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

System: Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM

RAxML-NG was called at 05-Jul-2021 05:14:22 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P51530/2_msa/P51530_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P51530/3_mltree/P51530 --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: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P51530/2_msa/P51530_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 619 sites

WARNING: Sequences tr_A0A2R8Q1I5_A0A2R8Q1I5_DANRE_7955 and tr_A0A2R8QJS2_A0A2R8QJS2_DANRE_7955 are exactly identical!
WARNING: Sequences tr_A0A2R8Q1I5_A0A2R8Q1I5_DANRE_7955 and tr_F1Q892_F1Q892_DANRE_7955 are exactly identical!
WARNING: Sequences tr_J3K905_J3K905_COCIM_246410 and tr_E9DI37_E9DI37_COCPS_443226 are exactly identical!
WARNING: Sequences tr_J3K905_J3K905_COCIM_246410 and tr_A0A0J6Y8E4_A0A0J6Y8E4_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B6QCK9_B6QCK9_TALMQ_441960 and tr_A0A093XID1_A0A093XID1_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_B2WIV2_B2WIV2_PYRTR_426418 and tr_A0A2W1DLH5_A0A2W1DLH5_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_C0NNJ3_C0NNJ3_AJECG_447093 and tr_C6HFT1_C6HFT1_AJECH_544712 are exactly identical!
WARNING: Sequences tr_C0NNJ3_C0NNJ3_AJECG_447093 and tr_F0UMG1_F0UMG1_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_B8PMG2_B8PMG2_POSPM_561896 and tr_A0A1X6N1E5_A0A1X6N1E5_9APHY_670580 are exactly identical!
WARNING: Sequences tr_B8N676_B8N676_ASPFN_332952 and tr_Q2UCH7_Q2UCH7_ASPOR_510516 are exactly identical!
WARNING: Sequences tr_B8N676_B8N676_ASPFN_332952 and tr_A0A1S9DQD0_A0A1S9DQD0_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_A0A179U8M2_A0A179U8M2_BLAGS_559298 and tr_C5GIH5_C5GIH5_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_F7E550_F7E550_ORNAN_9258 and tr_G3W9Z2_G3W9Z2_SARHA_9305 are exactly identical!
WARNING: Sequences tr_E9QTE7_E9QTE7_ASPFU_330879 and tr_A1D2B4_A1D2B4_NEOFI_331117 are exactly identical!
WARNING: Sequences tr_E9QTE7_E9QTE7_ASPFU_330879 and tr_A0A0S7DYZ0_A0A0S7DYZ0_9EURO_293939 are exactly identical!
WARNING: Sequences tr_C6HJ70_C6HJ70_AJECH_544712 and tr_F0UBM6_F0UBM6_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_J4KN16_J4KN16_BEAB2_655819 and tr_A0A0A2VX51_A0A0A2VX51_BEABA_1245745 are exactly identical!
WARNING: Sequences tr_J5JP07_J5JP07_BEAB2_655819 and tr_A0A0A2VUL1_A0A0A2VUL1_BEABA_1245745 are exactly identical!
WARNING: Sequences tr_J3NHF4_J3NHF4_GAGT3_644352 and tr_A0A0C4DZM6_A0A0C4DZM6_MAGP6_644358 are exactly identical!
WARNING: Sequences tr_A2QRH3_A2QRH3_ASPNC_425011 and tr_G7XNH3_G7XNH3_ASPKW_1033177 are exactly identical!
WARNING: Sequences tr_A2QRH3_A2QRH3_ASPNC_425011 and tr_G3YHG6_G3YHG6_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_A2QRH3_A2QRH3_ASPNC_425011 and tr_A0A100IJE5_A0A100IJE5_ASPNG_5061 are exactly identical!
WARNING: Sequences tr_A2QRH3_A2QRH3_ASPNC_425011 and tr_A0A146FTK0_A0A146FTK0_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_A0A1D5QWC5_A0A1D5QWC5_MACMU_9544 and tr_A0A2K6B619_A0A2K6B619_MACNE_9545 are exactly identical!
WARNING: Sequences tr_E6R3F9_E6R3F9_CRYGW_367775 and tr_A0A095CD96_A0A095CD96_CRYGR_294750 are exactly identical!
WARNING: Sequences tr_A0A0E0PDB1_A0A0E0PDB1_ORYRU_4529 and tr_A0A0D3FZH8_A0A0D3FZH8_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_F2SXP9_F2SXP9_TRIRC_559305 and tr_A0A178F795_A0A178F795_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_A0A0D2XQF9_A0A0D2XQF9_FUSO4_426428 and tr_A0A2H3HLU6_A0A2H3HLU6_FUSOX_327505 are exactly identical!
WARNING: Sequences sp_E1BMP7_DNA2_BOVIN_9913 and tr_K7DXW3_K7DXW3_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_L0P928_L0P928_PNEJ8_1209962 and tr_A0A0W4ZCZ9_A0A0W4ZCZ9_PNEJ7_1408657 are exactly identical!
WARNING: Sequences tr_L8FQX2_L8FQX2_PSED2_658429 and tr_A0A094CRK2_A0A094CRK2_9PEZI_1420910 are exactly identical!
WARNING: Sequences tr_L8FQX2_L8FQX2_PSED2_658429 and tr_A0A094GU29_A0A094GU29_9PEZI_1420912 are exactly identical!
WARNING: Sequences tr_L8FQX2_L8FQX2_PSED2_658429 and tr_A0A2P6FGT2_A0A2P6FGT2_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_W2PPM1_W2PPM1_PHYPN_761204 and tr_W2MKA1_W2MKA1_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_W2Q3V4_W2Q3V4_PHYPN_761204 and tr_A0A0W8CKT1_A0A0W8CKT1_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2Q3V4_W2Q3V4_PHYPN_761204 and tr_W2L3E7_W2L3E7_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A015KKB5_A0A015KKB5_9GLOM_1432141 and tr_A0A2H5RCW5_A0A2H5RCW5_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015LMI6_A0A015LMI6_9GLOM_1432141 and tr_A0A2H5U353_A0A2H5U353_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A078GC85_A0A078GC85_BRANA_3708 and tr_A0A0D3DYD3_A0A0D3DYD3_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A0A2KY17_A0A0A2KY17_PENIT_40296 and tr_A0A0A2IUG9_A0A0A2IUG9_PENEN_27334 are exactly identical!
WARNING: Sequences tr_A0A0F0IG97_A0A0F0IG97_ASPPU_1403190 and tr_A0A2G7G7H9_A0A2G7G7H9_9EURO_656916 are exactly identical!
WARNING: Sequences tr_A0A0F7VBZ6_A0A0F7VBZ6_9EURO_104259 and tr_A0A1Q5U250_A0A1Q5U250_9EURO_1316194 are exactly identical!
WARNING: Sequences tr_A0A0G4P8K6_A0A0G4P8K6_PENCA_1429867 and tr_A0A117NRI6_A0A117NRI6_9EURO_48697 are exactly identical!
WARNING: Sequences tr_A0A0G4P8K6_A0A0G4P8K6_PENCA_1429867 and tr_A0A1V6N9N4_A0A1V6N9N4_9EURO_60169 are exactly identical!
WARNING: Sequences tr_A0A0G4P8K6_A0A0G4P8K6_PENCA_1429867 and tr_A0A1V6R140_A0A1V6R140_9EURO_60172 are exactly identical!
WARNING: Sequences tr_A0A194WD92_A0A194WD92_9PEZI_105487 and tr_A0A194V3T5_A0A194V3T5_9PEZI_694573 are exactly identical!
WARNING: Sequences tr_A0A1S3U7R2_A0A1S3U7R2_VIGRR_3916 and tr_A0A3Q0EZM6_A0A3Q0EZM6_VIGRR_3916 are exactly identical!
WARNING: Sequences tr_A0A1S3U7R2_A0A1S3U7R2_VIGRR_3916 and tr_A0A3Q0F465_A0A3Q0F465_VIGRR_3916 are exactly identical!
WARNING: Sequences tr_A0A1R1X811_A0A1R1X811_9FUNG_133412 and tr_A0A1R1XL96_A0A1R1XL96_9FUNG_133412 are exactly identical!
WARNING: Sequences tr_A0A2D0QM64_A0A2D0QM64_ICTPU_7998 and tr_A0A2D0QMG9_A0A2D0QMG9_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QM64_A0A2D0QM64_ICTPU_7998 and tr_A0A2D0QMS6_A0A2D0QMS6_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QM64_A0A2D0QM64_ICTPU_7998 and tr_A0A2D0QQ61_A0A2D0QQ61_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2G3AF80_A0A2G3AF80_CAPAN_4072 and tr_A0A2G3DCA3_A0A2G3DCA3_CAPCH_80379 are exactly identical!
WARNING: Sequences tr_A0A2N5T4E6_A0A2N5T4E6_9BASI_200324 and tr_A0A2N5VCN6_A0A2N5VCN6_9BASI_200324 are exactly identical!
WARNING: Duplicate sequences found: 54

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P51530/3_mltree/P51530.raxml.reduced.phy

Alignment comprises 1 partitions and 618 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 619 / 618
Gaps: 5.56 %
Invariant sites: 0.97 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P51530/3_mltree/P51530.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 / 89 / 7120
[00:00:00] Data distribution: max. searches per worker: 20

Starting ML tree search with 20 distinct starting trees

[00:00:00 -1109288.009858] Initial branch length optimization
[00:00:05 -922134.791637] Model parameter optimization (eps = 10.000000)
[00:00:33 -920950.435578] AUTODETECT spr round 1 (radius: 5)
[00:02:25 -603849.339114] AUTODETECT spr round 2 (radius: 10)
[00:04:28 -449921.918134] AUTODETECT spr round 3 (radius: 15)
[00:06:43 -393098.539444] AUTODETECT spr round 4 (radius: 20)
[00:09:20 -343680.647693] AUTODETECT spr round 5 (radius: 25)
[00:11:55 -334309.275778] SPR radius for FAST iterations: 25 (autodetect)
[00:11:55 -334309.275778] Model parameter optimization (eps = 3.000000)
[00:12:09 -334221.002929] FAST spr round 1 (radius: 25)
[00:14:37 -291180.079083] FAST spr round 2 (radius: 25)
[00:16:27 -289749.187408] FAST spr round 3 (radius: 25)
[00:18:06 -289694.322530] FAST spr round 4 (radius: 25)
[00:19:33 -289683.771206] FAST spr round 5 (radius: 25)
[00:21:00 -289683.770772] Model parameter optimization (eps = 1.000000)
[00:21:10 -289681.608531] SLOW spr round 1 (radius: 5)
[00:23:11 -289585.680182] SLOW spr round 2 (radius: 5)
[00:25:03 -289582.519033] SLOW spr round 3 (radius: 5)
[00:26:50 -289582.518979] SLOW spr round 4 (radius: 10)
[00:28:41 -289582.518978] SLOW spr round 5 (radius: 15)
[00:31:48 -289582.518978] SLOW spr round 6 (radius: 20)
[00:35:47 -289582.518978] SLOW spr round 7 (radius: 25)
[00:40:35 -289582.518978] Model parameter optimization (eps = 0.100000)

[00:40:40] ML tree search #1, logLikelihood: -289582.482581

[00:40:40 -1113783.105559] Initial branch length optimization
[00:40:44 -918688.537025] Model parameter optimization (eps = 10.000000)
[00:41:08 -917564.685647] AUTODETECT spr round 1 (radius: 5)
[00:42:59 -629635.920202] AUTODETECT spr round 2 (radius: 10)
[00:45:07 -490463.577354] AUTODETECT spr round 3 (radius: 15)
[00:47:31 -389066.597503] AUTODETECT spr round 4 (radius: 20)
[00:49:46 -352786.706957] AUTODETECT spr round 5 (radius: 25)
[00:52:34 -344754.678474] SPR radius for FAST iterations: 25 (autodetect)
[00:52:34 -344754.678474] Model parameter optimization (eps = 3.000000)
[00:52:55 -344661.795527] FAST spr round 1 (radius: 25)
[00:55:26 -291623.391809] FAST spr round 2 (radius: 25)
[00:57:16 -289751.643787] FAST spr round 3 (radius: 25)
[00:58:55 -289669.256821] FAST spr round 4 (radius: 25)
[01:00:22 -289664.227106] FAST spr round 5 (radius: 25)
[01:01:38 -289664.226913] Model parameter optimization (eps = 1.000000)
[01:01:49 -289651.440436] SLOW spr round 1 (radius: 5)
[01:03:31 -289599.252008] SLOW spr round 2 (radius: 5)
[01:05:09 -289589.969380] SLOW spr round 3 (radius: 5)
[01:06:43 -289589.405337] SLOW spr round 4 (radius: 5)
[01:08:15 -289589.405303] SLOW spr round 5 (radius: 10)
[01:09:48 -289589.405303] SLOW spr round 6 (radius: 15)
[01:12:27 -289589.405303] SLOW spr round 7 (radius: 20)
[01:15:52 -289589.405303] SLOW spr round 8 (radius: 25)
[01:20:07 -289589.405303] Model parameter optimization (eps = 0.100000)

[01:20:14] ML tree search #2, logLikelihood: -289589.253397

[01:20:14 -1095750.859428] Initial branch length optimization
[01:20:17 -909933.390658] Model parameter optimization (eps = 10.000000)
[01:20:41 -908757.794258] AUTODETECT spr round 1 (radius: 5)
[01:22:32 -619559.983226] AUTODETECT spr round 2 (radius: 10)
[01:24:44 -475508.712488] AUTODETECT spr round 3 (radius: 15)
[01:27:26 -375312.332353] AUTODETECT spr round 4 (radius: 20)
[01:30:11 -343368.931015] AUTODETECT spr round 5 (radius: 25)
[01:33:10 -338342.911840] SPR radius for FAST iterations: 25 (autodetect)
[01:33:10 -338342.911840] Model parameter optimization (eps = 3.000000)
[01:33:25 -338274.624318] FAST spr round 1 (radius: 25)
[01:36:03 -292348.782300] FAST spr round 2 (radius: 25)
[01:38:01 -289776.333548] FAST spr round 3 (radius: 25)
[01:39:45 -289672.788676] FAST spr round 4 (radius: 25)
[01:41:21 -289652.577051] FAST spr round 5 (radius: 25)
[01:42:50 -289652.576719] Model parameter optimization (eps = 1.000000)
[01:43:02 -289650.043096] SLOW spr round 1 (radius: 5)
[01:45:08 -289592.316196] SLOW spr round 2 (radius: 5)
[01:47:01 -289587.667409] SLOW spr round 3 (radius: 5)
[01:48:48 -289587.076437] SLOW spr round 4 (radius: 5)
[01:50:40 -289587.076424] SLOW spr round 5 (radius: 10)
[01:52:36 -289586.617621] SLOW spr round 6 (radius: 5)
[01:55:00 -289581.334119] SLOW spr round 7 (radius: 5)
[01:57:06 -289581.334008] SLOW spr round 8 (radius: 10)
[01:59:05 -289581.334001] SLOW spr round 9 (radius: 15)
[02:02:15 -289581.333996] SLOW spr round 10 (radius: 20)
[02:06:23 -289581.333992] SLOW spr round 11 (radius: 25)
[02:11:23 -289581.333988] Model parameter optimization (eps = 0.100000)

[02:11:27] ML tree search #3, logLikelihood: -289581.311934

[02:11:27 -1107798.106065] Initial branch length optimization
[02:11:30 -914258.760634] Model parameter optimization (eps = 10.000000)
[02:11:57 -913178.178222] AUTODETECT spr round 1 (radius: 5)
[02:13:49 -628957.730033] AUTODETECT spr round 2 (radius: 10)
[02:15:57 -487567.625401] AUTODETECT spr round 3 (radius: 15)
[02:18:22 -415753.265027] AUTODETECT spr round 4 (radius: 20)
[02:20:47 -352994.204811] AUTODETECT spr round 5 (radius: 25)
[02:23:24 -336054.251935] SPR radius for FAST iterations: 25 (autodetect)
[02:23:24 -336054.251935] Model parameter optimization (eps = 3.000000)
[02:23:29 -336052.305851] FAST spr round 1 (radius: 25)
[02:25:55 -291364.936743] FAST spr round 2 (radius: 25)
[02:27:46 -289848.538385] FAST spr round 3 (radius: 25)
[02:29:22 -289761.526785] FAST spr round 4 (radius: 25)
[02:30:50 -289757.828464] FAST spr round 5 (radius: 25)
[02:32:14 -289757.828292] Model parameter optimization (eps = 1.000000)
[02:32:27 -289684.596893] SLOW spr round 1 (radius: 5)
[02:34:27 -289604.125691] SLOW spr round 2 (radius: 5)
[02:36:23 -289598.160519] SLOW spr round 3 (radius: 5)
[02:38:15 -289592.647186] SLOW spr round 4 (radius: 5)
[02:40:03 -289592.647131] SLOW spr round 5 (radius: 10)
[02:41:53 -289588.004938] SLOW spr round 6 (radius: 5)
[02:44:08 -289588.004242] SLOW spr round 7 (radius: 10)
[02:46:07 -289588.004203] SLOW spr round 8 (radius: 15)
[02:48:59 -289588.004197] SLOW spr round 9 (radius: 20)
[02:53:10 -289588.004192] SLOW spr round 10 (radius: 25)
[02:58:03 -289588.004188] Model parameter optimization (eps = 0.100000)

[02:58:09] ML tree search #4, logLikelihood: -289587.637992

[02:58:09 -1101401.717369] Initial branch length optimization
[02:58:12 -908826.956916] Model parameter optimization (eps = 10.000000)
[02:58:37 -907763.613923] AUTODETECT spr round 1 (radius: 5)
[03:00:11 -626827.508554] AUTODETECT spr round 2 (radius: 10)
[03:02:00 -467979.185277] AUTODETECT spr round 3 (radius: 15)
[03:04:02 -416698.357807] AUTODETECT spr round 4 (radius: 20)
[03:06:08 -381309.308626] AUTODETECT spr round 5 (radius: 25)
[03:08:26 -350897.413802] SPR radius for FAST iterations: 25 (autodetect)
[03:08:26 -350897.413802] Model parameter optimization (eps = 3.000000)
[03:08:32 -350893.785671] FAST spr round 1 (radius: 25)
[03:10:46 -291632.044327] FAST spr round 2 (radius: 25)
[03:12:26 -289840.645052] FAST spr round 3 (radius: 25)
[03:13:53 -289758.542365] FAST spr round 4 (radius: 25)
[03:15:09 -289754.484290] FAST spr round 5 (radius: 25)
[03:16:22 -289746.655813] FAST spr round 6 (radius: 25)
[03:17:33 -289746.653190] Model parameter optimization (eps = 1.000000)
[03:17:46 -289643.335578] SLOW spr round 1 (radius: 5)
[03:19:28 -289587.399472] SLOW spr round 2 (radius: 5)
[03:21:04 -289581.491029] SLOW spr round 3 (radius: 5)
[03:22:37 -289580.914215] SLOW spr round 4 (radius: 5)
[03:24:09 -289580.914199] SLOW spr round 5 (radius: 10)
[03:25:41 -289580.914194] SLOW spr round 6 (radius: 15)
[03:28:16 -289580.914189] SLOW spr round 7 (radius: 20)
[03:31:36 -289580.914184] SLOW spr round 8 (radius: 25)
[03:35:37 -289580.914180] Model parameter optimization (eps = 0.100000)

[03:35:41] ML tree search #5, logLikelihood: -289580.838384

[03:35:41 -1108055.034195] Initial branch length optimization
[03:35:44 -921102.084151] Model parameter optimization (eps = 10.000000)
[03:36:05 -919941.305560] AUTODETECT spr round 1 (radius: 5)
[03:37:41 -633298.774311] AUTODETECT spr round 2 (radius: 10)
[03:39:32 -476996.551621] AUTODETECT spr round 3 (radius: 15)
[03:41:43 -413873.072950] AUTODETECT spr round 4 (radius: 20)
[03:43:57 -384967.194016] AUTODETECT spr round 5 (radius: 25)
[03:46:18 -371575.606189] SPR radius for FAST iterations: 25 (autodetect)
[03:46:18 -371575.606189] Model parameter optimization (eps = 3.000000)
[03:46:34 -371444.446181] FAST spr round 1 (radius: 25)
[03:48:50 -294464.142161] FAST spr round 2 (radius: 25)
[03:50:26 -289903.839756] FAST spr round 3 (radius: 25)
[03:51:50 -289786.068370] FAST spr round 4 (radius: 25)
[03:53:09 -289750.530874] FAST spr round 5 (radius: 25)
[03:54:26 -289693.736198] FAST spr round 6 (radius: 25)
[03:55:38 -289693.735040] Model parameter optimization (eps = 1.000000)
[03:55:51 -289676.422792] SLOW spr round 1 (radius: 5)
[03:57:32 -289616.409741] SLOW spr round 2 (radius: 5)
[03:59:09 -289605.143305] SLOW spr round 3 (radius: 5)
[04:00:45 -289605.143135] SLOW spr round 4 (radius: 10)
[04:02:50 -289600.500769] SLOW spr round 5 (radius: 5)
[04:05:23 -289600.500741] SLOW spr round 6 (radius: 10)
[04:07:39 -289600.500736] SLOW spr round 7 (radius: 15)
[04:10:53 -289600.500731] SLOW spr round 8 (radius: 20)
[04:15:25 -289600.500726] SLOW spr round 9 (radius: 25)
[04:20:43 -289600.500722] Model parameter optimization (eps = 0.100000)

[04:20:51] ML tree search #6, logLikelihood: -289600.412963

[04:20:51 -1101852.602382] Initial branch length optimization
[04:20:55 -913323.762530] Model parameter optimization (eps = 10.000000)
[04:21:24 -912274.071000] AUTODETECT spr round 1 (radius: 5)
[04:23:29 -620119.331921] AUTODETECT spr round 2 (radius: 10)
[04:25:49 -473861.839632] AUTODETECT spr round 3 (radius: 15)
[04:28:22 -388942.488122] AUTODETECT spr round 4 (radius: 20)
[04:31:01 -347106.567777] AUTODETECT spr round 5 (radius: 25)
[04:33:55 -337398.563253] SPR radius for FAST iterations: 25 (autodetect)
[04:33:55 -337398.563253] Model parameter optimization (eps = 3.000000)
[04:34:01 -337395.988696] FAST spr round 1 (radius: 25)
[04:36:36 -291738.984553] FAST spr round 2 (radius: 25)
[04:38:43 -289907.773836] FAST spr round 3 (radius: 25)
[04:40:39 -289798.256810] FAST spr round 4 (radius: 25)
[04:42:23 -289777.214930] FAST spr round 5 (radius: 25)
[04:44:01 -289771.532112] FAST spr round 6 (radius: 25)
[04:45:37 -289771.531977] Model parameter optimization (eps = 1.000000)
[04:45:56 -289677.544635] SLOW spr round 1 (radius: 5)
[04:48:10 -289607.823601] SLOW spr round 2 (radius: 5)
[04:50:19 -289595.203518] SLOW spr round 3 (radius: 5)
[04:52:22 -289595.203422] SLOW spr round 4 (radius: 10)
[04:54:26 -289595.203414] SLOW spr round 5 (radius: 15)
[04:57:54 -289595.203409] SLOW spr round 6 (radius: 20)
[05:02:25 -289595.203405] SLOW spr round 7 (radius: 25)
[05:07:53 -289595.203401] Model parameter optimization (eps = 0.100000)

[05:07:58] ML tree search #7, logLikelihood: -289595.146662

[05:07:58 -1106463.978592] Initial branch length optimization
[05:08:01 -913178.449981] Model parameter optimization (eps = 10.000000)
[05:08:31 -912006.338242] AUTODETECT spr round 1 (radius: 5)
[05:10:37 -618791.044824] AUTODETECT spr round 2 (radius: 10)
[05:12:59 -485567.713488] AUTODETECT spr round 3 (radius: 15)
[05:15:33 -403665.444336] AUTODETECT spr round 4 (radius: 20)
[05:18:31 -362438.076874] AUTODETECT spr round 5 (radius: 25)
[05:21:49 -340535.427471] SPR radius for FAST iterations: 25 (autodetect)
[05:21:49 -340535.427471] Model parameter optimization (eps = 3.000000)
[05:22:06 -340437.024606] FAST spr round 1 (radius: 25)
[05:24:52 -291946.102672] FAST spr round 2 (radius: 25)
[05:26:59 -289889.844057] FAST spr round 3 (radius: 25)
[05:28:51 -289694.037169] FAST spr round 4 (radius: 25)
[05:30:33 -289664.574731] FAST spr round 5 (radius: 25)
[05:32:09 -289664.574121] Model parameter optimization (eps = 1.000000)
[05:32:14 -289663.960672] SLOW spr round 1 (radius: 5)
[05:34:30 -289576.481369] SLOW spr round 2 (radius: 5)
[05:36:39 -289571.759758] SLOW spr round 3 (radius: 5)
[05:38:42 -289571.759719] SLOW spr round 4 (radius: 10)
[05:40:47 -289571.759719] SLOW spr round 5 (radius: 15)
[05:44:15 -289571.759719] SLOW spr round 6 (radius: 20)
[05:48:43 -289571.759719] SLOW spr round 7 (radius: 25)
[05:54:05 -289571.759719] Model parameter optimization (eps = 0.100000)

[05:54:10] ML tree search #8, logLikelihood: -289571.696767

[05:54:10 -1099052.697825] Initial branch length optimization
[05:54:14 -908818.555339] Model parameter optimization (eps = 10.000000)
[05:54:44 -907703.277307] AUTODETECT spr round 1 (radius: 5)
[05:56:48 -613939.158546] AUTODETECT spr round 2 (radius: 10)
[05:59:13 -471671.476226] AUTODETECT spr round 3 (radius: 15)
[06:02:07 -406940.660518] AUTODETECT spr round 4 (radius: 20)
[06:04:53 -353524.095349] AUTODETECT spr round 5 (radius: 25)
[06:07:57 -339316.235908] SPR radius for FAST iterations: 25 (autodetect)
[06:07:57 -339316.235908] Model parameter optimization (eps = 3.000000)
[06:08:17 -339208.931834] FAST spr round 1 (radius: 25)
[06:11:08 -291425.573147] FAST spr round 2 (radius: 25)
[06:13:13 -289879.912358] FAST spr round 3 (radius: 25)
[06:15:10 -289746.049460] FAST spr round 4 (radius: 25)
[06:16:52 -289735.004222] FAST spr round 5 (radius: 25)
[06:18:29 -289735.001029] Model parameter optimization (eps = 1.000000)
[06:18:45 -289726.373672] SLOW spr round 1 (radius: 5)
[06:21:04 -289632.694812] SLOW spr round 2 (radius: 5)
[06:23:13 -289615.424938] SLOW spr round 3 (radius: 5)
[06:25:16 -289615.424792] SLOW spr round 4 (radius: 10)
[06:27:21 -289613.363307] SLOW spr round 5 (radius: 5)
[06:29:53 -289605.145771] SLOW spr round 6 (radius: 5)
[06:32:07 -289605.145752] SLOW spr round 7 (radius: 10)
[06:34:13 -289605.145747] SLOW spr round 8 (radius: 15)
[06:37:33 -289605.145743] SLOW spr round 9 (radius: 20)
[06:42:01 -289605.145738] SLOW spr round 10 (radius: 25)
[06:47:21 -289605.145733] Model parameter optimization (eps = 0.100000)

[06:47:31] ML tree search #9, logLikelihood: -289604.925341

[06:47:31 -1101555.197722] Initial branch length optimization
[06:47:34 -908123.570642] Model parameter optimization (eps = 10.000000)
[06:48:04 -907010.297981] AUTODETECT spr round 1 (radius: 5)
[06:50:11 -617000.625297] AUTODETECT spr round 2 (radius: 10)
[06:52:32 -492218.087759] AUTODETECT spr round 3 (radius: 15)
[06:55:05 -384150.859336] AUTODETECT spr round 4 (radius: 20)
[06:57:46 -340632.961350] AUTODETECT spr round 5 (radius: 25)
[07:00:12 -336638.352158] SPR radius for FAST iterations: 25 (autodetect)
[07:00:12 -336638.352158] Model parameter optimization (eps = 3.000000)
[07:00:25 -336558.048691] FAST spr round 1 (radius: 25)
[07:02:27 -291217.120170] FAST spr round 2 (radius: 25)
[07:04:06 -289806.651977] FAST spr round 3 (radius: 25)
[07:05:30 -289771.139761] FAST spr round 4 (radius: 25)
[07:06:49 -289755.235563] FAST spr round 5 (radius: 25)
[07:08:03 -289745.344927] FAST spr round 6 (radius: 25)
[07:09:16 -289743.654092] FAST spr round 7 (radius: 25)
[07:10:28 -289743.653685] Model parameter optimization (eps = 1.000000)
[07:10:37 -289742.371085] SLOW spr round 1 (radius: 5)
[07:12:21 -289645.278467] SLOW spr round 2 (radius: 5)
[07:13:59 -289616.055222] SLOW spr round 3 (radius: 5)
[07:15:34 -289615.722192] SLOW spr round 4 (radius: 5)
[07:17:07 -289615.722177] SLOW spr round 5 (radius: 10)
[07:18:42 -289614.940953] SLOW spr round 6 (radius: 5)
[07:20:38 -289614.940916] SLOW spr round 7 (radius: 10)
[07:22:23 -289614.940911] SLOW spr round 8 (radius: 15)
[07:24:50 -289614.940906] SLOW spr round 9 (radius: 20)
[07:28:28 -289614.940902] SLOW spr round 10 (radius: 25)
[07:33:51 -289614.940897] Model parameter optimization (eps = 0.100000)

[07:33:56] ML tree search #10, logLikelihood: -289614.881185

[07:33:56 -1102993.795416] Initial branch length optimization
[07:33:59 -917690.369270] Model parameter optimization (eps = 10.000000)
[07:34:39 -916482.041536] AUTODETECT spr round 1 (radius: 5)
[07:36:44 -621084.645002] AUTODETECT spr round 2 (radius: 10)
[07:39:06 -474278.980719] AUTODETECT spr round 3 (radius: 15)
[07:41:59 -401272.364676] AUTODETECT spr round 4 (radius: 20)
[07:44:44 -353482.491049] AUTODETECT spr round 5 (radius: 25)
[07:47:43 -346141.329232] SPR radius for FAST iterations: 25 (autodetect)
[07:47:43 -346141.329232] Model parameter optimization (eps = 3.000000)
[07:47:53 -346123.645931] FAST spr round 1 (radius: 25)
[07:50:48 -293962.269402] FAST spr round 2 (radius: 25)
[07:53:02 -289878.830250] FAST spr round 3 (radius: 25)
[07:54:59 -289727.261173] FAST spr round 4 (radius: 25)
[07:56:42 -289717.968416] FAST spr round 5 (radius: 25)
[07:58:19 -289716.290448] FAST spr round 6 (radius: 25)
[07:59:55 -289716.290424] Model parameter optimization (eps = 1.000000)
[08:00:08 -289637.733959] SLOW spr round 1 (radius: 5)
[08:02:24 -289588.248335] SLOW spr round 2 (radius: 5)
[08:04:31 -289583.662213] SLOW spr round 3 (radius: 5)
[08:06:34 -289583.662121] SLOW spr round 4 (radius: 10)
[08:08:37 -289583.662114] SLOW spr round 5 (radius: 15)
[08:12:02 -289583.662110] SLOW spr round 6 (radius: 20)
[08:16:28 -289583.662106] SLOW spr round 7 (radius: 25)
[08:21:48 -289583.662103] Model parameter optimization (eps = 0.100000)

[08:21:56] ML tree search #11, logLikelihood: -289583.533570

[08:21:56 -1108959.277988] Initial branch length optimization
[08:22:00 -920974.504118] Model parameter optimization (eps = 10.000000)
[08:22:27 -919807.972074] AUTODETECT spr round 1 (radius: 5)
[08:24:33 -602930.577664] AUTODETECT spr round 2 (radius: 10)
[08:26:54 -449096.157677] AUTODETECT spr round 3 (radius: 15)
[08:29:34 -353052.560778] AUTODETECT spr round 4 (radius: 20)
[08:32:25 -328168.821136] AUTODETECT spr round 5 (radius: 25)
[08:35:35 -326095.243015] SPR radius for FAST iterations: 25 (autodetect)
[08:35:35 -326095.243015] Model parameter optimization (eps = 3.000000)
[08:35:43 -326092.644374] FAST spr round 1 (radius: 25)
[08:38:30 -290815.414504] FAST spr round 2 (radius: 25)
[08:40:41 -289796.104309] FAST spr round 3 (radius: 25)
[08:42:37 -289730.575920] FAST spr round 4 (radius: 25)
[08:44:18 -289724.555138] FAST spr round 5 (radius: 25)
[08:45:55 -289723.745465] FAST spr round 6 (radius: 25)
[08:47:31 -289723.745346] Model parameter optimization (eps = 1.000000)
[08:47:43 -289646.645352] SLOW spr round 1 (radius: 5)
[08:50:01 -289587.279945] SLOW spr round 2 (radius: 5)
[08:52:11 -289581.932810] SLOW spr round 3 (radius: 5)
[08:54:13 -289581.932614] SLOW spr round 4 (radius: 10)
[08:56:16 -289579.233502] SLOW spr round 5 (radius: 5)
[08:58:48 -289575.556788] SLOW spr round 6 (radius: 5)
[09:01:02 -289575.556782] SLOW spr round 7 (radius: 10)
[09:03:09 -289575.426625] SLOW spr round 8 (radius: 5)
[09:05:40 -289575.271593] SLOW spr round 9 (radius: 5)
[09:07:54 -289575.271385] SLOW spr round 10 (radius: 10)
[09:10:00 -289575.271368] SLOW spr round 11 (radius: 15)
[09:13:20 -289575.271362] SLOW spr round 12 (radius: 20)
[09:17:44 -289575.271357] SLOW spr round 13 (radius: 25)
[09:22:57 -289575.271352] Model parameter optimization (eps = 0.100000)

[09:23:06] ML tree search #12, logLikelihood: -289574.980596

[09:23:07 -1108128.014735] Initial branch length optimization
[09:23:10 -920029.556723] Model parameter optimization (eps = 10.000000)
[09:23:45 -918787.782782] AUTODETECT spr round 1 (radius: 5)
[09:25:55 -612584.430968] AUTODETECT spr round 2 (radius: 10)
[09:28:12 -464565.191821] AUTODETECT spr round 3 (radius: 15)
[09:30:48 -398767.153965] AUTODETECT spr round 4 (radius: 20)
[09:33:37 -357002.016522] AUTODETECT spr round 5 (radius: 25)
[09:36:36 -339262.125170] SPR radius for FAST iterations: 25 (autodetect)
[09:36:36 -339262.125170] Model parameter optimization (eps = 3.000000)
[09:36:54 -339172.311805] FAST spr round 1 (radius: 25)
[09:39:39 -290941.081537] FAST spr round 2 (radius: 25)
[09:41:46 -289814.571063] FAST spr round 3 (radius: 25)
[09:43:42 -289681.395688] FAST spr round 4 (radius: 25)
[09:45:25 -289663.537451] FAST spr round 5 (radius: 25)
[09:47:02 -289663.537446] Model parameter optimization (eps = 1.000000)
[09:47:16 -289637.276430] SLOW spr round 1 (radius: 5)
[09:49:35 -289588.856512] SLOW spr round 2 (radius: 5)
[09:51:45 -289581.840477] SLOW spr round 3 (radius: 5)
[09:53:49 -289581.840406] SLOW spr round 4 (radius: 10)
[09:55:52 -289581.840406] SLOW spr round 5 (radius: 15)
[09:59:19 -289581.840406] SLOW spr round 6 (radius: 20)
[10:03:41 -289581.840406] SLOW spr round 7 (radius: 25)
[10:08:57 -289581.840406] Model parameter optimization (eps = 0.100000)

[10:09:04] ML tree search #13, logLikelihood: -289581.781188

[10:09:04 -1099995.109159] Initial branch length optimization
[10:09:07 -915573.020397] Model parameter optimization (eps = 10.000000)
[10:09:38 -914465.781119] AUTODETECT spr round 1 (radius: 5)
[10:11:46 -618013.868213] AUTODETECT spr round 2 (radius: 10)
[10:14:07 -473729.958803] AUTODETECT spr round 3 (radius: 15)
[10:16:45 -391986.544030] AUTODETECT spr round 4 (radius: 20)
[10:19:30 -353073.781131] AUTODETECT spr round 5 (radius: 25)
[10:22:26 -336135.063286] SPR radius for FAST iterations: 25 (autodetect)
[10:22:26 -336135.063286] Model parameter optimization (eps = 3.000000)
[10:22:34 -336130.881812] FAST spr round 1 (radius: 25)
[10:25:23 -291840.307773] FAST spr round 2 (radius: 25)
[10:27:31 -289946.866415] FAST spr round 3 (radius: 25)
[10:29:18 -289746.696152] FAST spr round 4 (radius: 25)
[10:30:34 -289730.272698] FAST spr round 5 (radius: 25)
[10:31:47 -289730.235221] Model parameter optimization (eps = 1.000000)
[10:31:58 -289646.794065] SLOW spr round 1 (radius: 5)
[10:33:39 -289582.969980] SLOW spr round 2 (radius: 5)
[10:35:16 -289573.274070] SLOW spr round 3 (radius: 5)
[10:36:49 -289573.273995] SLOW spr round 4 (radius: 10)
[10:38:23 -289573.273988] SLOW spr round 5 (radius: 15)
[10:41:05 -289573.273982] SLOW spr round 6 (radius: 20)
[10:45:22 -289573.273978] SLOW spr round 7 (radius: 25)
[10:50:30 -289573.273973] Model parameter optimization (eps = 0.100000)

[10:50:34] ML tree search #14, logLikelihood: -289573.216470

[10:50:34 -1111256.093805] Initial branch length optimization
[10:50:37 -912985.958141] Model parameter optimization (eps = 10.000000)
[10:51:12 -911867.609675] AUTODETECT spr round 1 (radius: 5)
[10:53:12 -621057.338295] AUTODETECT spr round 2 (radius: 10)
[10:55:00 -478706.305233] AUTODETECT spr round 3 (radius: 15)
[10:57:07 -409546.147900] AUTODETECT spr round 4 (radius: 20)
[10:59:34 -354977.220046] AUTODETECT spr round 5 (radius: 25)
[11:02:18 -342286.001704] SPR radius for FAST iterations: 25 (autodetect)
[11:02:18 -342286.001704] Model parameter optimization (eps = 3.000000)
[11:02:35 -342154.715184] FAST spr round 1 (radius: 25)
[11:05:14 -291049.416279] FAST spr round 2 (radius: 25)
[11:07:14 -289800.015024] FAST spr round 3 (radius: 25)
[11:08:59 -289696.322901] FAST spr round 4 (radius: 25)
[11:10:34 -289660.795324] FAST spr round 5 (radius: 25)
[11:12:05 -289660.794914] Model parameter optimization (eps = 1.000000)
[11:12:24 -289653.966865] SLOW spr round 1 (radius: 5)
[11:14:30 -289601.932434] SLOW spr round 2 (radius: 5)
[11:16:31 -289598.400414] SLOW spr round 3 (radius: 5)
[11:18:27 -289598.400107] SLOW spr round 4 (radius: 10)
[11:20:25 -289593.758147] SLOW spr round 5 (radius: 5)
[11:22:47 -289593.758019] SLOW spr round 6 (radius: 10)
[11:24:54 -289592.940027] SLOW spr round 7 (radius: 5)
[11:27:15 -289591.321668] SLOW spr round 8 (radius: 5)
[11:29:22 -289591.320015] SLOW spr round 9 (radius: 10)
[11:31:20 -289591.319921] SLOW spr round 10 (radius: 15)
[11:34:26 -289591.319912] SLOW spr round 11 (radius: 20)
[11:38:29 -289591.319908] SLOW spr round 12 (radius: 25)
[11:43:25 -289591.319904] Model parameter optimization (eps = 0.100000)

[11:43:34] ML tree search #15, logLikelihood: -289591.203632

[11:43:34 -1111724.385183] Initial branch length optimization
[11:43:38 -920910.043620] Model parameter optimization (eps = 10.000000)
[11:44:01 -919809.583616] AUTODETECT spr round 1 (radius: 5)
[11:45:56 -623173.652995] AUTODETECT spr round 2 (radius: 10)
[11:48:08 -480119.481511] AUTODETECT spr round 3 (radius: 15)
[11:50:49 -398672.381955] AUTODETECT spr round 4 (radius: 20)
[11:53:13 -345483.835042] AUTODETECT spr round 5 (radius: 25)
[11:56:05 -335674.278571] SPR radius for FAST iterations: 25 (autodetect)
[11:56:05 -335674.278571] Model parameter optimization (eps = 3.000000)
[11:56:24 -335561.224974] FAST spr round 1 (radius: 25)
[11:58:52 -291400.038401] FAST spr round 2 (radius: 25)
[12:00:45 -289785.980316] FAST spr round 3 (radius: 25)
[12:02:26 -289682.652715] FAST spr round 4 (radius: 25)
[12:03:55 -289680.732577] FAST spr round 5 (radius: 25)
[12:05:25 -289680.732140] Model parameter optimization (eps = 1.000000)
[12:05:38 -289676.276534] SLOW spr round 1 (radius: 5)
[12:07:44 -289614.828239] SLOW spr round 2 (radius: 5)
[12:09:38 -289599.068203] SLOW spr round 3 (radius: 5)
[12:11:30 -289586.886569] SLOW spr round 4 (radius: 5)
[12:13:22 -289586.885583] SLOW spr round 5 (radius: 10)
[12:15:21 -289582.243982] SLOW spr round 6 (radius: 5)
[12:17:44 -289582.243966] SLOW spr round 7 (radius: 10)
[12:19:53 -289582.243962] SLOW spr round 8 (radius: 15)
[12:22:53 -289582.243957] SLOW spr round 9 (radius: 20)
[12:27:02 -289582.243953] SLOW spr round 10 (radius: 25)
[12:31:48 -289582.243949] Model parameter optimization (eps = 0.100000)

[12:31:53] ML tree search #16, logLikelihood: -289582.145995

[12:31:53 -1105413.262389] Initial branch length optimization
[12:31:56 -918388.160417] Model parameter optimization (eps = 10.000000)
[12:32:36 -917265.687505] AUTODETECT spr round 1 (radius: 5)
[12:34:34 -624391.138980] AUTODETECT spr round 2 (radius: 10)
[12:36:48 -469453.405427] AUTODETECT spr round 3 (radius: 15)
[12:39:29 -378218.971420] AUTODETECT spr round 4 (radius: 20)
[12:42:01 -344338.133460] AUTODETECT spr round 5 (radius: 25)
[12:44:49 -335716.697758] SPR radius for FAST iterations: 25 (autodetect)
[12:44:49 -335716.697758] Model parameter optimization (eps = 3.000000)
[12:45:06 -335622.735009] FAST spr round 1 (radius: 25)
[12:47:35 -291456.683668] FAST spr round 2 (radius: 25)
[12:49:32 -289837.814119] FAST spr round 3 (radius: 25)
[12:51:18 -289744.011904] FAST spr round 4 (radius: 25)
[12:52:55 -289696.566681] FAST spr round 5 (radius: 25)
[12:54:30 -289680.424732] FAST spr round 6 (radius: 25)
[12:56:02 -289680.424724] Model parameter optimization (eps = 1.000000)
[12:56:16 -289667.731925] SLOW spr round 1 (radius: 5)
[12:58:21 -289601.968909] SLOW spr round 2 (radius: 5)
[13:00:24 -289595.074971] SLOW spr round 3 (radius: 5)
[13:02:22 -289594.185769] SLOW spr round 4 (radius: 5)
[13:04:17 -289594.185735] SLOW spr round 5 (radius: 10)
[13:06:13 -289590.120711] SLOW spr round 6 (radius: 5)
[13:08:38 -289588.551445] SLOW spr round 7 (radius: 5)
[13:10:47 -289588.551420] SLOW spr round 8 (radius: 10)
[13:12:48 -289588.551413] SLOW spr round 9 (radius: 15)
[13:16:00 -289588.551407] SLOW spr round 10 (radius: 20)
[13:20:09 -289588.551401] SLOW spr round 11 (radius: 25)
[13:25:00 -289588.551396] Model parameter optimization (eps = 0.100000)

[13:25:07] ML tree search #17, logLikelihood: -289588.261790

[13:25:07 -1102197.049338] Initial branch length optimization
[13:25:11 -916007.957646] Model parameter optimization (eps = 10.000000)
[13:25:39 -914661.344126] AUTODETECT spr round 1 (radius: 5)
[13:27:39 -615447.897766] AUTODETECT spr round 2 (radius: 10)
[13:29:50 -465626.463309] AUTODETECT spr round 3 (radius: 15)
[13:32:31 -401390.158988] AUTODETECT spr round 4 (radius: 20)
[13:35:08 -372109.419633] AUTODETECT spr round 5 (radius: 25)
[13:38:30 -350720.675833] SPR radius for FAST iterations: 25 (autodetect)
[13:38:30 -350720.675833] Model parameter optimization (eps = 3.000000)
[13:38:35 -350718.101398] FAST spr round 1 (radius: 25)
[13:41:17 -292335.684246] FAST spr round 2 (radius: 25)
[13:43:16 -289915.152143] FAST spr round 3 (radius: 25)
[13:45:03 -289758.977989] FAST spr round 4 (radius: 25)
[13:46:44 -289737.676330] FAST spr round 5 (radius: 25)
[13:48:18 -289735.345061] FAST spr round 6 (radius: 25)
[13:49:50 -289735.344159] Model parameter optimization (eps = 1.000000)
[13:50:05 -289661.604220] SLOW spr round 1 (radius: 5)
[13:52:13 -289598.013415] SLOW spr round 2 (radius: 5)
[13:54:17 -289591.917180] SLOW spr round 3 (radius: 5)
[13:56:14 -289589.432542] SLOW spr round 4 (radius: 5)
[13:58:11 -289589.432531] SLOW spr round 5 (radius: 10)
[14:00:10 -289588.953997] SLOW spr round 6 (radius: 5)
[14:02:38 -289586.371042] SLOW spr round 7 (radius: 5)
[14:04:47 -289586.369003] SLOW spr round 8 (radius: 10)
[14:06:47 -289586.368895] SLOW spr round 9 (radius: 15)
[14:10:03 -289586.368886] SLOW spr round 10 (radius: 20)
[14:14:24 -289586.368881] SLOW spr round 11 (radius: 25)
[14:19:38 -289586.368877] Model parameter optimization (eps = 0.100000)

[14:19:51] ML tree search #18, logLikelihood: -289586.204422

[14:19:51 -1109811.467630] Initial branch length optimization
[14:19:54 -913722.077185] Model parameter optimization (eps = 10.000000)
[14:20:22 -912693.373437] AUTODETECT spr round 1 (radius: 5)
[14:22:23 -618669.588847] AUTODETECT spr round 2 (radius: 10)
[14:24:38 -474470.833316] AUTODETECT spr round 3 (radius: 15)
[14:27:15 -395858.009960] AUTODETECT spr round 4 (radius: 20)
[14:29:43 -346373.301600] AUTODETECT spr round 5 (radius: 25)
[14:32:25 -334250.411532] SPR radius for FAST iterations: 25 (autodetect)
[14:32:25 -334250.411532] Model parameter optimization (eps = 3.000000)
[14:32:46 -334179.637061] FAST spr round 1 (radius: 25)
[14:35:25 -291776.197115] FAST spr round 2 (radius: 25)
[14:37:28 -289864.203940] FAST spr round 3 (radius: 25)
[14:39:22 -289744.482098] FAST spr round 4 (radius: 25)
[14:41:08 -289651.925739] FAST spr round 5 (radius: 25)
[14:42:43 -289645.233455] FAST spr round 6 (radius: 25)
[14:44:15 -289642.638383] FAST spr round 7 (radius: 25)
[14:45:45 -289642.638368] Model parameter optimization (eps = 1.000000)
[14:45:57 -289633.547439] SLOW spr round 1 (radius: 5)
[14:48:04 -289581.147824] SLOW spr round 2 (radius: 5)
[14:50:03 -289581.043905] SLOW spr round 3 (radius: 5)
[14:51:55 -289581.043795] SLOW spr round 4 (radius: 10)
[14:53:50 -289580.736086] SLOW spr round 5 (radius: 5)
[14:56:09 -289580.574003] SLOW spr round 6 (radius: 5)
[14:58:12 -289580.573850] SLOW spr round 7 (radius: 10)
[15:00:08 -289580.573843] SLOW spr round 8 (radius: 15)
[15:03:15 -289580.573843] SLOW spr round 9 (radius: 20)
[15:07:20 -289580.573843] SLOW spr round 10 (radius: 25)
[15:12:16 -289580.573843] Model parameter optimization (eps = 0.100000)

[15:12:21] ML tree search #19, logLikelihood: -289580.495529

[15:12:21 -1099249.529931] Initial branch length optimization
[15:12:25 -911721.186479] Model parameter optimization (eps = 10.000000)
[15:13:01 -910590.638557] AUTODETECT spr round 1 (radius: 5)
[15:14:58 -614839.036748] AUTODETECT spr round 2 (radius: 10)
[15:17:10 -481203.390669] AUTODETECT spr round 3 (radius: 15)
[15:19:50 -394952.884494] AUTODETECT spr round 4 (radius: 20)
[15:22:37 -338165.327844] AUTODETECT spr round 5 (radius: 25)
[15:25:36 -333447.046052] SPR radius for FAST iterations: 25 (autodetect)
[15:25:36 -333447.046052] Model parameter optimization (eps = 3.000000)
[15:25:41 -333445.164102] FAST spr round 1 (radius: 25)
[15:28:12 -291349.993067] FAST spr round 2 (radius: 25)
[15:30:11 -289872.499638] FAST spr round 3 (radius: 25)
[15:31:57 -289785.002614] FAST spr round 4 (radius: 25)
[15:33:29 -289785.001686] Model parameter optimization (eps = 1.000000)
[15:33:44 -289693.799613] SLOW spr round 1 (radius: 5)
[15:35:53 -289602.703854] SLOW spr round 2 (radius: 5)
[15:37:56 -289590.383230] SLOW spr round 3 (radius: 5)
[15:39:51 -289590.382892] SLOW spr round 4 (radius: 10)
[15:41:46 -289590.382868] SLOW spr round 5 (radius: 15)
[15:44:58 -289590.382862] SLOW spr round 6 (radius: 20)
[15:49:06 -289590.382858] SLOW spr round 7 (radius: 25)
[15:54:14 -289590.382854] Model parameter optimization (eps = 0.100000)

[15:54:20] ML tree search #20, logLikelihood: -289590.318387


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.180642,0.291135) (0.275587,0.418880) (0.310062,0.986747) (0.233709,2.250739) 
   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: -289571.696767

AIC score: 583153.393534 / AICc score: 8627213.393534 / BIC score: 592031.744606
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=619).
         This might lead to overfitting and compromise tree inference results!


Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P51530/3_mltree/P51530.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P51530/3_mltree/P51530.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P51530/3_mltree/P51530.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P51530/3_mltree/P51530.raxml.log

Analysis started: 05-Jul-2021 05:14:22 / finished: 05-Jul-2021 21:08:42

Elapsed time: 57260.413 seconds

Consumed energy: 4501.894 Wh (= 23 km in an electric car, or 113 km with an e-scooter!)