RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab.
Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml

System: Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM

RAxML-NG was called at 13-Jul-2021 02:14:46 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6ZQY2/2_msa/Q6ZQY2_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6ZQY2/3_mltree/Q6ZQY2 --seed 2 --threads 3 --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 (3 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6ZQY2/2_msa/Q6ZQY2_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 143 sites

WARNING: Sequences tr_M3XX36_M3XX36_MUSPF_9669 and tr_A0A2Y9ISS8_A0A2Y9ISS8_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3YUD1_M3YUD1_MUSPF_9669 and tr_A0A2Y9KH93_A0A2Y9KH93_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_D8RF61_D8RF61_SELML_88036 and tr_D8SDB4_D8SDB4_SELML_88036 are exactly identical!
WARNING: Sequences tr_G3RKC2_G3RKC2_GORGO_9595 and tr_H2QAG9_H2QAG9_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3RKC2_G3RKC2_GORGO_9595 and tr_A0A2R9B4T4_A0A2R9B4T4_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3SBY7_G3SBY7_GORGO_9595 and tr_H2QLA6_H2QLA6_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3SBY7_G3SBY7_GORGO_9595 and sp_Q6ZQY2_LR74B_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3SBY7_G3SBY7_GORGO_9595 and tr_A0A2R9C6J8_A0A2R9C6J8_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2Q8P1_H2Q8P1_PANTR_9598 and tr_A0A2R9BMG1_A0A2R9BMG1_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F6W880_F6W880_MACMU_9544 and tr_G7PB22_G7PB22_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F6W880_F6W880_MACMU_9544 and tr_A0A096NS71_A0A096NS71_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F6W880_F6W880_MACMU_9544 and tr_A0A0D9RHJ8_A0A0D9RHJ8_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F6W880_F6W880_MACMU_9544 and tr_A0A2K6BUC3_A0A2K6BUC3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F6W880_F6W880_MACMU_9544 and tr_A0A2K6A1Z2_A0A2K6A1Z2_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A0D2UMG9_A0A0D2UMG9_CAPO3_595528 and tr_A0A0D2UMJ9_A0A0D2UMJ9_CAPO3_595528 are exactly identical!
WARNING: Sequences tr_A0A0D2X580_A0A0D2X580_CAPO3_595528 and tr_A0A0D2X584_A0A0D2X584_CAPO3_595528 are exactly identical!
WARNING: Sequences tr_B3RKL5_B3RKL5_TRIAD_10228 and tr_A0A369RZZ0_A0A369RZZ0_9METZ_287889 are exactly identical!
WARNING: Sequences tr_B3RKS5_B3RKS5_TRIAD_10228 and tr_A0A369SDT3_A0A369SDT3_9METZ_287889 are exactly identical!
WARNING: Sequences tr_G7Q0D0_G7Q0D0_MACFA_9541 and tr_A0A0D9RC41_A0A0D9RC41_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G7Q0D0_G7Q0D0_MACFA_9541 and tr_A0A2K5P006_A0A2K5P006_CERAT_9531 are exactly identical!
WARNING: Sequences tr_R1DD06_R1DD06_EMIHU_2903 and tr_R1EKP1_R1EKP1_EMIHU_2903 are exactly identical!
WARNING: Sequences tr_R1DD06_R1DD06_EMIHU_2903 and tr_R1F231_R1F231_EMIHU_2903 are exactly identical!
WARNING: Sequences tr_W2PML8_W2PML8_PHYPN_761204 and tr_A0A0W8CLI8_A0A0W8CLI8_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2PML8_W2PML8_PHYPN_761204 and tr_W2KHL3_W2KHL3_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_W2QLS3_W2QLS3_PHYPN_761204 and tr_A0A0W8DPD5_A0A0W8DPD5_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2QLS3_W2QLS3_PHYPN_761204 and tr_W2LUG1_W2LUG1_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_W2RGE0_W2RGE0_PHYPN_761204 and tr_A0A0W8DN40_A0A0W8DN40_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2RGE0_W2RGE0_PHYPN_761204 and tr_W2M1S6_W2M1S6_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A1S3J761_A0A1S3J761_LINUN_7574 and tr_A0A1S3K5K4_A0A1S3K5K4_LINUN_7574 are exactly identical!
WARNING: Sequences tr_A0A1S3J7G8_A0A1S3J7G8_LINUN_7574 and tr_A0A1S3K5K9_A0A1S3K5K9_LINUN_7574 are exactly identical!
WARNING: Sequences tr_A0A1Y2GBL6_A0A1Y2GBL6_9FUNG_64571 and tr_A0A1Y2GDS3_A0A1Y2GDS3_9FUNG_64571 are exactly identical!
WARNING: Sequences tr_A0A1Y2GMS2_A0A1Y2GMS2_9FUNG_64571 and tr_A0A1Y2GP55_A0A1Y2GP55_9FUNG_64571 are exactly identical!
WARNING: Sequences tr_A0A2D0PJM6_A0A2D0PJM6_ICTPU_7998 and tr_A0A2D0PL88_A0A2D0PL88_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PJM6_A0A2D0PJM6_ICTPU_7998 and tr_A0A2D0PLC4_A0A2D0PLC4_ICTPU_7998 are exactly identical!
WARNING: Duplicate sequences found: 34

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6ZQY2/3_mltree/Q6ZQY2.raxml.reduced.phy

Alignment comprises 1 partitions and 143 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 143 / 143
Gaps: 6.42 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6ZQY2/3_mltree/Q6ZQY2.raxml.rba

Parallelization scheme autoconfig: 3 worker(s) x 1 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 / 143 / 11440
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -270207.952997] Initial branch length optimization
[00:00:02 -233215.452998] Model parameter optimization (eps = 10.000000)
[00:00:55 -231384.279186] AUTODETECT spr round 1 (radius: 5)
[00:03:33 -201349.062999] AUTODETECT spr round 2 (radius: 10)
[00:06:38 -171031.545698] AUTODETECT spr round 3 (radius: 15)
[00:10:15 -152059.006427] AUTODETECT spr round 4 (radius: 20)
[00:14:15 -146055.957345] AUTODETECT spr round 5 (radius: 25)
[00:18:35 -144305.000544] SPR radius for FAST iterations: 25 (autodetect)
[00:18:35 -144305.000544] Model parameter optimization (eps = 3.000000)
[00:18:43 -144303.706120] FAST spr round 1 (radius: 25)
[00:24:56 -135043.196261] FAST spr round 2 (radius: 25)
[00:29:32 -134481.544777] FAST spr round 3 (radius: 25)
[00:33:15 -134420.341134] FAST spr round 4 (radius: 25)
[00:36:18 -134412.163791] FAST spr round 5 (radius: 25)
[00:39:05 -134409.410159] FAST spr round 6 (radius: 25)
[00:41:41 -134407.505463] FAST spr round 7 (radius: 25)
[00:44:11 -134407.277071] FAST spr round 8 (radius: 25)
[00:46:37 -134407.276595] Model parameter optimization (eps = 1.000000)
[00:46:43 -134406.974559] SLOW spr round 1 (radius: 5)
[00:50:02 -134375.806379] SLOW spr round 2 (radius: 5)
[00:53:12 -134374.106645] SLOW spr round 3 (radius: 5)
[00:56:16 -134374.092322] SLOW spr round 4 (radius: 10)
[00:59:41 -134354.103520] SLOW spr round 5 (radius: 5)
[01:03:20 -134326.418674] SLOW spr round 6 (radius: 5)
[01:06:40 -134320.080804] SLOW spr round 7 (radius: 5)
[01:09:55 -134315.886062] SLOW spr round 8 (radius: 5)
[01:13:02 -134314.355289] SLOW spr round 9 (radius: 5)
[01:16:01 -134314.326035] SLOW spr round 10 (radius: 10)
[01:19:22 -134299.285294] SLOW spr round 11 (radius: 5)
[01:23:01 -134296.111232] SLOW spr round 12 (radius: 5)
[01:26:15 -134296.107680] SLOW spr round 13 (radius: 10)
[01:29:44 -134293.980421] SLOW spr round 14 (radius: 5)
[01:33:25 -134290.608357] SLOW spr round 15 (radius: 5)
[01:36:39 -134290.606999] SLOW spr round 16 (radius: 10)
[01:40:04 -134290.277259] SLOW spr round 17 (radius: 5)
[01:43:37 -134290.277047] SLOW spr round 18 (radius: 10)
[01:47:20 -134290.012311] SLOW spr round 19 (radius: 5)
[01:50:51 -134289.592697] SLOW spr round 20 (radius: 5)
[01:54:03 -134289.592684] SLOW spr round 21 (radius: 10)
[01:57:27 -134289.592684] SLOW spr round 22 (radius: 15)
[02:03:25 -134288.129116] SLOW spr round 23 (radius: 5)
[02:07:12 -134276.099478] SLOW spr round 24 (radius: 5)
[02:10:29 -134276.099148] SLOW spr round 25 (radius: 10)
[02:13:55 -134273.028897] SLOW spr round 26 (radius: 5)
[02:17:24 -134273.028874] SLOW spr round 27 (radius: 10)
[02:21:03 -134273.028874] SLOW spr round 28 (radius: 15)
[02:26:44 -134272.758406] SLOW spr round 29 (radius: 5)
[02:30:20 -134272.502004] SLOW spr round 30 (radius: 5)
[02:33:34 -134272.501380] SLOW spr round 31 (radius: 10)
[02:37:00 -134271.896739] SLOW spr round 32 (radius: 5)
[02:40:35 -134265.887043] SLOW spr round 33 (radius: 5)
[02:43:52 -134265.730463] SLOW spr round 34 (radius: 5)
[02:47:01 -134264.711156] SLOW spr round 35 (radius: 5)
[02:50:04 -134264.710522] SLOW spr round 36 (radius: 10)
[02:53:24 -134264.268342] SLOW spr round 37 (radius: 5)
[02:56:59 -134264.004828] SLOW spr round 38 (radius: 5)
[03:00:12 -134264.004174] SLOW spr round 39 (radius: 10)
[03:03:40 -134260.496989] SLOW spr round 40 (radius: 5)
[03:07:21 -134258.095387] SLOW spr round 41 (radius: 5)
[03:10:44 -134256.323990] SLOW spr round 42 (radius: 5)
[03:13:56 -134254.399610] SLOW spr round 43 (radius: 5)
[03:17:00 -134254.398418] SLOW spr round 44 (radius: 10)
[03:20:21 -134254.193219] SLOW spr round 45 (radius: 5)
[03:23:52 -134254.020081] SLOW spr round 46 (radius: 5)
[03:27:06 -134254.019753] SLOW spr round 47 (radius: 10)
[03:30:35 -134253.000860] SLOW spr round 48 (radius: 5)
[03:34:14 -134246.242846] SLOW spr round 49 (radius: 5)
[03:37:32 -134244.482068] SLOW spr round 50 (radius: 5)
[03:40:38 -134244.136870] SLOW spr round 51 (radius: 5)
[03:43:37 -134244.136240] SLOW spr round 52 (radius: 10)
[03:46:52 -134243.846331] SLOW spr round 53 (radius: 5)
[03:50:21 -134243.753422] SLOW spr round 54 (radius: 10)
[03:53:58 -134243.627242] SLOW spr round 55 (radius: 5)
[03:57:23 -134243.601020] SLOW spr round 56 (radius: 10)
[04:00:57 -134243.600763] SLOW spr round 57 (radius: 15)
[04:06:28 -134239.678080] SLOW spr round 58 (radius: 5)
[04:10:05 -134238.737171] SLOW spr round 59 (radius: 5)
[04:13:20 -134238.736228] SLOW spr round 60 (radius: 10)
[04:16:44 -134238.693994] SLOW spr round 61 (radius: 15)
[04:22:14 -134238.263267] SLOW spr round 62 (radius: 5)
[04:25:49 -134237.993521] SLOW spr round 63 (radius: 5)
[04:27:15] [worker #2] ML tree search #3, logLikelihood: -134276.410212
[04:29:02 -134237.993495] SLOW spr round 64 (radius: 10)
[04:32:24 -134237.583172] SLOW spr round 65 (radius: 5)
[04:35:50 -134237.581485] SLOW spr round 66 (radius: 10)
[04:39:24 -134237.581310] SLOW spr round 67 (radius: 15)
[04:44:48 -134237.581252] SLOW spr round 68 (radius: 20)
[04:52:35 -134237.308507] SLOW spr round 69 (radius: 5)
[04:56:11 -134237.307345] SLOW spr round 70 (radius: 10)
[05:00:01 -134237.307304] SLOW spr round 71 (radius: 15)
[05:05:25 -134237.307303] SLOW spr round 72 (radius: 20)
[05:13:24 -134236.400250] SLOW spr round 73 (radius: 5)
[05:17:10 -134235.129335] SLOW spr round 74 (radius: 5)
[05:20:30 -134235.128695] SLOW spr round 75 (radius: 10)
[05:23:57 -134235.049387] SLOW spr round 76 (radius: 15)
[05:29:30 -134235.049270] SLOW spr round 77 (radius: 20)
[05:37:20 -134235.049260] SLOW spr round 78 (radius: 25)
[05:46:50 -134222.293527] SLOW spr round 79 (radius: 5)
[05:50:39 -134218.252583] SLOW spr round 80 (radius: 5)
[05:54:04 -134217.430183] SLOW spr round 81 (radius: 5)
[05:57:11 -134217.430048] SLOW spr round 82 (radius: 10)
[06:00:28 -134217.392924] SLOW spr round 83 (radius: 15)
[06:06:10 -134217.391643] SLOW spr round 84 (radius: 20)
[06:14:12 -134217.391590] SLOW spr round 85 (radius: 25)
[06:23:55 -134217.391584] Model parameter optimization (eps = 0.100000)

[06:24:00] [worker #0] ML tree search #1, logLikelihood: -134217.358265

[06:24:00 -270570.154008] Initial branch length optimization
[06:24:03 -233944.780660] Model parameter optimization (eps = 10.000000)
[06:24:43 -232235.074526] AUTODETECT spr round 1 (radius: 5)
[06:27:22 -201907.917006] AUTODETECT spr round 2 (radius: 10)
[06:30:28 -170160.934155] AUTODETECT spr round 3 (radius: 15)
[06:34:03 -152010.096176] AUTODETECT spr round 4 (radius: 20)
[06:38:00 -147364.591677] AUTODETECT spr round 5 (radius: 25)
[06:41:59 -144056.537305] SPR radius for FAST iterations: 25 (autodetect)
[06:41:59 -144056.537305] Model parameter optimization (eps = 3.000000)
[06:42:06 -144055.465499] FAST spr round 1 (radius: 25)
[06:48:14 -134962.038291] FAST spr round 2 (radius: 25)
[06:53:03 -134446.326666] FAST spr round 3 (radius: 25)
[06:53:16] [worker #1] ML tree search #2, logLikelihood: -133997.868703
[06:56:51 -134385.789647] FAST spr round 4 (radius: 25)
[07:00:10 -134359.740844] FAST spr round 5 (radius: 25)
[07:02:58 -134353.000233] FAST spr round 6 (radius: 25)
[07:05:38 -134329.624872] FAST spr round 7 (radius: 25)
[07:08:07 -134327.116713] FAST spr round 8 (radius: 25)
[07:10:33 -134327.116626] Model parameter optimization (eps = 1.000000)
[07:10:55 -134191.067700] SLOW spr round 1 (radius: 5)
[07:14:13 -134120.429123] SLOW spr round 2 (radius: 5)
[07:17:20 -134112.847058] SLOW spr round 3 (radius: 5)
[07:20:26 -134110.710701] SLOW spr round 4 (radius: 5)
[07:23:23 -134110.710378] SLOW spr round 5 (radius: 10)
[07:26:43 -134098.664174] SLOW spr round 6 (radius: 5)
[07:30:19 -134096.260784] SLOW spr round 7 (radius: 5)
[07:33:39 -134093.898540] SLOW spr round 8 (radius: 5)
[07:36:44 -134093.898446] SLOW spr round 9 (radius: 10)
[07:40:10 -134085.765757] SLOW spr round 10 (radius: 5)
[07:43:47 -134083.557613] SLOW spr round 11 (radius: 5)
[07:47:01 -134082.190054] SLOW spr round 12 (radius: 5)
[07:50:05 -134082.189887] SLOW spr round 13 (radius: 10)
[07:53:26 -134080.790826] SLOW spr round 14 (radius: 5)
[07:57:00 -134078.586354] SLOW spr round 15 (radius: 5)
[08:00:12 -134078.561918] SLOW spr round 16 (radius: 10)
[08:03:39 -134077.225816] SLOW spr round 17 (radius: 5)
[08:07:10 -134075.855966] SLOW spr round 18 (radius: 5)
[08:10:18 -134075.854807] SLOW spr round 19 (radius: 10)
[08:13:43 -134074.890729] SLOW spr round 20 (radius: 5)
[08:17:08 -134074.860796] SLOW spr round 21 (radius: 10)
[08:20:52 -134068.617207] SLOW spr round 22 (radius: 5)
[08:24:23 -134061.839390] SLOW spr round 23 (radius: 5)
[08:27:33 -134061.035897] SLOW spr round 24 (radius: 5)
[08:30:34 -134060.754739] SLOW spr round 25 (radius: 5)
[08:33:32 -134060.754575] SLOW spr round 26 (radius: 10)
[08:36:50 -134058.317813] SLOW spr round 27 (radius: 5)
[08:40:22 -134057.002920] SLOW spr round 28 (radius: 5)
[08:43:37 -134056.059620] SLOW spr round 29 (radius: 5)
[08:46:43 -134055.437639] SLOW spr round 30 (radius: 5)
[08:49:41 -134055.437244] SLOW spr round 31 (radius: 10)
[08:52:55 -134054.987663] SLOW spr round 32 (radius: 5)
[08:56:21 -134054.639917] SLOW spr round 33 (radius: 5)
[08:59:39 -134048.164296] SLOW spr round 34 (radius: 5)
[09:02:42 -134047.268202] SLOW spr round 35 (radius: 5)
[09:05:41 -134046.141183] SLOW spr round 36 (radius: 5)
[09:08:38 -134046.141083] SLOW spr round 37 (radius: 10)
[09:11:52 -134045.621470] SLOW spr round 38 (radius: 5)
[09:15:22 -134044.307769] SLOW spr round 39 (radius: 5)
[09:18:34 -134042.738130] SLOW spr round 40 (radius: 5)
[09:21:36 -134042.738051] SLOW spr round 41 (radius: 10)
[09:23:39] [worker #2] ML tree search #6, logLikelihood: -134075.161254
[09:24:56 -134036.696319] SLOW spr round 42 (radius: 5)
[09:28:25 -134034.865616] SLOW spr round 43 (radius: 5)
[09:31:33 -134034.862885] SLOW spr round 44 (radius: 10)
[09:34:54 -134034.862408] SLOW spr round 45 (radius: 15)
[09:40:58 -134029.664276] SLOW spr round 46 (radius: 5)
[09:44:36 -134026.487576] SLOW spr round 47 (radius: 5)
[09:47:50 -134026.059357] SLOW spr round 48 (radius: 5)
[09:50:52 -134026.059221] SLOW spr round 49 (radius: 10)
[09:54:11 -134025.247020] SLOW spr round 50 (radius: 5)
[09:57:35 -134025.246102] SLOW spr round 51 (radius: 10)
[10:01:14 -134024.198859] SLOW spr round 52 (radius: 5)
[10:04:43 -134020.448769] SLOW spr round 53 (radius: 5)
[10:07:58 -134019.850796] SLOW spr round 54 (radius: 5)
[10:11:01 -134019.843987] SLOW spr round 55 (radius: 10)
[10:14:18 -134019.516519] SLOW spr round 56 (radius: 5)
[10:17:43 -134019.041732] SLOW spr round 57 (radius: 5)
[10:20:51 -134019.041697] SLOW spr round 58 (radius: 10)
[10:24:12 -134018.584495] SLOW spr round 59 (radius: 5)
[10:28:55 -134018.424405] SLOW spr round 60 (radius: 5)
[10:33:19 -134018.423953] SLOW spr round 61 (radius: 10)
[10:37:55 -134018.295772] SLOW spr round 62 (radius: 5)
[10:42:24 -134018.217529] SLOW spr round 63 (radius: 10)
[10:47:19 -134016.242618] SLOW spr round 64 (radius: 5)
[10:52:29 -134016.241791] SLOW spr round 65 (radius: 10)
[10:57:40 -134016.189969] SLOW spr round 66 (radius: 15)
[11:06:12 -134015.703006] SLOW spr round 67 (radius: 5)
[11:10:42 -134006.557198] SLOW spr round 68 (radius: 5)
[11:17:07 -134006.237178] SLOW spr round 69 (radius: 5)
[11:23:09 -134006.201988] SLOW spr round 70 (radius: 10)
[11:28:42 -134006.200448] SLOW spr round 71 (radius: 15)
[11:39:25 -134005.963262] SLOW spr round 72 (radius: 5)
[11:46:27 -134005.962008] SLOW spr round 73 (radius: 10)
[11:50:30 -134005.961556] SLOW spr round 74 (radius: 15)
[11:58:49 -134005.067033] SLOW spr round 75 (radius: 5)
[12:02:49 -134004.932798] SLOW spr round 76 (radius: 5)
[12:06:45 -134004.902995] SLOW spr round 77 (radius: 10)
[12:10:17 -134004.482041] SLOW spr round 78 (radius: 5)
[12:13:43 -134003.052768] SLOW spr round 79 (radius: 5)
[12:19:40 -134003.052293] SLOW spr round 80 (radius: 10)
[12:25:40 -134003.052254] SLOW spr round 81 (radius: 15)
[12:35:47 -134003.052251] SLOW spr round 82 (radius: 20)
[12:51:20 -134000.611231] SLOW spr round 83 (radius: 5)
[12:55:23 -133998.227742] SLOW spr round 84 (radius: 5)
[13:01:37 -133996.673689] SLOW spr round 85 (radius: 5)
[13:06:25 -133996.673672] SLOW spr round 86 (radius: 10)
[13:13:04 -133995.941453] SLOW spr round 87 (radius: 5)
[13:19:50 -133995.684042] SLOW spr round 88 (radius: 5)
[13:25:03 -133995.683966] SLOW spr round 89 (radius: 10)
[13:31:43 -133995.683964] SLOW spr round 90 (radius: 15)
[13:38:18 -133994.217738] SLOW spr round 91 (radius: 5)
[13:42:07 -133990.279838] SLOW spr round 92 (radius: 5)
[13:48:30 -133990.278902] SLOW spr round 93 (radius: 10)
[13:52:06 -133990.278878] SLOW spr round 94 (radius: 15)
[13:58:53 -133989.012016] SLOW spr round 95 (radius: 5)
[14:05:35 -133989.010357] SLOW spr round 96 (radius: 10)
[14:13:06 -133989.010317] SLOW spr round 97 (radius: 15)
[14:19:35 -133989.010316] SLOW spr round 98 (radius: 20)
[14:29:54 -133988.459318] SLOW spr round 99 (radius: 5)
[14:33:34 -133988.441008] SLOW spr round 100 (radius: 10)
[14:37:31 -133985.392881] SLOW spr round 101 (radius: 5)
[14:40:56 -133985.389069] SLOW spr round 102 (radius: 10)
[14:44:35 -133985.387806] SLOW spr round 103 (radius: 15)
[14:50:24 -133985.387325] SLOW spr round 104 (radius: 20)
[14:58:42 -133985.387141] SLOW spr round 105 (radius: 25)
[15:08:26 -133977.314443] SLOW spr round 106 (radius: 5)
[15:12:05 -133977.313860] SLOW spr round 107 (radius: 10)
[15:16:08 -133977.313831] SLOW spr round 108 (radius: 15)
[15:21:52 -133977.234958] SLOW spr round 109 (radius: 20)
[15:30:10 -133977.233830] SLOW spr round 110 (radius: 25)
[15:39:52 -133977.233793] Model parameter optimization (eps = 0.100000)

[15:40:12] [worker #0] ML tree search #4, logLikelihood: -133971.693707

[15:40:12 -270799.285780] Initial branch length optimization
[15:40:14 -233140.352507] Model parameter optimization (eps = 10.000000)
[15:41:06 -231347.880704] AUTODETECT spr round 1 (radius: 5)
[15:43:45 -202017.047260] AUTODETECT spr round 2 (radius: 10)
[15:46:52 -171657.708794] AUTODETECT spr round 3 (radius: 15)
[15:50:14 -154000.638359] AUTODETECT spr round 4 (radius: 20)
[15:54:02 -148547.006795] AUTODETECT spr round 5 (radius: 25)
[15:58:27 -146154.362617] SPR radius for FAST iterations: 25 (autodetect)
[15:58:27 -146154.362617] Model parameter optimization (eps = 3.000000)
[15:58:34 -146153.511064] FAST spr round 1 (radius: 25)
[16:04:39 -135710.997722] FAST spr round 2 (radius: 25)
[16:09:16 -134642.699962] FAST spr round 3 (radius: 25)
[16:11:36] [worker #2] ML tree search #9, logLikelihood: -134237.183206
[16:13:05 -134484.230568] FAST spr round 4 (radius: 25)
[16:16:19 -134437.766269] FAST spr round 5 (radius: 25)
[16:19:13 -134430.747610] FAST spr round 6 (radius: 25)
[16:21:57 -134423.010835] FAST spr round 7 (radius: 25)
[16:24:28 -134421.470503] FAST spr round 8 (radius: 25)
[16:26:54 -134421.470498] Model parameter optimization (eps = 1.000000)
[16:27:29 -134262.764129] SLOW spr round 1 (radius: 5)
[16:30:53 -134181.161630] SLOW spr round 2 (radius: 5)
[16:34:10 -134167.060372] SLOW spr round 3 (radius: 5)
[16:37:23 -134159.809468] SLOW spr round 4 (radius: 5)
[16:40:29 -134159.131698] SLOW spr round 5 (radius: 5)
[16:43:41 -134148.841618] SLOW spr round 6 (radius: 5)
[16:46:50 -134146.486640] SLOW spr round 7 (radius: 5)
[16:47:25] [worker #1] ML tree search #5, logLikelihood: -134189.978076
[16:49:55 -134145.813274] SLOW spr round 8 (radius: 5)
[16:52:58 -134145.812981] SLOW spr round 9 (radius: 10)
[16:56:26 -134138.794811] SLOW spr round 10 (radius: 5)
[17:00:00 -134137.686731] SLOW spr round 11 (radius: 5)
[17:03:13 -134137.686654] SLOW spr round 12 (radius: 10)
[17:06:44 -134137.599796] SLOW spr round 13 (radius: 15)
[17:13:01 -134131.152154] SLOW spr round 14 (radius: 5)
[17:16:46 -134122.072160] SLOW spr round 15 (radius: 5)
[17:20:02 -134122.072095] SLOW spr round 16 (radius: 10)
[17:23:39 -134118.166202] SLOW spr round 17 (radius: 5)
[17:27:16 -134116.062595] SLOW spr round 18 (radius: 5)
[17:30:30 -134116.062225] SLOW spr round 19 (radius: 10)
[17:34:04 -134114.304571] SLOW spr round 20 (radius: 5)
[17:37:36 -134114.208114] SLOW spr round 21 (radius: 10)
[17:41:26 -134113.182485] SLOW spr round 22 (radius: 5)
[17:44:56 -134112.682338] SLOW spr round 23 (radius: 5)
[17:48:22 -134112.682210] SLOW spr round 24 (radius: 10)
[17:54:29 -134112.550592] SLOW spr round 25 (radius: 5)
[17:58:53 -134112.550326] SLOW spr round 26 (radius: 10)
[18:04:03 -134112.550316] SLOW spr round 27 (radius: 15)
[18:11:13 -134110.666991] SLOW spr round 28 (radius: 5)
[18:15:12 -134105.997009] SLOW spr round 29 (radius: 5)
[18:19:22 -134105.115173] SLOW spr round 30 (radius: 5)
[18:25:05 -134105.094152] SLOW spr round 31 (radius: 10)
[18:28:46 -134103.071823] SLOW spr round 32 (radius: 5)
[18:33:09 -134100.896302] SLOW spr round 33 (radius: 5)
[18:37:08 -134100.895405] SLOW spr round 34 (radius: 10)
[18:42:01 -134099.805531] SLOW spr round 35 (radius: 5)
[18:48:14 -134099.804585] SLOW spr round 36 (radius: 10)
[18:52:02 -134099.804533] SLOW spr round 37 (radius: 15)
[18:58:28 -134095.445401] SLOW spr round 38 (radius: 5)
[19:02:45 -134091.197699] SLOW spr round 39 (radius: 5)
[19:06:26 -134091.196981] SLOW spr round 40 (radius: 10)
[19:10:58 -134090.845579] SLOW spr round 41 (radius: 5)
[19:15:05 -134087.744682] SLOW spr round 42 (radius: 5)
[19:19:04 -134087.710998] SLOW spr round 43 (radius: 10)
[19:24:58 -134087.434269] SLOW spr round 44 (radius: 5)
[19:31:04 -134087.427927] SLOW spr round 45 (radius: 10)
[19:36:57 -134087.427562] SLOW spr round 46 (radius: 15)
[19:43:01 -134085.729425] SLOW spr round 47 (radius: 5)
[19:47:01 -134084.335594] SLOW spr round 48 (radius: 5)
[19:51:23 -134084.335500] SLOW spr round 49 (radius: 10)
[19:55:45 -134084.278555] SLOW spr round 50 (radius: 15)
[20:02:33 -134084.278391] SLOW spr round 51 (radius: 20)
[20:10:58 -134076.229615] SLOW spr round 52 (radius: 5)
[20:15:14 -134075.615696] SLOW spr round 53 (radius: 5)
[20:18:31 -134075.615639] SLOW spr round 54 (radius: 10)
[20:22:03 -134075.615637] SLOW spr round 55 (radius: 15)
[20:28:07 -134075.615637] SLOW spr round 56 (radius: 20)
[20:36:28 -134075.615637] SLOW spr round 57 (radius: 25)
[20:46:35 -134074.692734] SLOW spr round 58 (radius: 5)
[20:50:23 -134072.285877] SLOW spr round 59 (radius: 5)
[20:53:49 -134070.705424] SLOW spr round 60 (radius: 5)
[20:56:56 -134070.705086] SLOW spr round 61 (radius: 10)
[21:00:21 -134070.705067] SLOW spr round 62 (radius: 15)
[21:06:27 -134070.705064] SLOW spr round 63 (radius: 20)
[21:14:37 -134070.705064] SLOW spr round 64 (radius: 25)
[21:24:34 -134070.705064] Model parameter optimization (eps = 0.100000)

[21:24:59] [worker #0] ML tree search #7, logLikelihood: -134066.238896

[21:24:59 -270048.858221] Initial branch length optimization
[21:25:02 -233079.143083] Model parameter optimization (eps = 10.000000)
[21:25:50 -231307.625377] AUTODETECT spr round 1 (radius: 5)
[21:28:28 -202766.432620] AUTODETECT spr round 2 (radius: 10)
[21:31:36 -170433.013353] AUTODETECT spr round 3 (radius: 15)
[21:34:56 -158370.332124] AUTODETECT spr round 4 (radius: 20)
[21:38:28 -153789.886650] AUTODETECT spr round 5 (radius: 25)
[21:42:29 -150929.622932] SPR radius for FAST iterations: 25 (autodetect)
[21:42:29 -150929.622932] Model parameter optimization (eps = 3.000000)
[21:43:04 -150802.593578] FAST spr round 1 (radius: 25)
[21:49:02 -137178.023427] FAST spr round 2 (radius: 25)
[21:53:25 -134944.943766] FAST spr round 3 (radius: 25)
[21:57:03 -134341.856905] FAST spr round 4 (radius: 25)
[22:00:09 -134281.866186] FAST spr round 5 (radius: 25)
[22:02:55 -134259.491903] FAST spr round 6 (radius: 25)
[22:05:26 -134258.383951] FAST spr round 7 (radius: 25)
[22:07:51 -134258.383779] Model parameter optimization (eps = 1.000000)
[22:07:58 -134257.932415] SLOW spr round 1 (radius: 5)
[22:11:07 -134228.693454] SLOW spr round 2 (radius: 5)
[22:14:14 -134222.256784] SLOW spr round 3 (radius: 5)
[22:17:16 -134214.176800] SLOW spr round 4 (radius: 5)
[22:20:15 -134212.435866] SLOW spr round 5 (radius: 5)
[22:23:14 -134209.234682] SLOW spr round 6 (radius: 5)
[22:26:06 -134209.233874] SLOW spr round 7 (radius: 10)
[22:29:18 -134203.138640] SLOW spr round 8 (radius: 5)
[22:32:47 -134199.364101] SLOW spr round 9 (radius: 5)
[22:35:58 -134194.881859] SLOW spr round 10 (radius: 5)
[22:38:56 -134193.558155] SLOW spr round 11 (radius: 5)
[22:41:50 -134193.557992] SLOW spr round 12 (radius: 10)
[22:44:58 -134188.881125] SLOW spr round 13 (radius: 5)
[22:48:26 -134182.448681] SLOW spr round 14 (radius: 5)
[22:51:33 -134181.873836] SLOW spr round 15 (radius: 5)
[22:54:29 -134181.873252] SLOW spr round 16 (radius: 10)
[22:57:39 -134181.107541] SLOW spr round 17 (radius: 5)
[23:01:06 -134177.749793] SLOW spr round 18 (radius: 5)
[23:04:12 -134177.149401] SLOW spr round 19 (radius: 5)
[23:07:08 -134177.149375] SLOW spr round 20 (radius: 10)
[23:10:19 -134172.673649] SLOW spr round 21 (radius: 5)
[23:13:47 -134162.895234] SLOW spr round 22 (radius: 5)
[23:16:51 -134162.894952] SLOW spr round 23 (radius: 10)
[23:20:06 -134160.563730] SLOW spr round 24 (radius: 5)
[23:23:31 -134153.753546] SLOW spr round 25 (radius: 5)
[23:26:35 -134153.753475] SLOW spr round 26 (radius: 10)
[23:29:48 -134145.987374] SLOW spr round 27 (radius: 5)
[23:33:17 -134134.428270] SLOW spr round 28 (radius: 5)
[23:36:17] [worker #2] ML tree search #12, logLikelihood: -134025.183878
[23:36:33 -134124.657890] SLOW spr round 29 (radius: 5)
[23:39:33 -134124.086955] SLOW spr round 30 (radius: 5)
[23:42:33 -134121.982322] SLOW spr round 31 (radius: 5)
[23:45:24 -134121.982231] SLOW spr round 32 (radius: 10)
[23:48:29 -134118.984852] SLOW spr round 33 (radius: 5)
[23:51:53 -134118.266215] SLOW spr round 34 (radius: 5)
[23:54:58 -134118.266142] SLOW spr round 35 (radius: 10)
[23:58:09 -134118.130693] SLOW spr round 36 (radius: 5)
[24:01:32 -134118.017144] SLOW spr round 37 (radius: 5)
[24:04:37 -134118.016148] SLOW spr round 38 (radius: 10)
[24:07:49 -134117.506625] SLOW spr round 39 (radius: 5)
[24:11:15 -134115.372152] SLOW spr round 40 (radius: 5)
[24:14:22 -134115.008055] SLOW spr round 41 (radius: 5)
[24:17:20 -134115.007293] SLOW spr round 42 (radius: 10)
[24:20:28 -134115.007260] SLOW spr round 43 (radius: 15)
[24:25:52 -134113.331495] SLOW spr round 44 (radius: 5)
[24:29:22 -134112.909407] SLOW spr round 45 (radius: 5)
[24:32:30 -134112.909063] SLOW spr round 46 (radius: 10)
[24:35:45 -134112.662568] SLOW spr round 47 (radius: 5)
[24:39:09 -134112.658707] SLOW spr round 48 (radius: 10)
[24:42:37 -134112.515712] SLOW spr round 49 (radius: 5)
[24:46:04 -134110.960725] SLOW spr round 50 (radius: 5)
[24:47:16] [worker #1] ML tree search #8, logLikelihood: -134479.244531
[24:49:16 -134109.135263] SLOW spr round 51 (radius: 5)
[24:52:19 -134109.089979] SLOW spr round 52 (radius: 10)
[24:55:27 -134108.497542] SLOW spr round 53 (radius: 5)
[24:58:51 -134108.496204] SLOW spr round 54 (radius: 10)
[25:02:19 -134108.496159] SLOW spr round 55 (radius: 15)
[25:07:33 -134107.452777] SLOW spr round 56 (radius: 5)
[25:11:10 -134106.259337] SLOW spr round 57 (radius: 5)
[25:14:20 -134106.258685] SLOW spr round 58 (radius: 10)
[25:17:35 -134105.883116] SLOW spr round 59 (radius: 5)
[25:21:03 -134104.134147] SLOW spr round 60 (radius: 5)
[25:24:12 -134104.113587] SLOW spr round 61 (radius: 10)
[25:27:26 -134104.113513] SLOW spr round 62 (radius: 15)
[25:32:54 -134103.610571] SLOW spr round 63 (radius: 5)
[25:36:25 -134103.606243] SLOW spr round 64 (radius: 10)
[25:40:05 -134103.335254] SLOW spr round 65 (radius: 5)
[25:43:27 -134103.334895] SLOW spr round 66 (radius: 10)
[25:46:56 -134103.300449] SLOW spr round 67 (radius: 15)
[25:52:14 -134103.300390] SLOW spr round 68 (radius: 20)
[25:59:29 -134099.796999] SLOW spr round 69 (radius: 5)
[26:03:06 -134099.229380] SLOW spr round 70 (radius: 5)
[26:06:18 -134099.229110] SLOW spr round 71 (radius: 10)
[26:09:40 -134098.581204] SLOW spr round 72 (radius: 5)
[26:13:04 -134098.578985] SLOW spr round 73 (radius: 10)
[26:16:37 -134098.578769] SLOW spr round 74 (radius: 15)
[26:21:54 -134098.429563] SLOW spr round 75 (radius: 5)
[26:25:35 -134096.335141] SLOW spr round 76 (radius: 5)
[26:28:47 -134096.334430] SLOW spr round 77 (radius: 10)
[26:32:07 -134096.334413] SLOW spr round 78 (radius: 15)
[26:37:34 -134096.334412] SLOW spr round 79 (radius: 20)
[26:44:57 -134096.202034] SLOW spr round 80 (radius: 5)
[26:48:32 -134096.201780] SLOW spr round 81 (radius: 10)
[26:52:21 -134094.984646] SLOW spr round 82 (radius: 5)
[26:55:44 -134094.978935] SLOW spr round 83 (radius: 10)
[26:59:15 -134094.978643] SLOW spr round 84 (radius: 15)
[27:04:35 -134094.978629] SLOW spr round 85 (radius: 20)
[27:11:59 -134094.978628] SLOW spr round 86 (radius: 25)
[27:21:15 -134093.060006] SLOW spr round 87 (radius: 5)
[27:24:53 -134091.345045] SLOW spr round 88 (radius: 5)
[27:28:07 -134091.344942] SLOW spr round 89 (radius: 10)
[27:31:27 -134091.344942] SLOW spr round 90 (radius: 15)
[27:36:50 -134089.128619] SLOW spr round 91 (radius: 5)
[27:40:25 -134088.620383] SLOW spr round 92 (radius: 5)
[27:43:36 -134088.620103] SLOW spr round 93 (radius: 10)
[27:46:55 -134088.620098] SLOW spr round 94 (radius: 15)
[27:52:20 -134088.620098] SLOW spr round 95 (radius: 20)
[27:59:41 -134088.620098] SLOW spr round 96 (radius: 25)
[28:08:51 -134088.620098] Model parameter optimization (eps = 0.100000)

[28:08:57] [worker #0] ML tree search #10, logLikelihood: -134088.597519

[28:08:57 -270831.671659] Initial branch length optimization
[28:08:59 -233814.317465] Model parameter optimization (eps = 10.000000)
[28:09:45 -232106.815019] AUTODETECT spr round 1 (radius: 5)
[28:12:21 -201605.829708] AUTODETECT spr round 2 (radius: 10)
[28:15:25 -170127.350777] AUTODETECT spr round 3 (radius: 15)
[28:18:45 -155111.533042] AUTODETECT spr round 4 (radius: 20)
[28:22:28 -150829.257393] AUTODETECT spr round 5 (radius: 25)
[28:26:22 -150002.121115] SPR radius for FAST iterations: 25 (autodetect)
[28:26:22 -150002.121115] Model parameter optimization (eps = 3.000000)
[28:26:59 -149774.035401] FAST spr round 1 (radius: 25)
[28:32:50 -139849.158662] FAST spr round 2 (radius: 25)
[28:37:13 -135246.818289] FAST spr round 3 (radius: 25)
[28:40:57 -134321.214295] FAST spr round 4 (radius: 25)
[28:43:32] [worker #2] ML tree search #15, logLikelihood: -134032.497884
[28:44:15 -134188.632076] FAST spr round 5 (radius: 25)
[28:47:07 -134152.965398] FAST spr round 6 (radius: 25)
[28:49:45 -134152.964402] Model parameter optimization (eps = 1.000000)
[28:50:05 -134145.162554] SLOW spr round 1 (radius: 5)
[28:53:23 -134107.870310] SLOW spr round 2 (radius: 5)
[28:56:32 -134102.681960] SLOW spr round 3 (radius: 5)
[28:59:30 -134102.681788] SLOW spr round 4 (radius: 10)
[29:02:49 -134093.273980] SLOW spr round 5 (radius: 5)
[29:06:22 -134087.950596] SLOW spr round 6 (radius: 5)
[29:09:28 -134087.950392] SLOW spr round 7 (radius: 10)
[29:12:50 -134081.530489] SLOW spr round 8 (radius: 5)
[29:16:17 -134073.188524] SLOW spr round 9 (radius: 5)
[29:19:24 -134073.188456] SLOW spr round 10 (radius: 10)
[29:21:31] [worker #1] ML tree search #11, logLikelihood: -134246.140474
[29:22:45 -134071.759215] SLOW spr round 11 (radius: 5)
[29:26:11 -134070.088946] SLOW spr round 12 (radius: 5)
[29:29:17 -134070.088417] SLOW spr round 13 (radius: 10)
[29:32:39 -134069.484327] SLOW spr round 14 (radius: 5)
[29:36:01 -134069.484021] SLOW spr round 15 (radius: 10)
[29:39:36 -134069.371629] SLOW spr round 16 (radius: 5)
[29:43:00 -134067.349164] SLOW spr round 17 (radius: 5)
[29:46:06 -134067.348586] SLOW spr round 18 (radius: 10)
[29:49:25 -134067.230953] SLOW spr round 19 (radius: 5)
[29:52:49 -134066.304470] SLOW spr round 20 (radius: 5)
[29:55:55 -134066.303114] SLOW spr round 21 (radius: 10)
[29:59:18 -134061.829754] SLOW spr round 22 (radius: 5)
[30:02:44 -134060.882089] SLOW spr round 23 (radius: 5)
[30:05:51 -134060.881720] SLOW spr round 24 (radius: 10)
[30:09:13 -134060.782616] SLOW spr round 25 (radius: 15)
[30:14:44 -134060.420649] SLOW spr round 26 (radius: 5)
[30:18:12 -134060.281703] SLOW spr round 27 (radius: 5)
[30:21:22 -134060.281427] SLOW spr round 28 (radius: 10)
[30:24:46 -134059.930063] SLOW spr round 29 (radius: 5)
[30:28:10 -134055.177093] SLOW spr round 30 (radius: 5)
[30:31:16 -134053.468390] SLOW spr round 31 (radius: 5)
[30:34:16 -134053.467758] SLOW spr round 32 (radius: 10)
[30:37:33 -134053.467741] SLOW spr round 33 (radius: 15)
[30:43:04 -134053.467740] SLOW spr round 34 (radius: 20)
[30:50:23 -134053.125582] SLOW spr round 35 (radius: 5)
[30:54:00 -134051.792486] SLOW spr round 36 (radius: 5)
[30:57:12 -134051.792135] SLOW spr round 37 (radius: 10)
[31:00:38 -134051.539469] SLOW spr round 38 (radius: 5)
[31:03:59 -134051.537067] SLOW spr round 39 (radius: 10)
[31:07:34 -134051.536792] SLOW spr round 40 (radius: 15)
[31:12:50 -134051.536758] SLOW spr round 41 (radius: 20)
[31:20:12 -134051.536753] SLOW spr round 42 (radius: 25)
[31:29:18 -134045.765075] SLOW spr round 43 (radius: 5)
[31:32:57 -134045.664549] SLOW spr round 44 (radius: 5)
[31:36:11 -134045.663825] SLOW spr round 45 (radius: 10)
[31:39:37 -134045.560622] SLOW spr round 46 (radius: 5)
[31:42:59 -134045.559126] SLOW spr round 47 (radius: 10)
[31:46:33 -134045.559031] SLOW spr round 48 (radius: 15)
[31:51:51 -134045.559018] SLOW spr round 49 (radius: 20)
[31:56:41] [worker #2] ML tree search #18, logLikelihood: -134106.005832
[31:59:11 -134045.452569] SLOW spr round 50 (radius: 5)
[32:02:46 -134044.249301] SLOW spr round 51 (radius: 5)
[32:06:00 -134043.651639] SLOW spr round 52 (radius: 5)
[32:09:00 -134043.650983] SLOW spr round 53 (radius: 10)
[32:12:14 -134043.650959] SLOW spr round 54 (radius: 15)
[32:17:40 -134043.650958] SLOW spr round 55 (radius: 20)
[32:24:53 -134043.650958] SLOW spr round 56 (radius: 25)
[32:33:50 -134043.650958] Model parameter optimization (eps = 0.100000)

[32:34:05] [worker #0] ML tree search #13, logLikelihood: -134043.037835

[32:34:05 -271240.011949] Initial branch length optimization
[32:34:08 -234179.390217] Model parameter optimization (eps = 10.000000)
[32:34:56 -232245.811535] AUTODETECT spr round 1 (radius: 5)
[32:37:32 -200986.541742] AUTODETECT spr round 2 (radius: 10)
[32:40:41 -169819.711371] AUTODETECT spr round 3 (radius: 15)
[32:44:02 -153315.198815] AUTODETECT spr round 4 (radius: 20)
[32:47:40 -147549.928848] AUTODETECT spr round 5 (radius: 25)
[32:51:59 -146344.961308] SPR radius for FAST iterations: 25 (autodetect)
[32:51:59 -146344.961308] Model parameter optimization (eps = 3.000000)
[32:52:07 -146342.510542] FAST spr round 1 (radius: 25)
[32:58:34 -136679.553060] FAST spr round 2 (radius: 25)
[33:02:56 -135360.361809] FAST spr round 3 (radius: 25)
[33:06:41 -134604.678663] FAST spr round 4 (radius: 25)
[33:09:57 -134366.674878] FAST spr round 5 (radius: 25)
[33:12:51 -134348.869661] FAST spr round 6 (radius: 25)
[33:15:32 -134334.350918] FAST spr round 7 (radius: 25)
[33:18:05 -134328.615922] FAST spr round 8 (radius: 25)
[33:20:34 -134324.486970] FAST spr round 9 (radius: 25)
[33:22:58 -134320.517231] FAST spr round 10 (radius: 25)
[33:25:21 -134317.784103] FAST spr round 11 (radius: 25)
[33:27:43 -134317.783805] Model parameter optimization (eps = 1.000000)
[33:27:48 -134317.682553] SLOW spr round 1 (radius: 5)
[33:30:59 -134277.827438] SLOW spr round 2 (radius: 5)
[33:34:07 -134263.515624] SLOW spr round 3 (radius: 5)
[33:37:09 -134261.588250] SLOW spr round 4 (radius: 5)
[33:40:09 -134259.784818] SLOW spr round 5 (radius: 5)
[33:43:04 -134259.783920] SLOW spr round 6 (radius: 10)
[33:46:27 -134246.561731] SLOW spr round 7 (radius: 5)
[33:50:02 -134240.208737] SLOW spr round 8 (radius: 5)
[33:53:11 -134240.205332] SLOW spr round 9 (radius: 10)
[33:56:38 -134232.695674] SLOW spr round 10 (radius: 5)
[34:00:13 -134231.450501] SLOW spr round 11 (radius: 5)
[34:03:26 -134231.447726] SLOW spr round 12 (radius: 10)
[34:06:53 -134229.549995] SLOW spr round 13 (radius: 5)
[34:10:25 -134228.568567] SLOW spr round 14 (radius: 5)
[34:13:37 -134228.568105] SLOW spr round 15 (radius: 10)
[34:17:30 -134228.568053] SLOW spr round 16 (radius: 15)
[34:23:19 -134225.302460] SLOW spr round 17 (radius: 5)
[34:27:07 -134224.743216] SLOW spr round 18 (radius: 5)
[34:28:44] [worker #1] ML tree search #14, logLikelihood: -134020.355279
[34:30:33 -134224.743206] SLOW spr round 19 (radius: 10)
[34:34:03 -134224.743203] SLOW spr round 20 (radius: 15)
[34:39:39 -134224.743201] SLOW spr round 21 (radius: 20)
[34:47:25 -134223.193420] SLOW spr round 22 (radius: 5)
[34:51:15 -134221.793170] SLOW spr round 23 (radius: 5)
[34:54:46 -134220.265087] SLOW spr round 24 (radius: 5)
[34:58:45 -134220.263124] SLOW spr round 25 (radius: 10)
[35:02:29 -134220.263075] SLOW spr round 26 (radius: 15)
[35:08:12 -134220.263075] SLOW spr round 27 (radius: 20)
[35:15:56 -134220.263075] SLOW spr round 28 (radius: 25)
[35:24:59 -134215.830238] SLOW spr round 29 (radius: 5)
[35:28:44 -134212.574286] SLOW spr round 30 (radius: 5)
[35:32:05 -134210.520934] SLOW spr round 31 (radius: 5)
[35:35:10 -134210.520810] SLOW spr round 32 (radius: 10)
[35:38:30 -134210.520810] SLOW spr round 33 (radius: 15)
[35:44:09 -134210.520810] SLOW spr round 34 (radius: 20)
[35:51:42 -134210.520810] SLOW spr round 35 (radius: 25)
[36:00:40 -134210.520810] Model parameter optimization (eps = 0.100000)

[36:00:49] [worker #0] ML tree search #16, logLikelihood: -134210.277160

[36:00:49 -270521.109577] Initial branch length optimization
[36:00:52 -232892.522562] Model parameter optimization (eps = 10.000000)
[36:01:40 -231123.477097] AUTODETECT spr round 1 (radius: 5)
[36:04:19 -200725.387777] AUTODETECT spr round 2 (radius: 10)
[36:07:23 -171111.787221] AUTODETECT spr round 3 (radius: 15)
[36:10:46 -155657.426932] AUTODETECT spr round 4 (radius: 20)
[36:14:35 -148272.937592] AUTODETECT spr round 5 (radius: 25)
[36:18:54 -145076.574486] SPR radius for FAST iterations: 25 (autodetect)
[36:18:54 -145076.574486] Model parameter optimization (eps = 3.000000)
[36:19:20 -144943.925447] FAST spr round 1 (radius: 25)
[36:26:01 -134986.973721] FAST spr round 2 (radius: 25)
[36:30:56 -134360.361226] FAST spr round 3 (radius: 25)
[36:34:52 -134313.865378] FAST spr round 4 (radius: 25)
[36:38:13 -134296.926981] FAST spr round 5 (radius: 25)
[36:41:12 -134281.176811] FAST spr round 6 (radius: 25)
[36:43:53 -134278.828305] FAST spr round 7 (radius: 25)
[36:46:29 -134277.139448] FAST spr round 8 (radius: 25)
[36:49:00 -134277.138918] Model parameter optimization (eps = 1.000000)
[36:49:07 -134277.105315] SLOW spr round 1 (radius: 5)
[36:52:26 -134243.283574] SLOW spr round 2 (radius: 5)
[36:55:39 -134238.810985] SLOW spr round 3 (radius: 5)
[36:58:47 -134238.231290] SLOW spr round 4 (radius: 5)
[37:01:49 -134238.231205] SLOW spr round 5 (radius: 10)
[37:05:10 -134236.277756] SLOW spr round 6 (radius: 5)
[37:08:41 -134235.255636] SLOW spr round 7 (radius: 5)
[37:11:59 -134234.750932] SLOW spr round 8 (radius: 5)
[37:15:07 -134233.426056] SLOW spr round 9 (radius: 5)
[37:18:11 -134233.425965] SLOW spr round 10 (radius: 10)
[37:21:31 -134232.220047] SLOW spr round 11 (radius: 5)
[37:24:59 -134232.101380] SLOW spr round 12 (radius: 5)
[37:28:11 -134232.100926] SLOW spr round 13 (radius: 10)
[37:31:38 -134231.875961] SLOW spr round 14 (radius: 5)
[37:35:09 -134231.873127] SLOW spr round 15 (radius: 10)
[37:38:54 -134231.873101] SLOW spr round 16 (radius: 15)
[37:44:27 -134224.594385] SLOW spr round 17 (radius: 5)
[37:48:14 -134215.966570] SLOW spr round 18 (radius: 5)
[37:51:38 -134211.784680] SLOW spr round 19 (radius: 5)
[37:54:56 -134209.270613] SLOW spr round 20 (radius: 5)
[37:58:04 -134209.073911] SLOW spr round 21 (radius: 5)
[38:01:07 -134209.073428] SLOW spr round 22 (radius: 10)
[38:04:28 -134205.632293] SLOW spr round 23 (radius: 5)
[38:08:06 -134201.295140] SLOW spr round 24 (radius: 5)
[38:11:20 -134201.294775] SLOW spr round 25 (radius: 10)
[38:14:52 -134200.400202] SLOW spr round 26 (radius: 5)
[38:18:30 -134198.744163] SLOW spr round 27 (radius: 5)
[38:19:48] [worker #1] ML tree search #17, logLikelihood: -134244.421284
[38:21:46 -134198.743450] SLOW spr round 28 (radius: 10)
[38:25:18 -134198.129991] SLOW spr round 29 (radius: 5)
[38:28:52 -134198.089140] SLOW spr round 30 (radius: 10)
[38:32:42 -134196.948602] SLOW spr round 31 (radius: 5)
[38:36:20 -134192.837985] SLOW spr round 32 (radius: 5)
[38:39:38 -134192.712241] SLOW spr round 33 (radius: 5)
[38:42:45 -134192.712110] SLOW spr round 34 (radius: 10)
[38:46:09 -134188.318711] SLOW spr round 35 (radius: 5)
[38:49:44 -134187.862631] SLOW spr round 36 (radius: 5)
[38:52:59 -134187.862502] SLOW spr round 37 (radius: 10)
[38:56:28 -134186.350848] SLOW spr round 38 (radius: 5)
[39:00:04 -134183.917093] SLOW spr round 39 (radius: 5)
[39:03:22 -134183.568159] SLOW spr round 40 (radius: 5)
[39:06:30 -134183.568138] SLOW spr round 41 (radius: 10)
[39:09:56 -134181.515488] SLOW spr round 42 (radius: 5)
[39:13:26 -134181.515053] SLOW spr round 43 (radius: 10)
[39:17:15 -134181.515035] SLOW spr round 44 (radius: 15)
[39:22:44 -134179.599679] SLOW spr round 45 (radius: 5)
[39:26:30 -134177.243206] SLOW spr round 46 (radius: 5)
[39:29:48 -134177.242687] SLOW spr round 47 (radius: 10)
[39:33:20 -134177.127782] SLOW spr round 48 (radius: 5)
[39:36:58 -134175.589057] SLOW spr round 49 (radius: 5)
[39:40:18 -134173.859763] SLOW spr round 50 (radius: 5)
[39:43:27 -134173.859247] SLOW spr round 51 (radius: 10)
[39:46:49 -134173.859234] SLOW spr round 52 (radius: 15)
[39:52:32 -134173.859222] SLOW spr round 53 (radius: 20)
[40:00:04 -134172.899522] SLOW spr round 54 (radius: 5)
[40:03:51 -134171.853479] SLOW spr round 55 (radius: 5)
[40:07:14 -134171.852823] SLOW spr round 56 (radius: 10)
[40:10:49 -134171.852801] SLOW spr round 57 (radius: 15)
[40:16:25 -134171.852789] SLOW spr round 58 (radius: 20)
[40:24:02 -134171.852777] SLOW spr round 59 (radius: 25)
[40:33:12 -134169.323493] SLOW spr round 60 (radius: 5)
[40:37:03 -134158.394242] SLOW spr round 61 (radius: 5)
[40:40:33 -134155.790658] SLOW spr round 62 (radius: 5)
[40:43:47 -134155.335245] SLOW spr round 63 (radius: 5)
[40:46:54 -134155.335123] SLOW spr round 64 (radius: 10)
[40:50:17 -134155.335109] SLOW spr round 65 (radius: 15)
[40:56:04 -134155.335098] SLOW spr round 66 (radius: 20)
[41:03:43 -134155.335086] SLOW spr round 67 (radius: 25)
[41:12:54 -134153.667470] SLOW spr round 68 (radius: 5)
[41:16:47 -134149.889213] SLOW spr round 69 (radius: 5)
[41:20:13 -134149.791442] SLOW spr round 70 (radius: 10)
[41:23:51 -134148.063974] SLOW spr round 71 (radius: 5)
[41:27:23 -134148.063627] SLOW spr round 72 (radius: 10)
[41:31:10 -134148.063587] SLOW spr round 73 (radius: 15)
[41:36:43 -134142.943941] SLOW spr round 74 (radius: 5)
[41:40:30 -134142.123589] SLOW spr round 75 (radius: 5)
[41:43:53 -134141.002082] SLOW spr round 76 (radius: 5)
[41:47:02 -134141.002029] SLOW spr round 77 (radius: 10)
[41:49:50] [worker #1] ML tree search #20, logLikelihood: -133984.354215
[41:50:27 -134141.002009] SLOW spr round 78 (radius: 15)
[41:56:13 -134140.726875] SLOW spr round 79 (radius: 5)
[41:59:56 -134138.375003] SLOW spr round 80 (radius: 5)
[42:03:12 -134138.374350] SLOW spr round 81 (radius: 10)
[42:06:41 -134138.374326] SLOW spr round 82 (radius: 15)
[42:12:18 -134138.374314] SLOW spr round 83 (radius: 20)
[42:19:54 -134138.374303] SLOW spr round 84 (radius: 25)
[42:28:55 -134138.374291] Model parameter optimization (eps = 0.100000)

[42:29:01] [worker #0] ML tree search #19, logLikelihood: -134138.288536


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.253856,0.772206) (0.228638,0.353282) (0.314707,1.285200) (0.202799,1.571683) 
   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: -133971.693707

AIC score: 271953.387415 / AICc score: 8316013.387415 / BIC score: 277893.890898
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=143).
         This might lead to overfitting and compromise tree inference results!


Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6ZQY2/3_mltree/Q6ZQY2.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6ZQY2/3_mltree/Q6ZQY2.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6ZQY2/3_mltree/Q6ZQY2.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6ZQY2/3_mltree/Q6ZQY2.raxml.log

Analysis started: 13-Jul-2021 02:14:46 / finished: 14-Jul-2021 20:43:48

Elapsed time: 152941.878 seconds