] SLOW spr round 13 (radius: 15)
[24:15:20 -457021.712657] SLOW spr round 14 (radius: 20)
[24:23:23 -457021.711695] SLOW spr round 15 (radius: 25)
[24:35:27 -457021.711597] Model parameter optimization (eps = 0.100000)

[24:35:43] ML tree search #14, logLikelihood: -457021.560675

[24:35:43 -1480707.746678] Initial branch length optimization
[24:35:52 -1233839.178488] Model parameter optimization (eps = 10.000000)
[24:37:11 -1228278.601415] AUTODETECT spr round 1 (radius: 5)
[24:39:53 -872232.422192] AUTODETECT spr round 2 (radius: 10)
[24:42:58 -642822.459663] AUTODETECT spr round 3 (radius: 15)
[24:46:15 -536418.461445] AUTODETECT spr round 4 (radius: 20)
[24:49:59 -509021.937750] AUTODETECT spr round 5 (radius: 25)
[24:54:22 -502715.819737] SPR radius for FAST iterations: 25 (autodetect)
[24:54:22 -502715.819737] Model parameter optimization (eps = 3.000000)
[24:55:16 -501576.049724] FAST spr round 1 (radius: 25)
[24:59:43 -458415.868173] FAST spr round 2 (radius: 25)
[25:03:13 -457306.745806] FAST spr round 3 (radius: 25)
[25:06:09 -457162.483201] FAST spr round 4 (radius: 25)
[25:08:44 -457117.499867] FAST spr round 5 (radius: 25)
[25:10:58 -457115.210307] FAST spr round 6 (radius: 25)
[25:13:06 -457114.838077] FAST spr round 7 (radius: 25)
[25:14:55 -457114.837204] Model parameter optimization (eps = 1.000000)
[25:15:10 -457108.893325] SLOW spr round 1 (radius: 5)
[25:17:44 -457020.721875] SLOW spr round 2 (radius: 5)
[25:20:18 -457006.208387] SLOW spr round 3 (radius: 5)
[25:22:45 -457001.704406] SLOW spr round 4 (radius: 5)
[25:25:07 -457001.703984] SLOW spr round 5 (radius: 10)
[25:27:41 -457000.758725] SLOW spr round 6 (radius: 5)
[25:30:38 -456997.138650] SLOW spr round 7 (radius: 5)
[25:33:23 -456988.662280] SLOW spr round 8 (radius: 5)
[25:35:51 -456988.662056] SLOW spr round 9 (radius: 10)
[25:38:28 -456988.661894] SLOW spr round 10 (radius: 15)
[25:43:01 -456988.191645] SLOW spr round 11 (radius: 5)
[25:46:01 -456988.191186] SLOW spr round 12 (radius: 10)
[25:49:09 -456988.190852] SLOW spr round 13 (radius: 15)
[25:53:26 -456988.112179] SLOW spr round 14 (radius: 20)
[26:00:29 -456988.111375] SLOW spr round 15 (radius: 25)
[26:11:16 -456988.110662] Model parameter optimization (eps = 0.100000)

[26:11:28] ML tree search #15, logLikelihood: -456987.982854

[26:11:28 -1470923.433784] Initial branch length optimization
[26:11:37 -1233753.138730] Model parameter optimization (eps = 10.000000)
[26:12:58 -1228116.177680] AUTODETECT spr round 1 (radius: 5)
[26:15:16 -867997.734490] AUTODETECT spr round 2 (radius: 10)
[26:17:51 -651854.721361] AUTODETECT spr round 3 (radius: 15)
[26:20:35 -552922.567475] AUTODETECT spr round 4 (radius: 20)
[26:23:45 -524784.138963] AUTODETECT spr round 5 (radius: 25)
[26:27:15 -514275.798141] SPR radius for FAST iterations: 25 (autodetect)
[26:27:15 -514275.798141] Model parameter optimization (eps = 3.000000)
[26:27:47 -513131.202326] FAST spr round 1 (radius: 25)
[26:31:34 -459615.609161] FAST spr round 2 (radius: 25)
[26:34:27 -457233.877340] FAST spr round 3 (radius: 25)
[26:36:51 -457155.083845] FAST spr round 4 (radius: 25)
[26:38:59 -457134.616666] FAST spr round 5 (radius: 25)
[26:40:54 -457131.876508] FAST spr round 6 (radius: 25)
[26:42:45 -457131.874268] Model parameter optimization (eps = 1.000000)
[26:43:02 -457123.389669] SLOW spr round 1 (radius: 5)
[26:45:27 -457025.026463] SLOW spr round 2 (radius: 5)
[26:47:56 -457015.530088] SLOW spr round 3 (radius: 5)
[26:50:21 -457015.519376] SLOW spr round 4 (radius: 10)
[26:52:56 -457014.048024] SLOW spr round 5 (radius: 5)
[26:55:50 -457013.913753] SLOW spr round 6 (radius: 5)
[26:58:24 -457013.913283] SLOW spr round 7 (radius: 10)
[27:01:08 -457011.743226] SLOW spr round 8 (radius: 5)
[27:03:59 -457011.231019] SLOW spr round 9 (radius: 5)
[27:06:33 -457011.230545] SLOW spr round 10 (radius: 10)
[27:09:14 -457011.230376] SLOW spr round 11 (radius: 15)
[27:13:29 -457007.030264] SLOW spr round 12 (radius: 5)
[27:16:30 -457005.365911] SLOW spr round 13 (radius: 5)
[27:19:09 -457005.363782] SLOW spr round 14 (radius: 10)
[27:21:54 -457005.363350] SLOW spr round 15 (radius: 15)
[27:26:07 -457004.887611] SLOW spr round 16 (radius: 5)
[27:29:07 -457004.887174] SLOW spr round 17 (radius: 10)
[27:32:13 -457004.886852] SLOW spr round 18 (radius: 15)
[27:36:19 -457004.886599] SLOW spr round 19 (radius: 20)
[27:42:44 -457004.886393] SLOW spr round 20 (radius: 25)
[27:52:25 -457004.869739] Model parameter optimization (eps = 0.100000)

[27:52:30] ML tree search #16, logLikelihood: -457004.795015

[27:52:30 -1467656.692162] Initial branch length optimization
[27:52:38 -1223817.486465] Model parameter optimization (eps = 10.000000)
[27:53:30 -1218615.397754] AUTODETECT spr round 1 (radius: 5)
[27:55:46 -864446.953747] AUTODETECT spr round 2 (radius: 10)
[27:58:22 -641955.758437] AUTODETECT spr round 3 (radius: 15)
[28:01:11 -545149.389346] AUTODETECT spr round 4 (radius: 20)
[28:05:06 -505422.658425] AUTODETECT spr round 5 (radius: 25)
[28:09:48 -502149.974631] SPR radius for FAST iterations: 25 (autodetect)
[28:09:48 -502149.974631] Model parameter optimization (eps = 3.000000)
[28:10:21 -501092.274210] FAST spr round 1 (radius: 25)
[28:14:10 -459156.269003] FAST spr round 2 (radius: 25)
[28:16:55 -457426.877371] FAST spr round 3 (radius: 25)
[28:19:21 -457232.627353] FAST spr round 4 (radius: 25)
[28:21:28 -457203.245395] FAST spr round 5 (radius: 25)
[28:23:29 -457164.442506] FAST spr round 6 (radius: 25)
[28:25:24 -457146.534942] FAST spr round 7 (radius: 25)
[28:27:14 -457146.532938] Model parameter optimization (eps = 1.000000)
[28:27:26 -457142.620221] SLOW spr round 1 (radius: 5)
[28:29:54 -457040.336970] SLOW spr round 2 (radius: 5)
[28:32:23 -457027.764004] SLOW spr round 3 (radius: 5)
[28:34:52 -457018.705148] SLOW spr round 4 (radius: 5)
[28:37:20 -457016.640924] SLOW spr round 5 (radius: 5)
[28:39:47 -457016.606696] SLOW spr round 6 (radius: 10)
[28:42:22 -457015.289232] SLOW spr round 7 (radius: 5)
[28:45:17 -457014.929993] SLOW spr round 8 (radius: 5)
[28:47:54 -457014.927983] SLOW spr round 9 (radius: 10)
[28:50:35 -457012.730364] SLOW spr round 10 (radius: 5)
[28:53:29 -457011.538875] SLOW spr round 11 (radius: 5)
[28:56:04 -457011.538689] SLOW spr round 12 (radius: 10)
[28:58:43 -457011.537137] SLOW spr round 13 (radius: 15)
[29:02:50 -457010.541428] SLOW spr round 14 (radius: 5)
[29:05:50 -457010.540569] SLOW spr round 15 (radius: 10)
[29:08:53 -457010.540354] SLOW spr round 16 (radius: 15)
[29:12:50 -457010.540262] SLOW spr round 17 (radius: 20)
[29:18:55 -457010.540215] SLOW spr round 18 (radius: 25)
[29:27:48 -457010.339358] SLOW spr round 19 (radius: 5)
[29:30:56 -457010.328488] SLOW spr round 20 (radius: 10)
[29:34:13 -457010.325378] SLOW spr round 21 (radius: 15)
[29:38:10 -457010.323792] SLOW spr round 22 (radius: 20)
[29:44:16 -457010.322979] SLOW spr round 23 (radius: 25)
[29:53:10 -457010.322558] Model parameter optimization (eps = 0.100000)

[29:53:22] ML tree search #17, logLikelihood: -457010.033278

[29:53:22 -1466023.543123] Initial branch length optimization
[29:53:30 -1228872.429544] Model parameter optimization (eps = 10.000000)
[29:55:02 -1223392.569121] AUTODETECT spr round 1 (radius: 5)
[29:57:21 -873662.477414] AUTODETECT spr round 2 (radius: 10)
[29:59:55 -644375.885772] AUTODETECT spr round 3 (radius: 15)
[30:02:45 -551571.206839] AUTODETECT spr round 4 (radius: 20)
[30:05:53 -522426.285429] AUTODETECT spr round 5 (radius: 25)
[30:09:13 -517825.377388] SPR radius for FAST iterations: 25 (autodetect)
[30:09:13 -517825.377388] Model parameter optimization (eps = 3.000000)
[30:09:44 -516719.053132] FAST spr round 1 (radius: 25)
[30:13:35 -462454.570050] FAST spr round 2 (radius: 25)
[30:16:34 -457507.401516] FAST spr round 3 (radius: 25)
[30:18:58 -457180.964313] FAST spr round 4 (radius: 25)
[30:21:05 -457167.226733] FAST spr round 5 (radius: 25)
[30:22:58 -457164.284619] FAST spr round 6 (radius: 25)
[30:24:47 -457164.282809] Model parameter optimization (eps = 1.000000)
[30:25:07 -457156.015981] SLOW spr round 1 (radius: 5)
[30:27:37 -457012.827972] SLOW spr round 2 (radius: 5)
[30:30:03 -457003.776416] SLOW spr round 3 (radius: 5)
[30:32:24 -457003.775182] SLOW spr round 4 (radius: 10)
[30:34:58 -457001.503808] SLOW spr round 5 (radius: 5)
[30:37:51 -457001.500113] SLOW spr round 6 (radius: 10)
[30:40:45 -457001.499330] SLOW spr round 7 (radius: 15)
[30:44:51 -457000.609093] SLOW spr round 8 (radius: 5)
[30:47:57 -456996.399494] SLOW spr round 9 (radius: 5)
[30:50:37 -456995.524230] SLOW spr round 10 (radius: 5)
[30:53:07 -456995.522678] SLOW spr round 11 (radius: 10)
[30:55:44 -456995.521900] SLOW spr round 12 (radius: 15)
[31:00:04 -456995.474843] SLOW spr round 13 (radius: 20)
[31:06:24 -456995.259981] SLOW spr round 14 (radius: 5)
[31:09:30 -456995.257897] SLOW spr round 15 (radius: 10)
[31:12:45 -456995.256964] SLOW spr round 16 (radius: 15)
[31:16:52 -456995.256240] SLOW spr round 17 (radius: 20)
[31:23:16 -456995.255618] SLOW spr round 18 (radius: 25)
[31:33:02 -456995.255047] Model parameter optimization (eps = 0.100000)

[31:33:18] ML tree search #18, logLikelihood: -456994.358123

[31:33:18 -1473497.461133] Initial branch length optimization
[31:33:25 -1226844.720692] Model parameter optimization (eps = 10.000000)
[31:34:33 -1221572.308075] AUTODETECT spr round 1 (radius: 5)
[31:36:51 -871681.846408] AUTODETECT spr round 2 (radius: 10)
[31:39:30 -615776.890501] AUTODETECT spr round 3 (radius: 15)
[31:42:16 -554156.636237] AUTODETECT spr round 4 (radius: 20)
[31:45:48 -516784.373377] AUTODETECT spr round 5 (radius: 25)
[31:50:00 -510675.902012] SPR radius for FAST iterations: 25 (autodetect)
[31:50:00 -510675.902012] Model parameter optimization (eps = 3.000000)
[31:50:32 -509549.704736] FAST spr round 1 (radius: 25)
[31:54:26 -459333.948904] FAST spr round 2 (radius: 25)
[31:57:31 -457223.162989] FAST spr round 3 (radius: 25)
[32:00:05 -457102.415709] FAST spr round 4 (radius: 25)
[32:02:11 -457087.803096] FAST spr round 5 (radius: 25)
[32:04:08 -457079.920703] FAST spr round 6 (radius: 25)
[32:05:57 -457079.919192] Model parameter optimization (eps = 1.000000)
[32:06:13 -457073.658267] SLOW spr round 1 (radius: 5)
[32:08:46 -456983.682998] SLOW spr round 2 (radius: 5)
[32:11:13 -456978.207248] SLOW spr round 3 (radius: 5)
[32:13:37 -456978.204640] SLOW spr round 4 (radius: 10)
[32:16:11 -456977.005909] SLOW spr round 5 (radius: 5)
[32:19:03 -456976.999281] SLOW spr round 6 (radius: 10)
[32:22:01 -456976.998130] SLOW spr round 7 (radius: 15)
[32:26:15 -456975.650130] SLOW spr round 8 (radius: 5)
[32:29:16 -456975.639241] SLOW spr round 9 (radius: 10)
[32:32:24 -456975.636618] SLOW spr round 10 (radius: 15)
[32:36:36 -456975.636076] SLOW spr round 11 (radius: 20)
[32:43:33 -456975.635973] SLOW spr round 12 (radius: 25)
[32:54:03 -456975.635949] Model parameter optimization (eps = 0.100000)

[32:54:12] ML tree search #19, logLikelihood: -456975.522658

[32:54:12 -1475724.631112] Initial branch length optimization
[32:54:20 -1224933.294745] Model parameter optimization (eps = 10.000000)
[32:55:33 -1219834.811890] AUTODETECT spr round 1 (radius: 5)
[32:57:51 -856166.908835] AUTODETECT spr round 2 (radius: 10)
[33:00:27 -618120.380604] AUTODETECT spr round 3 (radius: 15)
[33:03:17 -532918.231935] AUTODETECT spr round 4 (radius: 20)
[33:06:21 -511790.343278] AUTODETECT spr round 5 (radius: 25)
[33:10:29 -504936.866322] SPR radius for FAST iterations: 25 (autodetect)
[33:10:29 -504936.866322] Model parameter optimization (eps = 3.000000)
[33:11:12 -503772.450959] FAST spr round 1 (radius: 25)
[33:15:22 -458815.783943] FAST spr round 2 (radius: 25)
[33:18:28 -457173.862330] FAST spr round 3 (radius: 25)
[33:21:07 -457113.661318] FAST spr round 4 (radius: 25)
[33:23:11 -457105.621725] FAST spr round 5 (radius: 25)
[33:25:03 -457105.620297] Model parameter optimization (eps = 1.000000)
[33:25:22 -457099.225822] SLOW spr round 1 (radius: 5)
[33:27:51 -457005.751979] SLOW spr round 2 (radius: 5)
[33:30:16 -457003.197038] SLOW spr round 3 (radius: 5)
[33:32:39 -457001.492870] SLOW spr round 4 (radius: 5)
[33:35:01 -457001.492249] SLOW spr round 5 (radius: 10)
[33:37:35 -457000.031295] SLOW spr round 6 (radius: 5)
[33:40:26 -457000.024590] SLOW spr round 7 (radius: 10)
[33:43:21 -457000.023292] SLOW spr round 8 (radius: 15)
[33:47:29 -456999.794388] SLOW spr round 9 (radius: 5)
[33:50:30 -456999.743672] SLOW spr round 10 (radius: 10)
[33:53:37 -456999.741876] SLOW spr round 11 (radius: 15)
[33:57:45 -456999.741140] SLOW spr round 12 (radius: 20)
[34:04:12 -456999.740789] SLOW spr round 13 (radius: 25)
[34:13:45 -456999.598627] SLOW spr round 14 (radius: 5)
[34:17:10 -456999.579812] SLOW spr round 15 (radius: 10)
[34:22:20 -456999.579639] SLOW spr round 16 (radius: 15)
[34:26:23 -456999.579481] SLOW spr round 17 (radius: 20)
[34:32:47 -456999.579328] SLOW spr round 18 (radius: 25)
[34:42:18 -456999.525792] Model parameter optimization (eps = 0.100000)

[34:42:24] ML tree search #20, logLikelihood: -456999.461431


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.131956,0.674675) (0.085665,0.788789) (0.505811,0.830864) (0.276568,1.529972) 
   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: -456972.736126

AIC score: 917955.472252 / AICc score: 8962015.472252 / BIC score: 928338.455947
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=1311).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 44 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9C0A0/3_mltree/Q9C0A0.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9C0A0/3_mltree/Q9C0A0.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9C0A0/3_mltree/Q9C0A0.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9C0A0/3_mltree/Q9C0A0.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9C0A0/3_mltree/Q9C0A0.raxml.log

Analysis started: 03-Jul-2021 15:19:06 / finished: 05-Jul-2021 02:01:30

Elapsed time: 124944.579 seconds

Consumed energy: 10706.895 Wh (= 54 km in an electric car, or 268 km with an e-scooter!)