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 18-Jun-2021 08:00:57 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P35520/2_msa/P35520_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P35520/3_mltree/P35520 --seed 2 --threads 7 --tree rand{20} pars{20}

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

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P35520/2_msa/P35520_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 443 sites

WARNING: Sequences tr_A0A0E1RXA8_A0A0E1RXA8_COCIM_246410 and tr_A0A0J6Y8R5_A0A0J6Y8R5_COCIT_404692 are exactly identical!
WARNING: Sequences tr_J3KI41_J3KI41_COCIM_246410 and tr_A0A0J6XXC5_A0A0J6XXC5_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B6Q8U6_B6Q8U6_TALMQ_441960 and tr_A0A093VLK5_A0A093VLK5_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_B8NBZ9_B8NBZ9_ASPFN_332952 and tr_A0A0F0I4J3_A0A0F0I4J3_ASPPU_1403190 are exactly identical!
WARNING: Sequences tr_B8NBZ9_B8NBZ9_ASPFN_332952 and tr_A0A1S9DDX3_A0A1S9DDX3_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_A0A179V230_A0A179V230_BLAGS_559298 and tr_A0A179TU37_A0A179TU37_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_Q4CXR9_Q4CXR9_TRYCC_353153 and tr_Q4DF38_Q4DF38_TRYCC_353153 are exactly identical!
WARNING: Sequences tr_F9FKU0_F9FKU0_FUSOF_660025 and tr_A0A0D2XET1_A0A0D2XET1_FUSO4_426428 are exactly identical!
WARNING: Sequences tr_F9FKU0_F9FKU0_FUSOF_660025 and tr_N4UEW5_N4UEW5_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9FKU0_F9FKU0_FUSOF_660025 and tr_X0C2V0_X0C2V0_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9FKU0_F9FKU0_FUSOF_660025 and tr_A0A2H3T2R4_A0A2H3T2R4_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_F9FKU0_F9FKU0_FUSOF_660025 and tr_A0A2H3HL31_A0A2H3HL31_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_C6HT32_C6HT32_AJECH_544712 and tr_F0U9F4_F0U9F4_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_J4UHI8_J4UHI8_BEAB2_655819 and tr_A0A2N6N8X5_A0A2N6N8X5_BEABA_176275 are exactly identical!
WARNING: Sequences sp_P0DN79_CBSL_HUMAN_9606 and sp_P35520_CBS_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A2QKG7_A2QKG7_ASPNC_425011 and tr_G3XV50_G3XV50_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_A2QKG7_A2QKG7_ASPNC_425011 and tr_A0A319AG86_A0A319AG86_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_F7H3T2_F7H3T2_MACMU_9544 and tr_A0A2K6D991_A0A2K6D991_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7XHD7_G7XHD7_ASPKW_1033177 and tr_A0A317UYW7_A0A317UYW7_9EURO_1448314 are exactly identical!
WARNING: Sequences tr_B8B3S9_B8B3S9_ORYSI_39946 and tr_Q5Z8Y9_Q5Z8Y9_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_F4P4C4_F4P4C4_BATDJ_684364 and tr_A0A177WHG6_A0A177WHG6_BATDE_403673 are exactly identical!
WARNING: Sequences tr_E3MMP8_E3MMP8_CAERE_31234 and tr_A0A261CTT1_A0A261CTT1_9PELO_1503980 are exactly identical!
WARNING: Sequences tr_A8WRM3_A8WRM3_CAEBR_6238 and tr_A0A2G5SMB0_A0A2G5SMB0_9PELO_1611254 are exactly identical!
WARNING: Sequences tr_F2SCU1_F2SCU1_TRIRC_559305 and tr_A0A178ETH1_A0A178ETH1_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_B3S7J1_B3S7J1_TRIAD_10228 and tr_A0A369SM35_A0A369SM35_9METZ_287889 are exactly identical!
WARNING: Sequences tr_U5HEA6_U5HEA6_USTV1_683840 and tr_A0A2X0NVI0_A0A2X0NVI0_9BASI_796604 are exactly identical!
WARNING: Sequences tr_V2XBC2_V2XBC2_MONRO_1381753 and tr_A0A0W0FZ85_A0A0W0FZ85_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_W2PM91_W2PM91_PHYPN_761204 and tr_A0A0W8CA49_A0A0W8CA49_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2PM91_W2PM91_PHYPN_761204 and tr_W2KGB8_W2KGB8_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_W2QNX4_W2QNX4_PHYPN_761204 and tr_W2HD38_W2HD38_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_W2RD14_W2RD14_PHYPN_761204 and tr_A0A0W8CS04_A0A0W8CS04_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2RD14_W2RD14_PHYPN_761204 and tr_W2LEI1_W2LEI1_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A015JN67_A0A015JN67_9GLOM_1432141 and tr_U9TWG8_U9TWG8_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A0A1NEP6_A0A0A1NEP6_9FUNG_58291 and tr_A0A367K1Z4_A0A367K1Z4_9FUNG_86630 are exactly identical!
WARNING: Sequences tr_A0A151NQF2_A0A151NQF2_ALLMI_8496 and tr_A0A3Q0HIM3_A0A3Q0HIM3_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A0V1CES5_A0A0V1CES5_TRIBR_45882 and tr_A0A0V0UX03_A0A0V0UX03_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V1CES5_A0A0V1CES5_TRIBR_45882 and tr_A0A0V1P796_A0A0V1P796_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V1CES5_A0A0V1CES5_TRIBR_45882 and tr_A0A0V0TUD0_A0A0V0TUD0_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A226MTM8_A0A226MTM8_CALSU_9009 and tr_A0A226PJ63_A0A226PJ63_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2S7P969_A0A2S7P969_9HELO_2070414 and tr_A0A2S7Q571_A0A2S7Q571_9HELO_2070412 are exactly identical!
WARNING: Duplicate sequences found: 40

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P35520/3_mltree/P35520.raxml.reduced.phy

Alignment comprises 1 partitions and 443 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 443 / 443
Gaps: 9.06 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P35520/3_mltree/P35520.raxml.rba

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

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

[00:00:00] Generating 20 random starting tree(s) with 1001 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 64 / 5120
[00:00:00] Data distribution: max. searches per worker: 20

Starting ML tree search with 20 distinct starting trees

[00:00:00 -588923.518154] Initial branch length optimization
[00:00:02 -497996.387217] Model parameter optimization (eps = 10.000000)
[00:00:37 -496013.953717] AUTODETECT spr round 1 (radius: 5)
[00:02:13 -377491.829144] AUTODETECT spr round 2 (radius: 10)
[00:04:02 -297848.373403] AUTODETECT spr round 3 (radius: 15)
[00:05:59 -271702.422421] AUTODETECT spr round 4 (radius: 20)
[00:08:58 -234894.904764] AUTODETECT spr round 5 (radius: 25)
[00:11:44 -228892.569832] SPR radius for FAST iterations: 25 (autodetect)
[00:11:45 -228892.569832] Model parameter optimization (eps = 3.000000)
[00:12:04 -228631.696059] FAST spr round 1 (radius: 25)
[00:14:18 -188821.173622] FAST spr round 2 (radius: 25)
[00:16:03 -187338.517735] FAST spr round 3 (radius: 25)
[00:17:35 -187263.460853] FAST spr round 4 (radius: 25)
[00:18:58 -187249.615808] FAST spr round 5 (radius: 25)
[00:20:17 -187245.929451] FAST spr round 6 (radius: 25)
[00:21:34 -187245.929417] Model parameter optimization (eps = 1.000000)
[00:21:42 -187244.226560] SLOW spr round 1 (radius: 5)
[00:23:34 -187184.797410] SLOW spr round 2 (radius: 5)
[00:25:19 -187171.483929] SLOW spr round 3 (radius: 5)
[00:27:00 -187165.764945] SLOW spr round 4 (radius: 5)
[00:28:37 -187165.764932] SLOW spr round 5 (radius: 10)
[00:30:20 -187155.336831] SLOW spr round 6 (radius: 5)
[00:32:27 -187147.138548] SLOW spr round 7 (radius: 5)
[00:34:17 -187145.386047] SLOW spr round 8 (radius: 5)
[00:35:59 -187145.386034] SLOW spr round 9 (radius: 10)
[00:37:40 -187144.504549] SLOW spr round 10 (radius: 5)
[00:39:43 -187143.444258] SLOW spr round 11 (radius: 5)
[00:41:32 -187143.444250] SLOW spr round 12 (radius: 10)
[00:43:16 -187143.444249] SLOW spr round 13 (radius: 15)
[00:45:53 -187143.444249] SLOW spr round 14 (radius: 20)
[00:49:37 -187143.444248] SLOW spr round 15 (radius: 25)
[00:54:23 -187143.444247] Model parameter optimization (eps = 0.100000)

[00:54:27] ML tree search #1, logLikelihood: -187143.405299

[00:54:28 -587518.063589] Initial branch length optimization
[00:54:32 -496898.073696] Model parameter optimization (eps = 10.000000)
[00:55:02 -495013.840765] AUTODETECT spr round 1 (radius: 5)
[00:56:40 -382196.826424] AUTODETECT spr round 2 (radius: 10)
[00:58:31 -303100.933603] AUTODETECT spr round 3 (radius: 15)
[01:00:28 -270090.416758] AUTODETECT spr round 4 (radius: 20)
[01:02:54 -235551.381539] AUTODETECT spr round 5 (radius: 25)
[01:05:29 -224947.402471] SPR radius for FAST iterations: 25 (autodetect)
[01:05:29 -224947.402471] Model parameter optimization (eps = 3.000000)
[01:05:46 -224694.578433] FAST spr round 1 (radius: 25)
[01:07:58 -189479.461516] FAST spr round 2 (radius: 25)
[01:09:42 -187356.243425] FAST spr round 3 (radius: 25)
[01:11:14 -187245.689905] FAST spr round 4 (radius: 25)
[01:12:38 -187229.403000] FAST spr round 5 (radius: 25)
[01:13:59 -187220.926526] FAST spr round 6 (radius: 25)
[01:15:19 -187218.467379] FAST spr round 7 (radius: 25)
[01:16:36 -187218.467340] Model parameter optimization (eps = 1.000000)
[01:16:49 -187215.880851] SLOW spr round 1 (radius: 5)
[01:18:36 -187171.095204] SLOW spr round 2 (radius: 5)
[01:20:20 -187168.081085] SLOW spr round 3 (radius: 5)
[01:21:59 -187167.087741] SLOW spr round 4 (radius: 5)
[01:23:37 -187167.087701] SLOW spr round 5 (radius: 10)
[01:25:20 -187162.014164] SLOW spr round 6 (radius: 5)
[01:27:25 -187153.264542] SLOW spr round 7 (radius: 5)
[01:29:17 -187150.482973] SLOW spr round 8 (radius: 5)
[01:31:00 -187148.629232] SLOW spr round 9 (radius: 5)
[01:32:40 -187148.628838] SLOW spr round 10 (radius: 10)
[01:34:23 -187148.608184] SLOW spr round 11 (radius: 15)
[01:37:15 -187145.276884] SLOW spr round 12 (radius: 5)
[01:39:21 -187136.772342] SLOW spr round 13 (radius: 5)
[01:41:14 -187131.200737] SLOW spr round 14 (radius: 5)
[01:42:57 -187131.200393] SLOW spr round 15 (radius: 10)
[01:44:40 -187131.200392] SLOW spr round 16 (radius: 15)
[01:47:31 -187131.200391] SLOW spr round 17 (radius: 20)
[01:51:25 -187131.200391] SLOW spr round 18 (radius: 25)
[01:56:37 -187131.200391] Model parameter optimization (eps = 0.100000)

[01:56:44] ML tree search #2, logLikelihood: -187131.020265

[01:56:45 -588742.492919] Initial branch length optimization
[01:56:48 -498685.156375] Model parameter optimization (eps = 10.000000)
[01:57:27 -496665.237890] AUTODETECT spr round 1 (radius: 5)
[01:59:05 -377413.517615] AUTODETECT spr round 2 (radius: 10)
[02:00:55 -298067.958710] AUTODETECT spr round 3 (radius: 15)
[02:02:54 -250966.687390] AUTODETECT spr round 4 (radius: 20)
[02:05:19 -227741.492120] AUTODETECT spr round 5 (radius: 25)
[02:07:34 -217855.149022] SPR radius for FAST iterations: 25 (autodetect)
[02:07:34 -217855.149022] Model parameter optimization (eps = 3.000000)
[02:07:54 -217640.276698] FAST spr round 1 (radius: 25)
[02:09:58 -189355.850118] FAST spr round 2 (radius: 25)
[02:11:40 -187324.892963] FAST spr round 3 (radius: 25)
[02:13:10 -187237.098567] FAST spr round 4 (radius: 25)
[02:14:33 -187225.258048] FAST spr round 5 (radius: 25)
[02:15:53 -187225.257607] Model parameter optimization (eps = 1.000000)
[02:15:59 -187224.826516] SLOW spr round 1 (radius: 5)
[02:17:46 -187166.281020] SLOW spr round 2 (radius: 5)
[02:19:29 -187161.659452] SLOW spr round 3 (radius: 5)
[02:21:09 -187161.659439] SLOW spr round 4 (radius: 10)
[02:22:51 -187160.305342] SLOW spr round 5 (radius: 5)
[02:24:54 -187156.959998] SLOW spr round 6 (radius: 5)
[02:26:42 -187156.959914] SLOW spr round 7 (radius: 10)
[02:28:27 -187156.004090] SLOW spr round 8 (radius: 5)
[02:30:28 -187156.004089] SLOW spr round 9 (radius: 10)
[02:32:20 -187156.004089] SLOW spr round 10 (radius: 15)
[02:34:58 -187156.004089] SLOW spr round 11 (radius: 20)
[02:39:07 -187156.004089] SLOW spr round 12 (radius: 25)
[02:44:19 -187156.004089] Model parameter optimization (eps = 0.100000)

[02:44:26] ML tree search #3, logLikelihood: -187155.676147

[02:44:26 -589798.881362] Initial branch length optimization
[02:44:28 -498212.601436] Model parameter optimization (eps = 10.000000)
[02:45:02 -496254.035202] AUTODETECT spr round 1 (radius: 5)
[02:46:39 -383557.542816] AUTODETECT spr round 2 (radius: 10)
[02:48:33 -293010.085164] AUTODETECT spr round 3 (radius: 15)
[02:50:32 -251390.508966] AUTODETECT spr round 4 (radius: 20)
[02:53:18 -226253.492804] AUTODETECT spr round 5 (radius: 25)
[02:55:53 -220710.754584] SPR radius for FAST iterations: 25 (autodetect)
[02:55:53 -220710.754584] Model parameter optimization (eps = 3.000000)
[02:56:00 -220702.969949] FAST spr round 1 (radius: 25)
[02:58:14 -188960.270987] FAST spr round 2 (radius: 25)
[03:00:02 -187504.522574] FAST spr round 3 (radius: 25)
[03:01:40 -187408.009334] FAST spr round 4 (radius: 25)
[03:03:03 -187395.081343] FAST spr round 5 (radius: 25)
[03:04:23 -187388.475170] FAST spr round 6 (radius: 25)
[03:05:42 -187388.474721] Model parameter optimization (eps = 1.000000)
[03:06:00 -187219.529938] SLOW spr round 1 (radius: 5)
[03:07:50 -187168.165904] SLOW spr round 2 (radius: 5)
[03:09:33 -187161.188751] SLOW spr round 3 (radius: 5)
[03:11:14 -187158.088550] SLOW spr round 4 (radius: 5)
[03:12:53 -187158.088272] SLOW spr round 5 (radius: 10)
[03:14:37 -187147.066639] SLOW spr round 6 (radius: 5)
[03:16:45 -187135.842853] SLOW spr round 7 (radius: 5)
[03:18:35 -187135.842795] SLOW spr round 8 (radius: 10)
[03:20:20 -187134.875804] SLOW spr round 9 (radius: 5)
[03:22:23 -187134.875803] SLOW spr round 10 (radius: 10)
[03:24:16 -187134.875803] SLOW spr round 11 (radius: 15)
[03:26:54 -187134.875803] SLOW spr round 12 (radius: 20)
[03:31:01 -187134.875803] SLOW spr round 13 (radius: 25)
[03:36:11 -187134.875803] Model parameter optimization (eps = 0.100000)

[03:36:22] ML tree search #4, logLikelihood: -187134.169712

[03:36:22 -590535.287904] Initial branch length optimization
[03:36:25 -499030.115524] Model parameter optimization (eps = 10.000000)
[03:37:09 -497075.532842] AUTODETECT spr round 1 (radius: 5)
[03:38:47 -385071.915851] AUTODETECT spr round 2 (radius: 10)
[03:40:41 -285305.749781] AUTODETECT spr round 3 (radius: 15)
[03:42:46 -232996.290179] AUTODETECT spr round 4 (radius: 20)
[03:45:01 -221938.501787] AUTODETECT spr round 5 (radius: 25)
[03:47:45 -218293.796226] SPR radius for FAST iterations: 25 (autodetect)
[03:47:45 -218293.796226] Model parameter optimization (eps = 3.000000)
[03:48:01 -218090.570659] FAST spr round 1 (radius: 25)
[03:50:11 -189034.429714] FAST spr round 2 (radius: 25)
[03:51:54 -187297.035567] FAST spr round 3 (radius: 25)
[03:53:28 -187210.043772] FAST spr round 4 (radius: 25)
[03:54:49 -187207.347966] FAST spr round 5 (radius: 25)
[03:56:09 -187204.793007] FAST spr round 6 (radius: 25)
[03:57:26 -187204.792958] Model parameter optimization (eps = 1.000000)
[03:57:37 -187201.114558] SLOW spr round 1 (radius: 5)
[03:59:25 -187156.075330] SLOW spr round 2 (radius: 5)
[04:01:07 -187154.653464] SLOW spr round 3 (radius: 5)
[04:02:46 -187154.653377] SLOW spr round 4 (radius: 10)
[04:04:28 -187150.012810] SLOW spr round 5 (radius: 5)
[04:06:31 -187143.311893] SLOW spr round 6 (radius: 5)
[04:08:22 -187142.525149] SLOW spr round 7 (radius: 5)
[04:10:04 -187142.525145] SLOW spr round 8 (radius: 10)
[04:11:46 -187142.316398] SLOW spr round 9 (radius: 5)
[04:13:47 -187142.315933] SLOW spr round 10 (radius: 10)
[04:15:40 -187142.315917] SLOW spr round 11 (radius: 15)
[04:18:16 -187142.315916] SLOW spr round 12 (radius: 20)
[04:22:11 -187142.315916] SLOW spr round 13 (radius: 25)
[04:27:03 -187142.315916] Model parameter optimization (eps = 0.100000)

[04:27:07] ML tree search #5, logLikelihood: -187142.301982

[04:27:07 -588937.107803] Initial branch length optimization
[04:27:10 -498663.078375] Model parameter optimization (eps = 10.000000)
[04:27:39 -496782.783317] AUTODETECT spr round 1 (radius: 5)
[04:29:17 -383695.338544] AUTODETECT spr round 2 (radius: 10)
[04:31:12 -292082.131920] AUTODETECT spr round 3 (radius: 15)
[04:33:18 -235417.129369] AUTODETECT spr round 4 (radius: 20)
[04:35:55 -218892.607604] AUTODETECT spr round 5 (radius: 25)
[04:39:04 -213570.575118] SPR radius for FAST iterations: 25 (autodetect)
[04:39:04 -213570.575118] Model parameter optimization (eps = 3.000000)
[04:39:22 -213258.837394] FAST spr round 1 (radius: 25)
[04:41:31 -188286.588099] FAST spr round 2 (radius: 25)
[04:43:17 -187264.926576] FAST spr round 3 (radius: 25)
[04:44:50 -187212.390720] FAST spr round 4 (radius: 25)
[04:46:14 -187207.004428] FAST spr round 5 (radius: 25)
[04:47:34 -187207.004413] Model parameter optimization (eps = 1.000000)
[04:47:44 -187205.473668] SLOW spr round 1 (radius: 5)
[04:49:36 -187151.465887] SLOW spr round 2 (radius: 5)
[04:51:23 -187144.322464] SLOW spr round 3 (radius: 5)
[04:53:03 -187144.322401] SLOW spr round 4 (radius: 10)
[04:54:46 -187143.357583] SLOW spr round 5 (radius: 5)
[04:56:48 -187143.357582] SLOW spr round 6 (radius: 10)
[04:58:42 -187143.357582] SLOW spr round 7 (radius: 15)
[05:01:22 -187143.357582] SLOW spr round 8 (radius: 20)
[05:05:35 -187143.357582] SLOW spr round 9 (radius: 25)
[05:10:48 -187143.357582] Model parameter optimization (eps = 0.100000)

[05:10:57] ML tree search #6, logLikelihood: -187142.634278

[05:10:57 -591582.022020] Initial branch length optimization
[05:11:00 -498830.398592] Model parameter optimization (eps = 10.000000)
[05:11:22 -496853.834028] AUTODETECT spr round 1 (radius: 5)
[05:12:59 -380211.400306] AUTODETECT spr round 2 (radius: 10)
[05:14:53 -286930.760923] AUTODETECT spr round 3 (radius: 15)
[05:16:57 -229640.829341] AUTODETECT spr round 4 (radius: 20)
[05:19:11 -214369.694383] AUTODETECT spr round 5 (radius: 25)
[05:21:39 -209083.666866] SPR radius for FAST iterations: 25 (autodetect)
[05:21:39 -209083.666866] Model parameter optimization (eps = 3.000000)
[05:21:59 -208810.476934] FAST spr round 1 (radius: 25)
[05:24:05 -188173.573854] FAST spr round 2 (radius: 25)
[05:25:49 -187306.399552] FAST spr round 3 (radius: 25)
[05:27:21 -187268.334442] FAST spr round 4 (radius: 25)
[05:28:43 -187264.366696] FAST spr round 5 (radius: 25)
[05:30:03 -187264.366460] Model parameter optimization (eps = 1.000000)
[05:30:13 -187260.243186] SLOW spr round 1 (radius: 5)
[05:32:05 -187202.369054] SLOW spr round 2 (radius: 5)
[05:33:51 -187194.772409] SLOW spr round 3 (radius: 5)
[05:35:31 -187194.772277] SLOW spr round 4 (radius: 10)
[05:37:15 -187188.018688] SLOW spr round 5 (radius: 5)
[05:39:18 -187188.018522] SLOW spr round 6 (radius: 10)
[05:41:13 -187187.921499] SLOW spr round 7 (radius: 15)
[05:43:50 -187182.673467] SLOW spr round 8 (radius: 5)
[05:45:58 -187179.636756] SLOW spr round 9 (radius: 5)
[05:47:51 -187179.636550] SLOW spr round 10 (radius: 10)
[05:49:39 -187158.919541] SLOW spr round 11 (radius: 5)
[05:51:42 -187155.996718] SLOW spr round 12 (radius: 5)
[05:53:32 -187155.996699] SLOW spr round 13 (radius: 10)
[05:55:19 -187155.686303] SLOW spr round 14 (radius: 5)
[05:57:21 -187155.685843] SLOW spr round 15 (radius: 10)
[05:59:15 -187155.685827] SLOW spr round 16 (radius: 15)
[06:01:53 -187155.685827] SLOW spr round 17 (radius: 20)
[06:05:56 -187155.685827] SLOW spr round 18 (radius: 25)
[06:10:59 -187155.685827] Model parameter optimization (eps = 0.100000)

[06:11:04] ML tree search #7, logLikelihood: -187155.623970

[06:11:04 -588153.732439] Initial branch length optimization
[06:11:06 -496333.771491] Model parameter optimization (eps = 10.000000)
[06:11:33 -494382.236531] AUTODETECT spr round 1 (radius: 5)
[06:13:11 -378235.335410] AUTODETECT spr round 2 (radius: 10)
[06:15:03 -295829.521439] AUTODETECT spr round 3 (radius: 15)
[06:17:12 -234028.188461] AUTODETECT spr round 4 (radius: 20)
[06:19:39 -219049.060466] AUTODETECT spr round 5 (radius: 25)
[06:22:09 -212357.409676] SPR radius for FAST iterations: 25 (autodetect)
[06:22:09 -212357.409676] Model parameter optimization (eps = 3.000000)
[06:22:31 -212101.603733] FAST spr round 1 (radius: 25)
[06:24:34 -188640.435421] FAST spr round 2 (radius: 25)
[06:26:15 -187329.319385] FAST spr round 3 (radius: 25)
[06:27:47 -187221.915149] FAST spr round 4 (radius: 25)
[06:29:09 -187217.833772] FAST spr round 5 (radius: 25)
[06:30:29 -187217.667895] FAST spr round 6 (radius: 25)
[06:31:48 -187214.201173] FAST spr round 7 (radius: 25)
[06:33:06 -187214.200887] Model parameter optimization (eps = 1.000000)
[06:33:16 -187212.032414] SLOW spr round 1 (radius: 5)
[06:35:02 -187165.376335] SLOW spr round 2 (radius: 5)
[06:36:44 -187163.213971] SLOW spr round 3 (radius: 5)
[06:38:24 -187162.960325] SLOW spr round 4 (radius: 5)
[06:40:01 -187162.960267] SLOW spr round 5 (radius: 10)
[06:41:43 -187158.516451] SLOW spr round 6 (radius: 5)
[06:43:46 -187154.307630] SLOW spr round 7 (radius: 5)
[06:45:37 -187153.524655] SLOW spr round 8 (radius: 5)
[06:47:19 -187153.524652] SLOW spr round 9 (radius: 10)
[06:49:02 -187152.493309] SLOW spr round 10 (radius: 5)
[06:51:04 -187152.493176] SLOW spr round 11 (radius: 10)
[06:52:56 -187152.227547] SLOW spr round 12 (radius: 5)
[06:54:56 -187151.209669] SLOW spr round 13 (radius: 5)
[06:56:44 -187151.209411] SLOW spr round 14 (radius: 10)
[06:58:29 -187151.209409] SLOW spr round 15 (radius: 15)
[07:01:15 -187151.209409] SLOW spr round 16 (radius: 20)
[07:05:17 -187151.209409] SLOW spr round 17 (radius: 25)
[07:10:23 -187151.209409] Model parameter optimization (eps = 0.100000)

[07:10:28] ML tree search #8, logLikelihood: -187151.157187

[07:10:28 -586573.828371] Initial branch length optimization
[07:10:31 -496783.105057] Model parameter optimization (eps = 10.000000)
[07:11:01 -494819.462170] AUTODETECT spr round 1 (radius: 5)
[07:12:37 -376992.854230] AUTODETECT spr round 2 (radius: 10)
[07:14:28 -283034.506108] AUTODETECT spr round 3 (radius: 15)
[07:16:29 -243106.534600] AUTODETECT spr round 4 (radius: 20)
[07:18:52 -224154.933028] AUTODETECT spr round 5 (radius: 25)
[07:21:30 -218970.656071] SPR radius for FAST iterations: 25 (autodetect)
[07:21:30 -218970.656071] Model parameter optimization (eps = 3.000000)
[07:21:47 -218705.828497] FAST spr round 1 (radius: 25)
[07:23:58 -188438.888669] FAST spr round 2 (radius: 25)
[07:25:43 -187288.318399] FAST spr round 3 (radius: 25)
[07:27:17 -187240.856052] FAST spr round 4 (radius: 25)
[07:28:41 -187232.534272] FAST spr round 5 (radius: 25)
[07:30:02 -187223.150159] FAST spr round 6 (radius: 25)
[07:31:21 -187221.910941] FAST spr round 7 (radius: 25)
[07:32:40 -187221.910937] Model parameter optimization (eps = 1.000000)
[07:32:52 -187214.995714] SLOW spr round 1 (radius: 5)
[07:34:41 -187161.557657] SLOW spr round 2 (radius: 5)
[07:36:23 -187156.409750] SLOW spr round 3 (radius: 5)
[07:38:04 -187150.563258] SLOW spr round 4 (radius: 5)
[07:39:43 -187149.470818] SLOW spr round 5 (radius: 5)
[07:41:22 -187149.470764] SLOW spr round 6 (radius: 10)
[07:43:04 -187148.619877] SLOW spr round 7 (radius: 5)
[07:45:08 -187148.619370] SLOW spr round 8 (radius: 10)
[07:47:02 -187148.235698] SLOW spr round 9 (radius: 5)
[07:49:03 -187147.784395] SLOW spr round 10 (radius: 5)
[07:50:51 -187147.783119] SLOW spr round 11 (radius: 10)
[07:52:37 -187147.783051] SLOW spr round 12 (radius: 15)
[07:55:22 -187147.783047] SLOW spr round 13 (radius: 20)
[07:59:11 -187147.783047] SLOW spr round 14 (radius: 25)
[08:03:57 -187147.783047] Model parameter optimization (eps = 0.100000)

[08:04:05] ML tree search #9, logLikelihood: -187147.649268

[08:04:05 -590950.682469] Initial branch length optimization
[08:04:08 -499543.085548] Model parameter optimization (eps = 10.000000)
[08:04:44 -497586.601752] AUTODETECT spr round 1 (radius: 5)
[08:06:23 -380707.031637] AUTODETECT spr round 2 (radius: 10)
[08:08:15 -291090.350797] AUTODETECT spr round 3 (radius: 15)
[08:10:16 -247144.170516] AUTODETECT spr round 4 (radius: 20)
[08:12:31 -227120.375881] AUTODETECT spr round 5 (radius: 25)
[08:15:05 -222176.324098] SPR radius for FAST iterations: 25 (autodetect)
[08:15:05 -222176.324098] Model parameter optimization (eps = 3.000000)
[08:15:26 -221893.595215] FAST spr round 1 (radius: 25)
[08:17:38 -189895.315309] FAST spr round 2 (radius: 25)
[08:19:24 -187344.036611] FAST spr round 3 (radius: 25)
[08:20:57 -187236.760930] FAST spr round 4 (radius: 25)
[08:22:19 -187225.679340] FAST spr round 5 (radius: 25)
[08:23:38 -187225.679263] Model parameter optimization (eps = 1.000000)
[08:23:52 -187223.110489] SLOW spr round 1 (radius: 5)
[08:25:40 -187167.355043] SLOW spr round 2 (radius: 5)
[08:27:24 -187153.343009] SLOW spr round 3 (radius: 5)
[08:29:04 -187150.761511] SLOW spr round 4 (radius: 5)
[08:30:42 -187150.761386] SLOW spr round 5 (radius: 10)
[08:32:25 -187149.798873] SLOW spr round 6 (radius: 5)
[08:34:26 -187149.798873] SLOW spr round 7 (radius: 10)
[08:36:18 -187149.798873] SLOW spr round 8 (radius: 15)
[08:38:52 -187149.798873] SLOW spr round 9 (radius: 20)
[08:42:54 -187149.798873] SLOW spr round 10 (radius: 25)
[08:47:53 -187149.798873] Model parameter optimization (eps = 0.100000)

[08:48:06] ML tree search #10, logLikelihood: -187149.290672

[08:48:06 -588340.998181] Initial branch length optimization
[08:48:08 -496294.348377] Model parameter optimization (eps = 10.000000)
[08:48:49 -494392.654775] AUTODETECT spr round 1 (radius: 5)
[08:50:27 -379532.974048] AUTODETECT spr round 2 (radius: 10)
[08:52:20 -286511.140680] AUTODETECT spr round 3 (radius: 15)
[08:54:26 -244250.039029] AUTODETECT spr round 4 (radius: 20)
[08:56:50 -220526.868190] AUTODETECT spr round 5 (radius: 25)
[08:59:12 -217038.905811] SPR radius for FAST iterations: 25 (autodetect)
[08:59:12 -217038.905811] Model parameter optimization (eps = 3.000000)
[08:59:28 -216812.772683] FAST spr round 1 (radius: 25)
[09:01:38 -188827.107307] FAST spr round 2 (radius: 25)
[09:03:24 -187408.693699] FAST spr round 3 (radius: 25)
[09:05:01 -187274.271314] FAST spr round 4 (radius: 25)
[09:06:27 -187260.374938] FAST spr round 5 (radius: 25)
[09:07:47 -187259.904895] FAST spr round 6 (radius: 25)
[09:09:05 -187259.904881] Model parameter optimization (eps = 1.000000)
[09:09:17 -187258.072544] SLOW spr round 1 (radius: 5)
[09:11:06 -187215.255984] SLOW spr round 2 (radius: 5)
[09:12:50 -187202.790441] SLOW spr round 3 (radius: 5)
[09:14:30 -187198.124051] SLOW spr round 4 (radius: 5)
[09:16:08 -187198.124033] SLOW spr round 5 (radius: 10)
[09:17:51 -187193.239209] SLOW spr round 6 (radius: 5)
[09:19:54 -187191.426928] SLOW spr round 7 (radius: 5)
[09:21:44 -187191.426776] SLOW spr round 8 (radius: 10)
[09:23:30 -187190.476856] SLOW spr round 9 (radius: 5)
[09:25:32 -187190.476854] SLOW spr round 10 (radius: 10)
[09:27:25 -187190.476854] SLOW spr round 11 (radius: 15)
[09:30:01 -187190.476854] SLOW spr round 12 (radius: 20)
[09:33:49 -187190.476854] SLOW spr round 13 (radius: 25)
[09:38:29 -187190.476854] Model parameter optimization (eps = 0.100000)

[09:38:33] ML tree search #11, logLikelihood: -187190.432332

[09:38:33 -589413.511437] Initial branch length optimization
[09:38:36 -498226.885113] Model parameter optimization (eps = 10.000000)
[09:39:07 -496234.771603] AUTODETECT spr round 1 (radius: 5)
[09:40:45 -381957.283832] AUTODETECT spr round 2 (radius: 10)
[09:42:36 -293831.787130] AUTODETECT spr round 3 (radius: 15)
[09:44:37 -239915.334288] AUTODETECT spr round 4 (radius: 20)
[09:47:00 -219168.319860] AUTODETECT spr round 5 (radius: 25)
[09:49:31 -214908.111205] SPR radius for FAST iterations: 25 (autodetect)
[09:49:31 -214908.111205] Model parameter optimization (eps = 3.000000)
[09:49:49 -214633.070557] FAST spr round 1 (radius: 25)
[09:51:58 -188154.427781] FAST spr round 2 (radius: 25)
[09:53:40 -187326.825100] FAST spr round 3 (radius: 25)
[09:55:13 -187260.518113] FAST spr round 4 (radius: 25)
[09:56:34 -187260.517753] Model parameter optimization (eps = 1.000000)
[09:56:47 -187257.905062] SLOW spr round 1 (radius: 5)
[09:58:40 -187184.330329] SLOW spr round 2 (radius: 5)
[10:00:28 -187163.001671] SLOW spr round 3 (radius: 5)
[10:02:11 -187153.700699] SLOW spr round 4 (radius: 5)
[10:03:50 -187153.700649] SLOW spr round 5 (radius: 10)
[10:05:33 -187149.677640] SLOW spr round 6 (radius: 5)
[10:07:38 -187146.125209] SLOW spr round 7 (radius: 5)
[10:09:31 -187144.235712] SLOW spr round 8 (radius: 5)
[10:11:14 -187144.235604] SLOW spr round 9 (radius: 10)
[10:12:57 -187143.265670] SLOW spr round 10 (radius: 5)
[10:15:00 -187143.265668] SLOW spr round 11 (radius: 10)
[10:16:54 -187143.265667] SLOW spr round 12 (radius: 15)
[10:19:29 -187143.265665] SLOW spr round 13 (radius: 20)
[10:23:19 -187143.265664] SLOW spr round 14 (radius: 25)
[10:27:55 -187143.265662] Model parameter optimization (eps = 0.100000)

[10:27:59] ML tree search #12, logLikelihood: -187143.222221

[10:27:59 -590782.443311] Initial branch length optimization
[10:28:02 -497619.680996] Model parameter optimization (eps = 10.000000)
[10:28:38 -495717.703146] AUTODETECT spr round 1 (radius: 5)
[10:30:16 -381021.696540] AUTODETECT spr round 2 (radius: 10)
[10:32:08 -298508.598034] AUTODETECT spr round 3 (radius: 15)
[10:34:08 -246595.702511] AUTODETECT spr round 4 (radius: 20)
[10:36:30 -226959.634844] AUTODETECT spr round 5 (radius: 25)
[10:39:08 -219019.455697] SPR radius for FAST iterations: 25 (autodetect)
[10:39:08 -219019.455697] Model parameter optimization (eps = 3.000000)
[10:39:30 -218791.123463] FAST spr round 1 (radius: 25)
[10:41:41 -188621.260646] FAST spr round 2 (radius: 25)
[10:43:28 -187346.139841] FAST spr round 3 (radius: 25)
[10:45:03 -187244.782380] FAST spr round 4 (radius: 25)
[10:46:28 -187220.828719] FAST spr round 5 (radius: 25)
[10:47:48 -187219.490681] FAST spr round 6 (radius: 25)
[10:49:07 -187215.458085] FAST spr round 7 (radius: 25)
[10:50:26 -187215.458041] Model parameter optimization (eps = 1.000000)
[10:50:36 -187213.904541] SLOW spr round 1 (radius: 5)
[10:52:27 -187163.619552] SLOW spr round 2 (radius: 5)
[10:54:12 -187157.435467] SLOW spr round 3 (radius: 5)
[10:55:51 -187157.435467] SLOW spr round 4 (radius: 10)
[10:57:34 -187157.435467] SLOW spr round 5 (radius: 15)
[11:00:28 -187157.435467] SLOW spr round 6 (radius: 20)
[11:04:28 -187157.435466] SLOW spr round 7 (radius: 25)
[11:09:37 -187157.435466] Model parameter optimization (eps = 0.100000)

[11:09:44] ML tree search #13, logLikelihood: -187157.210284

[11:09:44 -587047.994437] Initial branch length optimization
[11:09:47 -497634.613886] Model parameter optimization (eps = 10.000000)
[11:10:12 -495710.143629] AUTODETECT spr round 1 (radius: 5)
[11:11:50 -378571.448779] AUTODETECT spr round 2 (radius: 10)
[11:13:43 -291620.977134] AUTODETECT spr round 3 (radius: 15)
[11:15:47 -255465.846507] AUTODETECT spr round 4 (radius: 20)
[11:18:24 -227457.515760] AUTODETECT spr round 5 (radius: 25)
[11:20:53 -220228.035746] SPR radius for FAST iterations: 25 (autodetect)
[11:20:53 -220228.035746] Model parameter optimization (eps = 3.000000)
[11:21:10 -219968.385704] FAST spr round 1 (radius: 25)
[11:23:25 -188667.089124] FAST spr round 2 (radius: 25)
[11:25:11 -187314.560458] FAST spr round 3 (radius: 25)
[11:26:46 -187252.875054] FAST spr round 4 (radius: 25)
[11:28:12 -187227.237912] FAST spr round 5 (radius: 25)
[11:29:32 -187224.099286] FAST spr round 6 (radius: 25)
[11:30:51 -187224.099263] Model parameter optimization (eps = 1.000000)
[11:31:02 -187221.690937] SLOW spr round 1 (radius: 5)
[11:32:52 -187159.870826] SLOW spr round 2 (radius: 5)
[11:34:36 -187154.167867] SLOW spr round 3 (radius: 5)
[11:36:15 -187154.167744] SLOW spr round 4 (radius: 10)
[11:37:58 -187145.032747] SLOW spr round 5 (radius: 5)
[11:40:02 -187144.282328] SLOW spr round 6 (radius: 5)
[11:41:51 -187144.282302] SLOW spr round 7 (radius: 10)
[11:43:37 -187144.282300] SLOW spr round 8 (radius: 15)
[11:46:23 -187144.282299] SLOW spr round 9 (radius: 20)
[11:50:22 -187143.737680] SLOW spr round 10 (radius: 5)
[11:52:30 -187143.737617] SLOW spr round 11 (radius: 10)
[11:54:31 -187143.737614] SLOW spr round 12 (radius: 15)
[11:57:06 -187143.737612] SLOW spr round 13 (radius: 20)
[12:01:12 -187143.737610] SLOW spr round 14 (radius: 25)
[12:06:12 -187143.737609] Model parameter optimization (eps = 0.100000)

[12:06:19] ML tree search #14, logLikelihood: -187143.658903

[12:06:19 -589525.260035] Initial branch length optimization
[12:06:21 -497532.012637] Model parameter optimization (eps = 10.000000)
[12:06:54 -495634.629905] AUTODETECT spr round 1 (radius: 5)
[12:08:32 -377323.051286] AUTODETECT spr round 2 (radius: 10)
[12:10:22 -291006.917912] AUTODETECT spr round 3 (radius: 15)
[12:12:29 -236004.850322] AUTODETECT spr round 4 (radius: 20)
[12:14:59 -220494.175252] AUTODETECT spr round 5 (radius: 25)
[12:17:33 -217558.363699] SPR radius for FAST iterations: 25 (autodetect)
[12:17:33 -217558.363699] Model parameter optimization (eps = 3.000000)
[12:17:51 -217323.481109] FAST spr round 1 (radius: 25)
[12:20:04 -189136.613608] FAST spr round 2 (radius: 25)
[12:21:51 -187328.043783] FAST spr round 3 (radius: 25)
[12:23:24 -187216.325529] FAST spr round 4 (radius: 25)
[12:24:47 -187205.009043] FAST spr round 5 (radius: 25)
[12:26:06 -187205.008854] Model parameter optimization (eps = 1.000000)
[12:26:11 -187204.729518] SLOW spr round 1 (radius: 5)
[12:28:03 -187160.693083] SLOW spr round 2 (radius: 5)
[12:29:48 -187145.099758] SLOW spr round 3 (radius: 5)
[12:31:27 -187145.099725] SLOW spr round 4 (radius: 10)
[12:33:10 -187142.987054] SLOW spr round 5 (radius: 5)
[12:35:16 -187133.807517] SLOW spr round 6 (radius: 5)
[12:37:07 -187130.864069] SLOW spr round 7 (radius: 5)
[12:38:50 -187130.626645] SLOW spr round 8 (radius: 5)
[12:40:30 -187130.626644] SLOW spr round 9 (radius: 10)
[12:42:13 -187128.855952] SLOW spr round 10 (radius: 5)
[12:44:16 -187126.474923] SLOW spr round 11 (radius: 5)
[12:46:05 -187126.474918] SLOW spr round 12 (radius: 10)
[12:47:49 -187126.474917] SLOW spr round 13 (radius: 15)
[12:50:31 -187126.474917] SLOW spr round 14 (radius: 20)
[12:54:23 -187126.474917] SLOW spr round 15 (radius: 25)
[12:59:18 -187126.474917] Model parameter optimization (eps = 0.100000)

[12:59:23] ML tree search #15, logLikelihood: -187126.255716

[12:59:23 -590308.576531] Initial branch length optimization
[12:59:26 -495809.181239] Model parameter optimization (eps = 10.000000)
[13:00:00 -493977.920605] AUTODETECT spr round 1 (radius: 5)
[13:01:37 -384185.539924] AUTODETECT spr round 2 (radius: 10)
[13:03:29 -300317.427721] AUTODETECT spr round 3 (radius: 15)
[13:05:33 -244867.779497] AUTODETECT spr round 4 (radius: 20)
[13:07:44 -225794.161478] AUTODETECT spr round 5 (radius: 25)
[13:10:03 -221812.400406] SPR radius for FAST iterations: 25 (autodetect)
[13:10:03 -221812.400406] Model parameter optimization (eps = 3.000000)
[13:10:22 -221454.226567] FAST spr round 1 (radius: 25)
[13:12:30 -189930.808293] FAST spr round 2 (radius: 25)
[13:14:16 -187494.442185] FAST spr round 3 (radius: 25)
[13:15:50 -187265.890686] FAST spr round 4 (radius: 25)
[13:17:16 -187221.687160] FAST spr round 5 (radius: 25)
[13:18:37 -187218.101303] FAST spr round 6 (radius: 25)
[13:19:56 -187212.473971] FAST spr round 7 (radius: 25)
[13:21:14 -187212.473818] Model parameter optimization (eps = 1.000000)
[13:21:17 -187212.402579] SLOW spr round 1 (radius: 5)
[13:23:04 -187173.254828] SLOW spr round 2 (radius: 5)
[13:24:47 -187165.154266] SLOW spr round 3 (radius: 5)
[13:26:25 -187165.154239] SLOW spr round 4 (radius: 10)
[13:28:05 -187161.610678] SLOW spr round 5 (radius: 5)
[13:30:08 -187159.381107] SLOW spr round 6 (radius: 5)
[13:31:58 -187157.272631] SLOW spr round 7 (radius: 5)
[13:33:39 -187157.272503] SLOW spr round 8 (radius: 10)
[13:35:21 -187157.272499] SLOW spr round 9 (radius: 15)
[13:38:04 -187155.148424] SLOW spr round 10 (radius: 5)
[13:40:08 -187144.721508] SLOW spr round 11 (radius: 5)
[13:41:57 -187144.634648] SLOW spr round 12 (radius: 10)
[13:43:42 -187144.634610] SLOW spr round 13 (radius: 15)
[13:46:19 -187144.634610] SLOW spr round 14 (radius: 20)
[13:50:06 -187144.634610] SLOW spr round 15 (radius: 25)
[13:54:57 -187144.634610] Model parameter optimization (eps = 0.100000)

[13:55:09] ML tree search #16, logLikelihood: -187137.420398

[13:55:09 -587703.506956] Initial branch length optimization
[13:55:11 -498064.169418] Model parameter optimization (eps = 10.000000)
[13:55:42 -496116.981841] AUTODETECT spr round 1 (radius: 5)
[13:57:20 -384740.339399] AUTODETECT spr round 2 (radius: 10)
[13:59:10 -301417.875950] AUTODETECT spr round 3 (radius: 15)
[14:01:11 -249337.671478] AUTODETECT spr round 4 (radius: 20)
[14:03:26 -226537.700512] AUTODETECT spr round 5 (radius: 25)
[14:06:07 -217920.864516] SPR radius for FAST iterations: 25 (autodetect)
[14:06:07 -217920.864516] Model parameter optimization (eps = 3.000000)
[14:06:24 -217643.590374] FAST spr round 1 (radius: 25)
[14:08:35 -188275.475190] FAST spr round 2 (radius: 25)
[14:10:13 -187288.863367] FAST spr round 3 (radius: 25)
[14:11:43 -187229.575744] FAST spr round 4 (radius: 25)
[14:13:04 -187229.537403] Model parameter optimization (eps = 1.000000)
[14:13:16 -187226.603414] SLOW spr round 1 (radius: 5)
[14:15:06 -187171.383022] SLOW spr round 2 (radius: 5)
[14:16:52 -187151.426798] SLOW spr round 3 (radius: 5)
[14:18:33 -187147.734672] SLOW spr round 4 (radius: 5)
[14:20:15 -187142.059962] SLOW spr round 5 (radius: 5)
[14:21:53 -187142.059862] SLOW spr round 6 (radius: 10)
[14:23:35 -187137.217980] SLOW spr round 7 (radius: 5)
[14:25:38 -187135.108897] SLOW spr round 8 (radius: 5)
[14:27:27 -187135.108841] SLOW spr round 9 (radius: 10)
[14:29:12 -187135.108841] SLOW spr round 10 (radius: 15)
[14:31:58 -187132.261582] SLOW spr round 11 (radius: 5)
[14:34:05 -187127.006563] SLOW spr round 12 (radius: 5)
[14:35:58 -187127.006415] SLOW spr round 13 (radius: 10)
[14:37:43 -187127.006414] SLOW spr round 14 (radius: 15)
[14:40:28 -187127.006414] SLOW spr round 15 (radius: 20)
[14:44:32 -187127.006414] SLOW spr round 16 (radius: 25)
[14:49:45 -187127.006414] Model parameter optimization (eps = 0.100000)

[14:49:52] ML tree search #17, logLikelihood: -187126.373554

[14:49:52 -592158.667371] Initial branch length optimization
[14:49:55 -501211.321380] Model parameter optimization (eps = 10.000000)
[14:50:32 -499145.603105] AUTODETECT spr round 1 (radius: 5)
[14:52:09 -384703.939802] AUTODETECT spr round 2 (radius: 10)
[14:54:00 -295230.435727] AUTODETECT spr round 3 (radius: 15)
[14:56:04 -241590.980112] AUTODETECT spr round 4 (radius: 20)
[14:58:16 -225757.212261] AUTODETECT spr round 5 (radius: 25)
[15:00:38 -219120.270243] SPR radius for FAST iterations: 25 (autodetect)
[15:00:38 -219120.270243] Model parameter optimization (eps = 3.000000)
[15:00:58 -218888.063774] FAST spr round 1 (radius: 25)
[15:03:08 -189869.956625] FAST spr round 2 (radius: 25)
[15:04:54 -187632.159801] FAST spr round 3 (radius: 25)
[15:06:28 -187246.132609] FAST spr round 4 (radius: 25)
[15:07:53 -187220.213496] FAST spr round 5 (radius: 25)
[15:09:13 -187218.162601] FAST spr round 6 (radius: 25)
[15:10:31 -187218.162536] Model parameter optimization (eps = 1.000000)
[15:10:42 -187215.533259] SLOW spr round 1 (radius: 5)
[15:12:32 -187174.395931] SLOW spr round 2 (radius: 5)
[15:14:15 -187172.051992] SLOW spr round 3 (radius: 5)
[15:15:54 -187172.051955] SLOW spr round 4 (radius: 10)
[15:17:36 -187172.051955] SLOW spr round 5 (radius: 15)
[15:20:22 -187172.051955] SLOW spr round 6 (radius: 20)
[15:24:09 -187172.051955] SLOW spr round 7 (radius: 25)
[15:29:03 -187172.051955] Model parameter optimization (eps = 0.100000)

[15:29:07] ML tree search #18, logLikelihood: -187172.007128

[15:29:07 -589691.332482] Initial branch length optimization
[15:29:09 -498973.874757] Model parameter optimization (eps = 10.000000)
[15:29:35 -497010.437706] AUTODETECT spr round 1 (radius: 5)
[15:31:13 -378318.832178] AUTODETECT spr round 2 (radius: 10)
[15:33:04 -301536.994194] AUTODETECT spr round 3 (radius: 15)
[15:35:09 -250396.978569] AUTODETECT spr round 4 (radius: 20)
[15:37:33 -225724.014437] AUTODETECT spr round 5 (radius: 25)
[15:40:06 -220483.315160] SPR radius for FAST iterations: 25 (autodetect)
[15:40:06 -220483.315160] Model parameter optimization (eps = 3.000000)
[15:40:23 -220195.076347] FAST spr round 1 (radius: 25)
[15:42:36 -188761.999120] FAST spr round 2 (radius: 25)
[15:44:16 -187340.450660] FAST spr round 3 (radius: 25)
[15:45:49 -187242.499419] FAST spr round 4 (radius: 25)
[15:47:12 -187232.458391] FAST spr round 5 (radius: 25)
[15:48:32 -187232.232540] FAST spr round 6 (radius: 25)
[15:49:50 -187232.232081] Model parameter optimization (eps = 1.000000)
[15:49:55 -187231.943027] SLOW spr round 1 (radius: 5)
[15:51:46 -187180.940074] SLOW spr round 2 (radius: 5)
[15:53:30 -187162.630272] SLOW spr round 3 (radius: 5)
[15:55:11 -187158.456485] SLOW spr round 4 (radius: 5)
[15:56:49 -187158.456468] SLOW spr round 5 (radius: 10)
[15:58:31 -187157.495593] SLOW spr round 6 (radius: 5)
[16:00:34 -187155.120479] SLOW spr round 7 (radius: 5)
[16:02:24 -187155.120475] SLOW spr round 8 (radius: 10)
[16:04:09 -187155.056237] SLOW spr round 9 (radius: 15)
[16:06:50 -187155.055786] SLOW spr round 10 (radius: 20)
[16:10:29 -187153.420628] SLOW spr round 11 (radius: 5)
[16:12:37 -187152.420429] SLOW spr round 12 (radius: 5)
[16:14:30 -187152.420328] SLOW spr round 13 (radius: 10)
[16:16:17 -187151.585015] SLOW spr round 14 (radius: 5)
[16:18:18 -187151.584831] SLOW spr round 15 (radius: 10)
[16:20:08 -187151.500528] SLOW spr round 16 (radius: 15)
[16:22:43 -187151.499942] SLOW spr round 17 (radius: 20)
[16:26:35 -187151.499929] SLOW spr round 18 (radius: 25)
[16:31:20 -187151.499929] Model parameter optimization (eps = 0.100000)

[16:31:28] ML tree search #19, logLikelihood: -187151.282755

[16:31:28 -591771.441362] Initial branch length optimization
[16:31:30 -500321.692967] Model parameter optimization (eps = 10.000000)
[16:31:58 -498326.600627] AUTODETECT spr round 1 (radius: 5)
[16:33:35 -381953.845847] AUTODETECT spr round 2 (radius: 10)
[16:35:31 -288590.353320] AUTODETECT spr round 3 (radius: 15)
[16:37:30 -241964.725167] AUTODETECT spr round 4 (radius: 20)
[16:39:42 -223131.805498] AUTODETECT spr round 5 (radius: 25)
[16:42:18 -216992.837851] SPR radius for FAST iterations: 25 (autodetect)
[16:42:18 -216992.837851] Model parameter optimization (eps = 3.000000)
[16:42:33 -216727.522594] FAST spr round 1 (radius: 25)
[16:44:45 -188321.957231] FAST spr round 2 (radius: 25)
[16:46:30 -187339.061037] FAST spr round 3 (radius: 25)
[16:48:01 -187258.182879] FAST spr round 4 (radius: 25)
[16:49:25 -187241.942503] FAST spr round 5 (radius: 25)
[16:50:45 -187241.942443] Model parameter optimization (eps = 1.000000)
[16:50:52 -187241.169475] SLOW spr round 1 (radius: 5)
[16:52:41 -187192.296672] SLOW spr round 2 (radius: 5)
[16:54:26 -187176.839238] SLOW spr round 3 (radius: 5)
[16:56:08 -187168.932379] SLOW spr round 4 (radius: 5)
[16:57:47 -187168.200311] SLOW spr round 5 (radius: 5)
[16:59:26 -187168.200286] SLOW spr round 6 (radius: 10)
[17:01:09 -187161.231009] SLOW spr round 7 (radius: 5)
[17:03:13 -187156.759064] SLOW spr round 8 (radius: 5)
[17:05:02 -187156.759007] SLOW spr round 9 (radius: 10)
[17:06:48 -187155.031321] SLOW spr round 10 (radius: 5)
[17:08:50 -187153.570490] SLOW spr round 11 (radius: 5)
[17:10:39 -187153.570477] SLOW spr round 12 (radius: 10)
[17:12:24 -187153.570477] SLOW spr round 13 (radius: 15)
[17:15:05 -187153.570477] SLOW spr round 14 (radius: 20)
[17:18:55 -187153.570477] SLOW spr round 15 (radius: 25)
[17:23:49 -187153.570477] Model parameter optimization (eps = 0.100000)

[17:23:58] ML tree search #20, logLikelihood: -187153.460088


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.218300,0.400961) (0.282521,0.480810) (0.278968,0.971025) (0.220211,2.296642) 
   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: -187126.255716

AIC score: 378262.511433 / AICc score: 8422322.511433 / BIC score: 386470.118822
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=443).
         This might lead to overfitting and compromise tree inference results!


Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P35520/3_mltree/P35520.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P35520/3_mltree/P35520.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P35520/3_mltree/P35520.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P35520/3_mltree/P35520.raxml.log

Analysis started: 18-Jun-2021 08:00:57 / finished: 19-Jun-2021 01:24:56

Elapsed time: 62638.390 seconds