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 24-Jun-2021 06:11:58 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q15835/2_msa/Q15835_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q15835/3_mltree/Q15835 --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/Q15835/2_msa/Q15835_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 585 sites

WARNING: Sequences tr_B4QSM6_B4QSM6_DROSI_7240 and sp_P32866_GPRK2_DROME_7227 are exactly identical!
WARNING: Sequences tr_B4QSM6_B4QSM6_DROSI_7240 and tr_B4I027_B4I027_DROSE_7238 are exactly identical!
WARNING: Sequences tr_B4QXQ5_B4QXQ5_DROSI_7240 and tr_B4HLD8_B4HLD8_DROSE_7238 are exactly identical!
WARNING: Sequences tr_A0A1D5PP79_A0A1D5PP79_CHICK_9031 and tr_A0A218V572_A0A218V572_9PASE_299123 are exactly identical!
WARNING: Sequences tr_G3QL13_G3QL13_GORGO_9595 and tr_K7DA70_K7DA70_PANTR_9598 are exactly identical!
WARNING: Sequences tr_H2NCP1_H2NCP1_PONAB_9601 and tr_A0A096N611_A0A096N611_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_H2NCP1_H2NCP1_PONAB_9601 and tr_A0A0D9R809_A0A0D9R809_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_H2NCP1_H2NCP1_PONAB_9601 and tr_A0A2K5L0Z3_A0A2K5L0Z3_CERAT_9531 are exactly identical!
WARNING: Sequences tr_H2NCP1_H2NCP1_PONAB_9601 and tr_A0A2K6AR56_A0A2K6AR56_MACNE_9545 are exactly identical!
WARNING: Sequences tr_Q29BB5_Q29BB5_DROPS_46245 and tr_B4GYT9_B4GYT9_DROPE_7234 are exactly identical!
WARNING: Sequences tr_H2Q482_H2Q482_PANTR_9598 and sp_P25098_ARBK1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2Q7U6_H2Q7U6_PANTR_9598 and tr_A0A2R8ZIW3_A0A2R8ZIW3_PANPA_9597 are exactly identical!
WARNING: Sequences tr_K7B2K4_K7B2K4_PANTR_9598 and sp_P35626_ARBK2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_K7B2K4_K7B2K4_PANTR_9598 and tr_A0A0D9RCS3_A0A0D9RCS3_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_K7B2K4_K7B2K4_PANTR_9598 and tr_A0A2K6BHH5_A0A2K6BHH5_MACNE_9545 are exactly identical!
WARNING: Sequences tr_K7B2K4_K7B2K4_PANTR_9598 and tr_A0A2R9A3T4_A0A2R9A3T4_PANPA_9597 are exactly identical!
WARNING: Sequences tr_K7BG59_K7BG59_PANTR_9598 and tr_A0A2R9A0D5_A0A2R9A0D5_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A158NFW2_A0A158NFW2_ATTCE_12957 and tr_A0A195E6Z4_A0A195E6Z4_9HYME_471704 are exactly identical!
WARNING: Sequences tr_A0A158NFW2_A0A158NFW2_ATTCE_12957 and tr_A0A195B2L3_A0A195B2L3_9HYME_520822 are exactly identical!
WARNING: Sequences tr_F6SX33_F6SX33_MACMU_9544 and tr_A0A2K6B128_A0A2K6B128_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7E0C1_F7E0C1_MACMU_9544 and tr_G7P015_G7P015_MACFA_9541 are exactly identical!
WARNING: Sequences tr_H9EU39_H9EU39_MACMU_9544 and tr_G7NZU6_G7NZU6_MACFA_9541 are exactly identical!
WARNING: Sequences tr_H9EU39_H9EU39_MACMU_9544 and tr_A0A096NG19_A0A096NG19_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_H9EU39_H9EU39_MACMU_9544 and tr_A0A0D9RKU2_A0A0D9RKU2_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_H9EU39_H9EU39_MACMU_9544 and tr_A0A2K5MBX9_A0A2K5MBX9_CERAT_9531 are exactly identical!
WARNING: Sequences tr_H9EU39_H9EU39_MACMU_9544 and tr_A0A2K6A1K4_A0A2K6A1K4_MANLE_9568 are exactly identical!
WARNING: Sequences tr_H0Z6Q4_H0Z6Q4_TAEGU_59729 and tr_A0A218UUU4_A0A218UUU4_9PASE_299123 are exactly identical!
WARNING: Sequences tr_E3MMQ6_E3MMQ6_CAERE_31234 and tr_A0A261CPL9_A0A261CPL9_9PELO_1503980 are exactly identical!
WARNING: Sequences tr_M3W092_M3W092_FELCA_9685 and tr_A0A2Y9JMQ3_A0A2Y9JMQ3_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_U3K1T7_U3K1T7_FICAL_59894 and tr_A0A091ENH3_A0A091ENH3_CORBR_85066 are exactly identical!
WARNING: Sequences tr_U3K1T7_U3K1T7_FICAL_59894 and tr_A0A093QGV9_A0A093QGV9_9PASS_328815 are exactly identical!
WARNING: Sequences tr_U3IST7_U3IST7_ANAPL_8839 and tr_A0A091G3N7_A0A091G3N7_9AVES_55661 are exactly identical!
WARNING: Sequences tr_A0A096NTY7_A0A096NTY7_PAPAN_9555 and tr_A0A2K5L696_A0A2K5L696_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A0D9R8V9_A0A0D9R8V9_CHLSB_60711 and tr_A0A2K5MXF0_A0A2K5MXF0_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A091UM58_A0A091UM58_NIPNI_128390 and tr_A0A087R8T8_A0A087R8T8_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091WUH3_A0A091WUH3_NIPNI_128390 and tr_A0A099ZZL1_A0A099ZZL1_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A0V0S7L4_A0A0V0S7L4_9BILA_6336 and tr_A0A0V1DGE5_A0A0V1DGE5_TRIBR_45882 are exactly identical!
WARNING: Sequences tr_A0A0V0S7L4_A0A0V0S7L4_9BILA_6336 and tr_A0A0V0VYU3_A0A0V0VYU3_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V0S7L4_A0A0V0S7L4_9BILA_6336 and tr_A0A0V0ZRE6_A0A0V0ZRE6_9BILA_990121 are exactly identical!
WARNING: Sequences tr_A0A0V0S7L4_A0A0V0S7L4_9BILA_6336 and tr_A0A0V1NVT5_A0A0V1NVT5_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V0S7L4_A0A0V0S7L4_9BILA_6336 and tr_A0A0V0TRZ5_A0A0V0TRZ5_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A0V1EVP4_A0A0V1EVP4_TRIPS_6337 and tr_A0A0V1MHY7_A0A0V1MHY7_9BILA_268474 are exactly identical!
WARNING: Sequences tr_A0A0V1EVP4_A0A0V1EVP4_TRIPS_6337 and tr_A0A0V1I3Q2_A0A0V1I3Q2_9BILA_268475 are exactly identical!
WARNING: Sequences tr_A0A1S4CHI3_A0A1S4CHI3_TOBAC_4097 and tr_A0A1U7YIA2_A0A1U7YIA2_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1U7Q2D0_A0A1U7Q2D0_MESAU_10036 and sp_Q64682_ARBK1_MESAU_10036 are exactly identical!
WARNING: Sequences tr_A0A226MV43_A0A226MV43_CALSU_9009 and tr_A0A226PZV1_A0A226PZV1_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A226N183_A0A226N183_CALSU_9009 and tr_A0A226PLK4_A0A226PLK4_COLVI_9014 are exactly identical!
WARNING: Duplicate sequences found: 47

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/Q15835/3_mltree/Q15835.raxml.reduced.phy

Alignment comprises 1 partitions and 585 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 585 / 585
Gaps: 12.64 %
Invariant sites: 0.00 %


NOTE: Binary MSA file already exists: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q15835/3_mltree/Q15835.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 / 84 / 6720
[00:00:00] Data distribution: max. searches per worker: 20

Starting ML tree search with 20 distinct starting trees

[00:00:00 -873468.873255] Initial branch length optimization
[00:00:04 -721393.427961] Model parameter optimization (eps = 10.000000)
[00:00:39 -719402.661126] AUTODETECT spr round 1 (radius: 5)
[00:02:55 -454291.292397] AUTODETECT spr round 2 (radius: 10)
[00:05:24 -313755.942531] AUTODETECT spr round 3 (radius: 15)
[00:08:02 -248204.495562] AUTODETECT spr round 4 (radius: 20)
[00:10:48 -219016.445262] AUTODETECT spr round 5 (radius: 25)
[00:13:41 -215366.848494] SPR radius for FAST iterations: 25 (autodetect)
[00:13:41 -215366.848494] Model parameter optimization (eps = 3.000000)
[00:14:03 -215206.455566] FAST spr round 1 (radius: 25)
[00:16:37 -186477.304702] FAST spr round 2 (radius: 25)
[00:18:45 -185392.563585] FAST spr round 3 (radius: 25)
[00:20:43 -185262.975811] FAST spr round 4 (radius: 25)
[00:22:37 -185242.507269] FAST spr round 5 (radius: 25)
[00:24:30 -185224.598914] FAST spr round 6 (radius: 25)
[00:26:19 -185224.598364] Model parameter optimization (eps = 1.000000)
[00:26:37 -185207.178491] SLOW spr round 1 (radius: 5)
[00:28:55 -185154.879497] SLOW spr round 2 (radius: 5)
[00:31:15 -185134.384491] SLOW spr round 3 (radius: 5)
[00:33:27 -185134.362671] SLOW spr round 4 (radius: 10)
[00:35:38 -185132.747495] SLOW spr round 5 (radius: 5)
[00:38:16 -185132.747484] SLOW spr round 6 (radius: 10)
[00:40:37 -185132.747484] SLOW spr round 7 (radius: 15)
[00:43:41 -185132.747484] SLOW spr round 8 (radius: 20)
[00:48:35 -185132.747484] SLOW spr round 9 (radius: 25)
[00:55:00 -185131.547282] SLOW spr round 10 (radius: 5)
[00:57:47 -185127.864931] SLOW spr round 11 (radius: 5)
[01:00:13 -185127.857178] SLOW spr round 12 (radius: 10)
[01:02:28 -185127.856673] SLOW spr round 13 (radius: 15)
[01:05:28 -185127.856673] SLOW spr round 14 (radius: 20)
[01:10:15 -185127.856673] SLOW spr round 15 (radius: 25)
[01:16:47 -185127.856673] Model parameter optimization (eps = 0.100000)

[01:16:57] ML tree search #1, logLikelihood: -185127.663044

[01:16:57 -866696.661081] Initial branch length optimization
[01:17:02 -714586.279683] Model parameter optimization (eps = 10.000000)
[01:17:46 -712707.051182] AUTODETECT spr round 1 (radius: 5)
[01:20:06 -459489.908453] AUTODETECT spr round 2 (radius: 10)
[01:22:42 -324421.614541] AUTODETECT spr round 3 (radius: 15)
[01:25:24 -250819.907419] AUTODETECT spr round 4 (radius: 20)
[01:28:21 -229837.869447] AUTODETECT spr round 5 (radius: 25)
[01:31:15 -225637.648190] SPR radius for FAST iterations: 25 (autodetect)
[01:31:15 -225637.648190] Model parameter optimization (eps = 3.000000)
[01:31:44 -225506.736285] FAST spr round 1 (radius: 25)
[01:34:15 -188440.185171] FAST spr round 2 (radius: 25)
[01:36:22 -185392.698811] FAST spr round 3 (radius: 25)
[01:38:20 -185211.780733] FAST spr round 4 (radius: 25)
[01:40:16 -185182.515020] FAST spr round 5 (radius: 25)
[01:42:05 -185178.861213] FAST spr round 6 (radius: 25)
[01:43:53 -185176.720779] FAST spr round 7 (radius: 25)
[01:45:40 -185176.719987] Model parameter optimization (eps = 1.000000)
[01:46:02 -185156.301019] SLOW spr round 1 (radius: 5)
[01:48:17 -185120.232201] SLOW spr round 2 (radius: 5)
[01:50:33 -185117.865017] SLOW spr round 3 (radius: 5)
[01:52:49 -185115.283762] SLOW spr round 4 (radius: 5)
[01:55:00 -185115.283632] SLOW spr round 5 (radius: 10)
[01:57:12 -185115.283509] SLOW spr round 6 (radius: 15)
[02:00:25 -185115.283389] SLOW spr round 7 (radius: 20)
[02:04:59 -185115.283274] SLOW spr round 8 (radius: 25)
[02:11:10 -185115.283162] Model parameter optimization (eps = 0.100000)

[02:11:16] ML tree search #2, logLikelihood: -185115.223284

[02:11:17 -864586.902087] Initial branch length optimization
[02:11:20 -712165.222343] Model parameter optimization (eps = 10.000000)
[02:11:55 -710188.511326] AUTODETECT spr round 1 (radius: 5)
[02:14:09 -456493.611549] AUTODETECT spr round 2 (radius: 10)
[02:16:34 -332551.365683] AUTODETECT spr round 3 (radius: 15)
[02:19:16 -262963.192220] AUTODETECT spr round 4 (radius: 20)
[02:21:57 -216429.844768] AUTODETECT spr round 5 (radius: 25)
[02:25:02 -215234.562139] SPR radius for FAST iterations: 25 (autodetect)
[02:25:02 -215234.562139] Model parameter optimization (eps = 3.000000)
[02:25:31 -215078.220373] FAST spr round 1 (radius: 25)
[02:27:59 -186211.436042] FAST spr round 2 (radius: 25)
[02:30:07 -185297.276620] FAST spr round 3 (radius: 25)
[02:32:06 -185225.689247] FAST spr round 4 (radius: 25)
[02:33:55 -185225.687369] Model parameter optimization (eps = 1.000000)
[02:34:16 -185207.914818] SLOW spr round 1 (radius: 5)
[02:36:33 -185156.801996] SLOW spr round 2 (radius: 5)
[02:38:45 -185154.787391] SLOW spr round 3 (radius: 5)
[02:40:52 -185154.787179] SLOW spr round 4 (radius: 10)
[02:42:59 -185151.468489] SLOW spr round 5 (radius: 5)
[02:45:33 -185151.468379] SLOW spr round 6 (radius: 10)
[02:47:51 -185151.468287] SLOW spr round 7 (radius: 15)
[02:50:46 -185151.290379] SLOW spr round 8 (radius: 5)
[02:53:26 -185151.288170] SLOW spr round 9 (radius: 10)
[02:55:49 -185151.288135] SLOW spr round 10 (radius: 15)
[02:58:41 -185151.288100] SLOW spr round 11 (radius: 20)
[03:06:02 -185151.288066] SLOW spr round 12 (radius: 25)
[03:15:29 -185150.091097] SLOW spr round 13 (radius: 5)
[03:19:06 -185146.391704] SLOW spr round 14 (radius: 5)
[03:22:22 -185146.391668] SLOW spr round 15 (radius: 10)
[03:25:08 -185146.391634] SLOW spr round 16 (radius: 15)
[03:29:11 -185146.391600] SLOW spr round 17 (radius: 20)
[03:35:30 -185146.391565] SLOW spr round 18 (radius: 25)
[03:43:48 -185146.391531] Model parameter optimization (eps = 0.100000)

[03:43:58] ML tree search #3, logLikelihood: -185146.282068

[03:43:58 -874513.365056] Initial branch length optimization
[03:44:03 -719037.140657] Model parameter optimization (eps = 10.000000)
[03:44:47 -717108.933759] AUTODETECT spr round 1 (radius: 5)
[03:48:11 -463821.831165] AUTODETECT spr round 2 (radius: 10)
[03:51:57 -309680.375614] AUTODETECT spr round 3 (radius: 15)
[03:55:27 -264079.579115] AUTODETECT spr round 4 (radius: 20)
[03:59:18 -240238.055120] AUTODETECT spr round 5 (radius: 25)
[04:03:28 -230926.043056] SPR radius for FAST iterations: 25 (autodetect)
[04:03:28 -230926.043056] Model parameter optimization (eps = 3.000000)
[04:03:55 -230767.377675] FAST spr round 1 (radius: 25)
[04:07:29 -192620.129291] FAST spr round 2 (radius: 25)
[04:10:11 -187253.454003] FAST spr round 3 (radius: 25)
[04:12:47 -185555.946786] FAST spr round 4 (radius: 25)
[04:15:08 -185260.762215] FAST spr round 5 (radius: 25)
[04:17:41 -185215.675951] FAST spr round 6 (radius: 25)
[04:20:02 -185210.328414] FAST spr round 7 (radius: 25)
[04:22:23 -185210.328369] Model parameter optimization (eps = 1.000000)
[04:22:45 -185191.803621] SLOW spr round 1 (radius: 5)
[04:25:43 -185135.909628] SLOW spr round 2 (radius: 5)
[04:28:24 -185128.535982] SLOW spr round 3 (radius: 5)
[04:31:24 -185127.110872] SLOW spr round 4 (radius: 5)
[04:34:15 -185127.110697] SLOW spr round 5 (radius: 10)
[04:36:50 -185121.477668] SLOW spr round 6 (radius: 5)
[04:40:01 -185121.476541] SLOW spr round 7 (radius: 10)
[04:42:50 -185121.476462] SLOW spr round 8 (radius: 15)
[04:46:38 -185121.476426] SLOW spr round 9 (radius: 20)
[04:52:28 -185119.157549] SLOW spr round 10 (radius: 5)
[04:55:52 -185116.494872] SLOW spr round 11 (radius: 5)
[04:58:53 -185116.494257] SLOW spr round 12 (radius: 10)
[05:01:41 -185116.494224] SLOW spr round 13 (radius: 15)
[05:05:19 -185116.494191] SLOW spr round 14 (radius: 20)
[05:11:01 -185116.494158] SLOW spr round 15 (radius: 25)
[05:19:04 -185116.494125] Model parameter optimization (eps = 0.100000)

[05:19:10] ML tree search #4, logLikelihood: -185116.435574

[05:19:10 -865385.252046] Initial branch length optimization
[05:19:14 -715115.884544] Model parameter optimization (eps = 10.000000)
[05:19:43 -713112.087339] AUTODETECT spr round 1 (radius: 5)
[05:23:03 -457532.665459] AUTODETECT spr round 2 (radius: 10)
[05:26:42 -317387.040782] AUTODETECT spr round 3 (radius: 15)
[05:30:03 -252622.417288] AUTODETECT spr round 4 (radius: 20)
[05:33:53 -228780.250330] AUTODETECT spr round 5 (radius: 25)
[05:37:58 -214310.919650] SPR radius for FAST iterations: 25 (autodetect)
[05:37:58 -214310.919650] Model parameter optimization (eps = 3.000000)
[05:38:30 -214101.883077] FAST spr round 1 (radius: 25)
[05:41:56 -186278.729264] FAST spr round 2 (radius: 25)
[05:44:42 -185295.295243] FAST spr round 3 (radius: 25)
[05:47:11 -185199.582926] FAST spr round 4 (radius: 25)

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 25-Jun-2021 04:54:51 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q15835/2_msa/Q15835_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q15835/3_mltree/Q15835 --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

WARNING: The model you specified on the command line (LG4X) will be ignored 
         since the binary MSA file already contains a model definition.
         If you want to change the model, please re-run RAxML-NG 
         with the original PHYLIP/FASTA alignment and --redo option.

[00:00:00] Loading binary alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q15835/3_mltree/Q15835.raxml.rba
[00:00:00] Alignment comprises 1001 taxa, 1 partitions and 585 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 585 / 585
Gaps: 12.64 %
Invariant sites: 0.00 %


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

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

[00:00:00] NOTE: Resuming execution from checkpoint (logLH: -185199.58, ML trees: 4, bootstraps: 0)
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 84 / 6720
[00:00:00] Data distribution: max. searches per worker: 16

Starting ML tree search with 20 distinct starting trees

[00:00:00 -185199.582926] SPR radius for FAST iterations: 25 (autodetect)
[00:00:00 -185199.582926] FAST spr round 4 (radius: 25)
[00:01:29 -185195.159451] FAST spr round 5 (radius: 25)
[00:02:55 -185195.158536] Model parameter optimization (eps = 1.000000)
[00:03:10 -185187.933909] SLOW spr round 1 (radius: 5)
[00:05:05 -185155.876113] SLOW spr round 2 (radius: 5)
[00:06:56 -185147.802578] SLOW spr round 3 (radius: 5)
[00:08:44 -185146.591164] SLOW spr round 4 (radius: 5)
[00:10:29 -185146.579295] SLOW spr round 5 (radius: 10)
[00:12:14 -185143.601826] SLOW spr round 6 (radius: 5)
[00:14:22 -185143.600585] SLOW spr round 7 (radius: 10)
[00:16:17 -185143.599314] SLOW spr round 8 (radius: 15)
[00:18:47 -185143.598238] SLOW spr round 9 (radius: 20)
[00:22:48 -185143.598215] SLOW spr round 10 (radius: 25)
[00:28:02 -185143.598215] Model parameter optimization (eps = 0.100000)

[00:28:08] ML tree search #5, logLikelihood: -185143.564527

[00:28:08 -871683.308839] Initial branch length optimization
[00:28:12 -724621.170100] Model parameter optimization (eps = 10.000000)
[00:28:54 -722533.853637] AUTODETECT spr round 1 (radius: 5)
[00:30:48 -456332.315373] AUTODETECT spr round 2 (radius: 10)
[00:32:55 -328999.180078] AUTODETECT spr round 3 (radius: 15)
[00:35:15 -282462.542069] AUTODETECT spr round 4 (radius: 20)
[00:38:00 -236506.430288] AUTODETECT spr round 5 (radius: 25)
[00:40:50 -225887.706235] SPR radius for FAST iterations: 25 (autodetect)
[00:40:50 -225887.706235] Model parameter optimization (eps = 3.000000)
[00:41:12 -225680.815622] FAST spr round 1 (radius: 25)
[00:43:24 -187188.405924] FAST spr round 2 (radius: 25)
[00:45:12 -185286.635724] FAST spr round 3 (radius: 25)
[00:46:50 -185191.021216] FAST spr round 4 (radius: 25)
[00:48:21 -185176.853798] FAST spr round 5 (radius: 25)
[00:49:48 -185176.852763] Model parameter optimization (eps = 1.000000)
[00:50:02 -185168.845431] SLOW spr round 1 (radius: 5)
[00:51:56 -185123.653546] SLOW spr round 2 (radius: 5)
[00:53:45 -185120.362328] SLOW spr round 3 (radius: 5)
[00:55:30 -185120.361643] SLOW spr round 4 (radius: 10)
[00:57:16 -185118.752408] SLOW spr round 5 (radius: 5)
[00:59:26 -185118.745524] SLOW spr round 6 (radius: 10)
[01:01:20 -185118.744980] SLOW spr round 7 (radius: 15)
[01:03:50 -185118.744426] SLOW spr round 8 (radius: 20)
[01:07:43 -185118.743856] SLOW spr round 9 (radius: 25)
[01:12:45 -185118.743267] Model parameter optimization (eps = 0.100000)

[01:12:50] ML tree search #6, logLikelihood: -185118.650832

[01:12:50 -871882.421355] Initial branch length optimization
[01:12:54 -717668.841150] Model parameter optimization (eps = 10.000000)
[01:13:22 -715678.797513] AUTODETECT spr round 1 (radius: 5)
[01:15:14 -452529.193954] AUTODETECT spr round 2 (radius: 10)
[01:17:20 -317142.310984] AUTODETECT spr round 3 (radius: 15)
[01:19:29 -260573.830259] AUTODETECT spr round 4 (radius: 20)
[01:22:02 -231288.168331] AUTODETECT spr round 5 (radius: 25)
[01:25:16 -220108.893775] SPR radius for FAST iterations: 25 (autodetect)
[01:25:17 -220108.893775] Model parameter optimization (eps = 3.000000)
[01:25:37 -219962.191323] FAST spr round 1 (radius: 25)
[01:27:56 -189068.079130] FAST spr round 2 (radius: 25)
[01:29:51 -185599.262281] FAST spr round 3 (radius: 25)
[01:31:36 -185224.762943] FAST spr round 4 (radius: 25)
[01:33:16 -185207.815703] FAST spr round 5 (radius: 25)
[01:34:51 -185206.362172] FAST spr round 6 (radius: 25)
[01:36:26 -185206.361919] Model parameter optimization (eps = 1.000000)
[01:36:47 -185160.051473] SLOW spr round 1 (radius: 5)
[01:38:49 -185120.319361] SLOW spr round 2 (radius: 5)
[01:40:44 -185118.700610] SLOW spr round 3 (radius: 5)
[01:42:30 -185118.700564] SLOW spr round 4 (radius: 10)
[01:44:15 -185118.700344] SLOW spr round 5 (radius: 15)
[01:46:54 -185118.700303] SLOW spr round 6 (radius: 20)
[01:50:42 -185117.539078] SLOW spr round 7 (radius: 5)
[01:53:01 -185113.867604] SLOW spr round 8 (radius: 5)
[01:55:03 -185113.867580] SLOW spr round 9 (radius: 10)
[01:56:53 -185113.867557] SLOW spr round 10 (radius: 15)
[01:59:26 -185113.867535] SLOW spr round 11 (radius: 20)
[02:03:21 -185113.867513] SLOW spr round 12 (radius: 25)
[02:08:33 -185113.867493] Model parameter optimization (eps = 0.100000)

[02:08:38] ML tree search #7, logLikelihood: -185113.838532

[02:08:38 -870653.612955] Initial branch length optimization
[02:08:43 -714086.569456] Model parameter optimization (eps = 10.000000)
[02:09:22 -712136.181814] AUTODETECT spr round 1 (radius: 5)
[02:11:17 -462499.540139] AUTODETECT spr round 2 (radius: 10)
[02:13:26 -331604.950646] AUTODETECT spr round 3 (radius: 15)
[02:15:52 -272294.232094] AUTODETECT spr round 4 (radius: 20)
[02:18:25 -227721.827438] AUTODETECT spr round 5 (radius: 25)
[02:20:56 -220479.815545] SPR radius for FAST iterations: 25 (autodetect)
[02:20:56 -220479.815545] Model parameter optimization (eps = 3.000000)
[02:21:16 -220343.954762] FAST spr round 1 (radius: 25)
[02:23:23 -186877.836852] FAST spr round 2 (radius: 25)
[02:25:07 -185309.754969] FAST spr round 3 (radius: 25)
[02:26:43 -185209.508696] FAST spr round 4 (radius: 25)
[02:28:14 -185197.064488] FAST spr round 5 (radius: 25)
[02:29:42 -185195.869035] FAST spr round 6 (radius: 25)
[02:31:09 -185195.868004] Model parameter optimization (eps = 1.000000)
[02:31:24 -185174.250168] SLOW spr round 1 (radius: 5)
[02:33:17 -185129.207953] SLOW spr round 2 (radius: 5)
[02:35:05 -185128.744243] SLOW spr round 3 (radius: 5)
[02:36:51 -185128.743861] SLOW spr round 4 (radius: 10)
[02:38:37 -185123.941692] SLOW spr round 5 (radius: 5)
[02:40:46 -185123.941507] SLOW spr round 6 (radius: 10)
[02:42:43 -185123.941392] SLOW spr round 7 (radius: 15)
[02:45:12 -185119.266672] SLOW spr round 8 (radius: 5)
[02:47:29 -185119.264437] SLOW spr round 9 (radius: 10)
[02:49:30 -185119.264403] SLOW spr round 10 (radius: 15)
[02:51:58 -185119.264370] SLOW spr round 11 (radius: 20)
[02:56:01 -185117.987285] SLOW spr round 12 (radius: 5)
[02:58:20 -185114.299433] SLOW spr round 13 (radius: 5)
[03:00:23 -185114.290529] SLOW spr round 14 (radius: 10)
[03:02:14 -185114.290494] SLOW spr round 15 (radius: 15)
[03:04:46 -185114.290461] SLOW spr round 16 (radius: 20)
[03:08:45 -185114.290428] SLOW spr round 17 (radius: 25)
[03:14:19 -185114.290395] Model parameter optimization (eps = 0.100000)

[03:14:24] ML tree search #8, logLikelihood: -185114.211879

[03:14:24 -863452.988473] Initial branch length optimization
[03:14:28 -712417.512458] Model parameter optimization (eps = 10.000000)
[03:15:05 -710373.799746] AUTODETECT spr round 1 (radius: 5)
[03:16:59 -466853.510559] AUTODETECT spr round 2 (radius: 10)
[03:19:05 -348570.917903] AUTODETECT spr round 3 (radius: 15)
[03:21:24 -269817.231683] AUTODETECT spr round 4 (radius: 20)
[03:23:51 -233859.491964] AUTODETECT spr round 5 (radius: 25)
[03:26:56 -225093.038994] SPR radius for FAST iterations: 25 (autodetect)
[03:26:56 -225093.038994] Model parameter optimization (eps = 3.000000)
[03:27:12 -224970.426152] FAST spr round 1 (radius: 25)
[03:29:28 -187531.103220] FAST spr round 2 (radius: 25)
[03:31:11 -185359.197902] FAST spr round 3 (radius: 25)
[03:32:48 -185226.259077] FAST spr round 4 (radius: 25)
[03:34:21 -185214.610406] FAST spr round 5 (radius: 25)
[03:35:50 -185213.776705] FAST spr round 6 (radius: 25)
[03:37:16 -185212.819432] FAST spr round 7 (radius: 25)
[03:38:42 -185212.807879] Model parameter optimization (eps = 1.000000)
[03:38:56 -185196.540643] SLOW spr round 1 (radius: 5)
[03:40:50 -185150.649404] SLOW spr round 2 (radius: 5)
[03:42:39 -185146.325249] SLOW spr round 3 (radius: 5)
[03:44:27 -185144.390431] SLOW spr round 4 (radius: 5)
[03:46:13 -185143.360161] SLOW spr round 5 (radius: 5)
[03:47:58 -185143.359987] SLOW spr round 6 (radius: 10)
[03:49:43 -185143.359942] SLOW spr round 7 (radius: 15)
[03:52:22 -185143.359942] SLOW spr round 8 (radius: 20)
[03:56:12 -185140.856273] SLOW spr round 9 (radius: 5)
[03:58:30 -185138.196179] SLOW spr round 10 (radius: 5)
[04:00:32 -185138.187408] SLOW spr round 11 (radius: 10)
[04:02:24 -185138.186892] SLOW spr round 12 (radius: 15)
[04:05:05 -185138.186892] SLOW spr round 13 (radius: 20)
[04:09:10 -185138.186892] SLOW spr round 14 (radius: 25)
[04:14:27 -185138.186892] Model parameter optimization (eps = 0.100000)

[04:14:34] ML tree search #9, logLikelihood: -185138.127727

[04:14:34 -873670.674776] Initial branch length optimization
[04:14:37 -718832.118083] Model parameter optimization (eps = 10.000000)
[04:15:04 -716859.858407] AUTODETECT spr round 1 (radius: 5)
[04:16:57 -463730.234895] AUTODETECT spr round 2 (radius: 10)
[04:19:04 -319098.523499] AUTODETECT spr round 3 (radius: 15)
[04:21:19 -255541.235089] AUTODETECT spr round 4 (radius: 20)
[04:23:57 -227090.995783] AUTODETECT spr round 5 (radius: 25)
[04:26:58 -215330.871085] SPR radius for FAST iterations: 25 (autodetect)
[04:26:58 -215330.871085] Model parameter optimization (eps = 3.000000)
[04:27:22 -215191.015518] FAST spr round 1 (radius: 25)
[04:29:33 -186226.015029] FAST spr round 2 (radius: 25)
[04:31:19 -185336.798336] FAST spr round 3 (radius: 25)
[04:32:59 -185237.700831] FAST spr round 4 (radius: 25)
[04:34:31 -185202.043236] FAST spr round 5 (radius: 25)
[04:35:59 -185194.903850] FAST spr round 6 (radius: 25)
[04:37:25 -185194.903679] Model parameter optimization (eps = 1.000000)
[04:37:38 -185191.216454] SLOW spr round 1 (radius: 5)
[04:39:33 -185144.427701] SLOW spr round 2 (radius: 5)
[04:41:24 -185126.514654] SLOW spr round 3 (radius: 5)
[04:43:12 -185124.649732] SLOW spr round 4 (radius: 5)
[04:44:58 -185124.649279] SLOW spr round 5 (radius: 10)
[04:46:44 -185121.729725] SLOW spr round 6 (radius: 5)
[04:48:54 -185121.727526] SLOW spr round 7 (radius: 10)
[04:50:49 -185121.727406] SLOW spr round 8 (radius: 15)
[04:53:19 -185121.727292] SLOW spr round 9 (radius: 20)
[04:57:21 -185121.727181] SLOW spr round 10 (radius: 25)
[05:02:33 -185116.588054] SLOW spr round 11 (radius: 5)
[05:04:51 -185116.587745] SLOW spr round 12 (radius: 10)
[05:06:55 -185116.587641] SLOW spr round 13 (radius: 15)
[05:09:22 -185116.587540] SLOW spr round 14 (radius: 20)
[05:13:24 -185116.587441] SLOW spr round 15 (radius: 25)
[05:18:37 -185116.587343] Model parameter optimization (eps = 0.100000)

[05:18:48] ML tree search #10, logLikelihood: -185116.304282

[05:18:48 -864916.130606] Initial branch length optimization
[05:18:52 -711817.311630] Model parameter optimization (eps = 10.000000)
[05:19:21 -709942.941998] AUTODETECT spr round 1 (radius: 5)
[05:21:16 -462061.188862] AUTODETECT spr round 2 (radius: 10)
[05:23:22 -323400.568789] AUTODETECT spr round 3 (radius: 15)
[05:25:32 -265227.863224] AUTODETECT spr round 4 (radius: 20)
[05:27:55 -238615.061404] AUTODETECT spr round 5 (radius: 25)
[05:30:37 -224522.332988] SPR radius for FAST iterations: 25 (autodetect)
[05:30:37 -224522.332988] Model parameter optimization (eps = 3.000000)
[05:30:54 -224402.247790] FAST spr round 1 (radius: 25)
[05:33:08 -186737.781755] FAST spr round 2 (radius: 25)
[05:34:52 -185325.081167] FAST spr round 3 (radius: 25)
[05:36:29 -185198.052548] FAST spr round 4 (radius: 25)
[05:38:00 -185194.287680] FAST spr round 5 (radius: 25)
[05:39:26 -185194.286561] Model parameter optimization (eps = 1.000000)
[05:39:42 -185177.989498] SLOW spr round 1 (radius: 5)
[05:41:36 -185143.987550] SLOW spr round 2 (radius: 5)
[05:43:27 -185140.768752] SLOW spr round 3 (radius: 5)
[05:45:14 -185140.732514] SLOW spr round 4 (radius: 10)
[05:47:01 -185140.732264] SLOW spr round 5 (radius: 15)
[05:49:39 -185140.732230] SLOW spr round 6 (radius: 20)
[05:53:26 -185140.732196] SLOW spr round 7 (radius: 25)
[05:58:36 -185140.732163] Model parameter optimization (eps = 0.100000)

[05:58:48] ML tree search #11, logLikelihood: -185140.368963

[05:58:48 -866590.380109] Initial branch length optimization
[05:58:51 -716886.980003] Model parameter optimization (eps = 10.000000)
[05:59:19 -714920.505016] AUTODETECT spr round 1 (radius: 5)
[06:01:12 -468763.068562] AUTODETECT spr round 2 (radius: 10)
[06:03:20 -330958.750563] AUTODETECT spr round 3 (radius: 15)
[06:05:33 -273315.687204] AUTODETECT spr round 4 (radius: 20)
[06:07:59 -241155.371134] AUTODETECT spr round 5 (radius: 25)
[06:10:32 -221800.498518] SPR radius for FAST iterations: 25 (autodetect)
[06:10:32 -221800.498518] Model parameter optimization (eps = 3.000000)
[06:10:52 -221659.972642] FAST spr round 1 (radius: 25)
[06:13:05 -187121.160306] FAST spr round 2 (radius: 25)
[06:14:53 -185361.563710] FAST spr round 3 (radius: 25)
[06:16:33 -185240.035810] FAST spr round 4 (radius: 25)
[06:18:05 -185219.272338] FAST spr round 5 (radius: 25)
[06:19:33 -185219.271914] Model parameter optimization (eps = 1.000000)
[06:19:47 -185210.055615] SLOW spr round 1 (radius: 5)
[06:21:43 -185158.378746] SLOW spr round 2 (radius: 5)
[06:23:36 -185136.455740] SLOW spr round 3 (radius: 5)
[06:25:23 -185135.082702] SLOW spr round 4 (radius: 5)
[06:27:08 -185135.082601] SLOW spr round 5 (radius: 10)
[06:28:56 -185130.403359] SLOW spr round 6 (radius: 5)
[06:31:05 -185129.344957] SLOW spr round 7 (radius: 5)
[06:33:03 -185128.376554] SLOW spr round 8 (radius: 5)
[06:34:54 -185128.285833] SLOW spr round 9 (radius: 10)
[06:36:41 -185128.285800] SLOW spr round 10 (radius: 15)
[06:39:18 -185128.285767] SLOW spr round 11 (radius: 20)
[06:43:03 -185128.285735] SLOW spr round 12 (radius: 25)
[06:48:05 -185128.285702] Model parameter optimization (eps = 0.100000)

[06:48:13] ML tree search #12, logLikelihood: -185128.133141

[06:48:13 -864733.889116] Initial branch length optimization
[06:48:17 -712502.098734] Model parameter optimization (eps = 10.000000)
[06:48:54 -710555.901978] AUTODETECT spr round 1 (radius: 5)
[06:50:47 -447217.474698] AUTODETECT spr round 2 (radius: 10)
[06:52:54 -302590.623135] AUTODETECT spr round 3 (radius: 15)
[06:55:05 -236145.537061] AUTODETECT spr round 4 (radius: 20)
[06:57:28 -213684.309225] AUTODETECT spr round 5 (radius: 25)
[07:00:53 -210523.030499] SPR radius for FAST iterations: 25 (autodetect)
[07:00:53 -210523.030499] Model parameter optimization (eps = 3.000000)
[07:01:11 -210381.120190] FAST spr round 1 (radius: 25)
[07:03:21 -186045.034843] FAST spr round 2 (radius: 25)
[07:05:10 -185278.990104] FAST spr round 3 (radius: 25)
[07:06:45 -185224.142451] FAST spr round 4 (radius: 25)
[07:08:13 -185224.140994] Model parameter optimization (eps = 1.000000)
[07:08:27 -185220.558427] SLOW spr round 1 (radius: 5)
[07:10:23 -185138.029665] SLOW spr round 2 (radius: 5)
[07:12:14 -185135.055015] SLOW spr round 3 (radius: 5)
[07:14:01 -185135.054589] SLOW spr round 4 (radius: 10)
[07:15:46 -185135.054500] SLOW spr round 5 (radius: 15)
[07:18:25 -185135.054464] SLOW spr round 6 (radius: 20)
[07:22:13 -185135.054430] SLOW spr round 7 (radius: 25)
[07:27:27 -185135.054395] Model parameter optimization (eps = 0.100000)

[07:27:35] ML tree search #13, logLikelihood: -185134.885092

[07:27:35 -868775.416134] Initial branch length optimization
[07:27:39 -718605.633584] Model parameter optimization (eps = 10.000000)
[07:28:12 -716693.782053] AUTODETECT spr round 1 (radius: 5)
[07:30:06 -452550.477019] AUTODETECT spr round 2 (radius: 10)
[07:32:12 -319205.226701] AUTODETECT spr round 3 (radius: 15)
[07:34:23 -268203.679559] AUTODETECT spr round 4 (radius: 20)
[07:36:50 -243773.233475] AUTODETECT spr round 5 (radius: 25)
[07:39:47 -225666.177301] SPR radius for FAST iterations: 25 (autodetect)
[07:39:47 -225666.177301] Model parameter optimization (eps = 3.000000)
[07:40:05 -225522.371152] FAST spr round 1 (radius: 25)
[07:42:22 -188027.893780] FAST spr round 2 (radius: 25)
[07:44:03 -185460.226588] FAST spr round 3 (radius: 25)
[07:45:41 -185227.717761] FAST spr round 4 (radius: 25)
[07:47:12 -185204.165733] FAST spr round 5 (radius: 25)
[07:48:39 -185204.164358] Model parameter optimization (eps = 1.000000)
[07:48:55 -185176.576687] SLOW spr round 1 (radius: 5)
[07:50:50 -185123.120065] SLOW spr round 2 (radius: 5)
[07:52:40 -185117.841133] SLOW spr round 3 (radius: 5)
[07:54:26 -185117.840780] SLOW spr round 4 (radius: 10)
[07:56:13 -185112.880962] SLOW spr round 5 (radius: 5)
[07:58:23 -185112.078540] SLOW spr round 6 (radius: 5)
[08:00:20 -185112.078420] SLOW spr round 7 (radius: 10)
[08:02:09 -185112.078323] SLOW spr round 8 (radius: 15)
[08:04:45 -185111.908580] SLOW spr round 9 (radius: 5)
[08:07:02 -185111.906343] SLOW spr round 10 (radius: 10)
[08:09:03 -185111.906324] SLOW spr round 11 (radius: 15)
[08:11:34 -185111.906306] SLOW spr round 12 (radius: 20)
[08:15:39 -185111.906289] SLOW spr round 13 (radius: 25)
[08:20:53 -185111.906272] Model parameter optimization (eps = 0.100000)

[08:21:05] ML tree search #14, logLikelihood: -185111.451643

[08:21:05 -867696.488089] Initial branch length optimization
[08:21:08 -712600.164477] Model parameter optimization (eps = 10.000000)
[08:21:42 -710639.070635] AUTODETECT spr round 1 (radius: 5)
[08:23:34 -446527.120655] AUTODETECT spr round 2 (radius: 10)
[08:25:41 -316918.447226] AUTODETECT spr round 3 (radius: 15)
[08:27:55 -271086.379711] AUTODETECT spr round 4 (radius: 20)
[08:30:16 -244037.959897] AUTODETECT spr round 5 (radius: 25)
[08:33:10 -223625.487558] SPR radius for FAST iterations: 25 (autodetect)
[08:33:10 -223625.487558] Model parameter optimization (eps = 3.000000)
[08:33:30 -223431.203058] FAST spr round 1 (radius: 25)
[08:35:39 -186963.941811] FAST spr round 2 (radius: 25)
[08:37:26 -185357.060143] FAST spr round 3 (radius: 25)
[08:39:04 -185203.881987] FAST spr round 4 (radius: 25)
[08:40:34 -185196.346057] FAST spr round 5 (radius: 25)
[08:42:01 -185196.345452] Model parameter optimization (eps = 1.000000)
[08:42:19 -185181.990606] SLOW spr round 1 (radius: 5)
[08:44:14 -185133.372233] SLOW spr round 2 (radius: 5)
[08:46:06 -185128.634626] SLOW spr round 3 (radius: 5)
[08:47:53 -185128.634508] SLOW spr round 4 (radius: 10)
[08:49:39 -185128.634502] SLOW spr round 5 (radius: 15)
[08:52:20 -185124.019637] SLOW spr round 6 (radius: 5)
[08:54:38 -185124.019434] SLOW spr round 7 (radius: 10)
[08:56:42 -185124.019433] SLOW spr round 8 (radius: 15)
[08:59:15 -185123.849599] SLOW spr round 9 (radius: 5)
[09:01:35 -185123.847500] SLOW spr round 10 (radius: 10)
[09:03:39 -185123.847500] SLOW spr round 11 (radius: 15)
[09:06:11 -185123.847500] SLOW spr round 12 (radius: 20)
[09:10:10 -185121.412186] SLOW spr round 13 (radius: 5)
[09:12:31 -185118.756614] SLOW spr round 14 (radius: 5)
[09:14:35 -185118.747361] SLOW spr round 15 (radius: 10)
[09:16:28 -185118.747359] SLOW spr round 16 (radius: 15)
[09:19:03 -185118.747359] SLOW spr round 17 (radius: 20)
[09:22:55 -185118.747359] SLOW spr round 18 (radius: 25)
[09:28:04 -185118.747359] Model parameter optimization (eps = 0.100000)

[09:28:12] ML tree search #15, logLikelihood: -185118.676400

[09:28:12 -866894.241894] Initial branch length optimization
[09:28:18 -714256.615105] Model parameter optimization (eps = 10.000000)
[09:28:56 -712273.237822] AUTODETECT spr round 1 (radius: 5)
[09:30:54 -464231.025910] AUTODETECT spr round 2 (radius: 10)
[09:33:08 -325578.756165] AUTODETECT spr round 3 (radius: 15)
[09:35:25 -264392.915388] AUTODETECT spr round 4 (radius: 20)
[09:38:05 -228348.064159] AUTODETECT spr round 5 (radius: 25)
[09:40:53 -217132.099770] SPR radius for FAST iterations: 25 (autodetect)
[09:40:53 -217132.099770] Model parameter optimization (eps = 3.000000)
[09:41:10 -216982.019823] FAST spr round 1 (radius: 25)
[09:43:23 -186339.269366] FAST spr round 2 (radius: 25)
[09:45:15 -185304.216970] FAST spr round 3 (radius: 25)
[09:46:58 -185202.583085] FAST spr round 4 (radius: 25)
[09:48:36 -185187.306180] FAST spr round 5 (radius: 25)
[09:50:07 -185186.120741] FAST spr round 6 (radius: 25)
[09:51:36 -185186.120588] Model parameter optimization (eps = 1.000000)
[09:51:53 -185174.874330] SLOW spr round 1 (radius: 5)
[09:53:52 -185133.474050] SLOW spr round 2 (radius: 5)
[09:55:46 -185130.104599] SLOW spr round 3 (radius: 5)
[09:57:38 -185130.104394] SLOW spr round 4 (radius: 10)
[09:59:33 -185126.540789] SLOW spr round 5 (radius: 5)
[10:01:48 -185126.540108] SLOW spr round 6 (radius: 10)
[10:03:50 -185126.540070] SLOW spr round 7 (radius: 15)
[10:06:29 -185121.930772] SLOW spr round 8 (radius: 5)
[10:08:51 -185121.930539] SLOW spr round 9 (radius: 10)
[10:10:59 -185121.930505] SLOW spr round 10 (radius: 15)
[10:13:37 -185121.930472] SLOW spr round 11 (radius: 20)
[10:17:50 -185121.930439] SLOW spr round 12 (radius: 25)
[10:23:14 -185116.706390] SLOW spr round 13 (radius: 5)
[10:25:37 -185116.706189] SLOW spr round 14 (radius: 10)
[10:27:47 -185116.706156] SLOW spr round 15 (radius: 15)
[10:30:23 -185116.706123] SLOW spr round 16 (radius: 20)
[10:34:34 -185116.706089] SLOW spr round 17 (radius: 25)
[10:39:55 -185116.706056] Model parameter optimization (eps = 0.100000)

[10:40:00] ML tree search #16, logLikelihood: -185116.686646

[10:40:00 -868607.305938] Initial branch length optimization
[10:40:05 -720245.555489] Model parameter optimization (eps = 10.000000)
[10:40:53 -718291.232201] AUTODETECT spr round 1 (radius: 5)
[10:42:49 -465806.896650] AUTODETECT spr round 2 (radius: 10)
[10:44:58 -341906.000506] AUTODETECT spr round 3 (radius: 15)
[10:47:24 -270725.037870] AUTODETECT spr round 4 (radius: 20)
[10:49:54 -239766.558384] AUTODETECT spr round 5 (radius: 25)
[10:52:53 -225011.818022] SPR radius for FAST iterations: 25 (autodetect)
[10:52:53 -225011.818022] Model parameter optimization (eps = 3.000000)
[10:53:14 -224869.668457] FAST spr round 1 (radius: 25)
[10:55:24 -186931.466968] FAST spr round 2 (radius: 25)
[10:57:09 -185341.559157] FAST spr round 3 (radius: 25)
[10:58:47 -185201.883059] FAST spr round 4 (radius: 25)
[11:00:22 -185182.958531] FAST spr round 5 (radius: 25)
[11:01:53 -185181.060284] FAST spr round 6 (radius: 25)
[11:03:20 -185181.058530] Model parameter optimization (eps = 1.000000)
[11:03:36 -185165.105254] SLOW spr round 1 (radius: 5)
[11:05:32 -185127.517362] SLOW spr round 2 (radius: 5)
[11:07:23 -185126.966784] SLOW spr round 3 (radius: 5)
[11:09:11 -185126.966778] SLOW spr round 4 (radius: 10)
[11:11:00 -185126.966778] SLOW spr round 5 (radius: 15)
[11:13:45 -185126.966778] SLOW spr round 6 (radius: 20)
[11:17:55 -185126.966778] SLOW spr round 7 (radius: 25)
[11:23:42 -185126.966778] Model parameter optimization (eps = 0.100000)

[11:23:46] ML tree search #17, logLikelihood: -185126.944178

[11:23:46 -864087.710066] Initial branch length optimization
[11:23:50 -709961.216110] Model parameter optimization (eps = 10.000000)
[11:24:19 -707964.924606] AUTODETECT spr round 1 (radius: 5)
[11:26:18 -458476.196021] AUTODETECT spr round 2 (radius: 10)
[11:28:28 -316748.675426] AUTODETECT spr round 3 (radius: 15)
[11:30:47 -249214.721823] AUTODETECT spr round 4 (radius: 20)
[11:33:25 -222869.034724] AUTODETECT spr round 5 (radius: 25)
[11:36:14 -215440.217591] SPR radius for FAST iterations: 25 (autodetect)
[11:36:14 -215440.217591] Model parameter optimization (eps = 3.000000)
[11:36:35 -215300.275100] FAST spr round 1 (radius: 25)
[11:38:45 -186720.746211] FAST spr round 2 (radius: 25)
[11:40:34 -185297.478283] FAST spr round 3 (radius: 25)
[11:42:17 -185183.502893] FAST spr round 4 (radius: 25)
[11:43:50 -185182.871117] FAST spr round 5 (radius: 25)
[11:45:20 -185182.870589] Model parameter optimization (eps = 1.000000)
[11:45:35 -185173.605942] SLOW spr round 1 (radius: 5)
[11:47:35 -185133.348487] SLOW spr round 2 (radius: 5)
[11:49:32 -185119.663165] SLOW spr round 3 (radius: 5)
[11:51:25 -185119.662728] SLOW spr round 4 (radius: 10)
[11:53:16 -185116.017186] SLOW spr round 5 (radius: 5)
[11:55:32 -185115.987372] SLOW spr round 6 (radius: 10)
[11:57:33 -185115.987302] SLOW spr round 7 (radius: 15)
[12:00:10 -185115.987235] SLOW spr round 8 (radius: 20)
[12:04:16 -185115.987170] SLOW spr round 9 (radius: 25)
[12:09:36 -185115.987107] Model parameter optimization (eps = 0.100000)

[12:09:47] ML tree search #18, logLikelihood: -185115.809506

[12:09:47 -869305.708776] Initial branch length optimization
[12:09:51 -714637.332851] Model parameter optimization (eps = 10.000000)
[12:10:42 -712746.595886] AUTODETECT spr round 1 (radius: 5)
[12:12:41 -456796.311338] AUTODETECT spr round 2 (radius: 10)
[12:14:52 -320369.112952] AUTODETECT spr round 3 (radius: 15)
[12:17:09 -259341.591134] AUTODETECT spr round 4 (radius: 20)
[12:19:55 -229816.804975] AUTODETECT spr round 5 (radius: 25)
[12:22:53 -218115.371828] SPR radius for FAST iterations: 25 (autodetect)
[12:22:53 -218115.371828] Model parameter optimization (eps = 3.000000)
[12:23:13 -217997.160565] FAST spr round 1 (radius: 25)
[12:25:25 -186994.057909] FAST spr round 2 (radius: 25)
[12:27:19 -185338.435530] FAST spr round 3 (radius: 25)
[12:29:01 -185214.389892] FAST spr round 4 (radius: 25)
[12:30:35 -185201.370413] FAST spr round 5 (radius: 25)
[12:32:06 -185201.087893] FAST spr round 6 (radius: 25)
[12:33:36 -185201.087354] Model parameter optimization (eps = 1.000000)
[12:33:52 -185192.283584] SLOW spr round 1 (radius: 5)
[12:35:46 -185134.481664] SLOW spr round 2 (radius: 5)
[12:37:39 -185123.502979] SLOW spr round 3 (radius: 5)
[12:39:30 -185123.468175] SLOW spr round 4 (radius: 10)
[12:41:21 -185118.144525] SLOW spr round 5 (radius: 5)
[12:43:35 -185118.144097] SLOW spr round 6 (radius: 10)
[12:45:34 -185118.143775] SLOW spr round 7 (radius: 15)
[12:48:09 -185117.973691] SLOW spr round 8 (radius: 5)
[12:50:29 -185117.971478] SLOW spr round 9 (radius: 10)
[12:52:34 -185117.971465] SLOW spr round 10 (radius: 15)
[12:55:07 -185117.971453] SLOW spr round 11 (radius: 20)
[12:59:18 -185115.654413] SLOW spr round 12 (radius: 5)
[13:01:38 -185112.994902] SLOW spr round 13 (radius: 5)
[13:03:45 -185112.985772] SLOW spr round 14 (radius: 10)
[13:05:42 -185112.985760] SLOW spr round 15 (radius: 15)
[13:08:22 -185112.985750] SLOW spr round 16 (radius: 20)
[13:12:31 -185112.985732] SLOW spr round 17 (radius: 25)
[13:18:01 -185112.985722] Model parameter optimization (eps = 0.100000)

[13:18:10] ML tree search #19, logLikelihood: -185112.777528

[13:18:10 -872838.392082] Initial branch length optimization
[13:18:14 -716825.842434] Model parameter optimization (eps = 10.000000)
[13:18:48 -714884.684923] AUTODETECT spr round 1 (radius: 5)
[13:20:45 -459528.482988] AUTODETECT spr round 2 (radius: 10)
[13:22:57 -325883.648191] AUTODETECT spr round 3 (radius: 15)
[13:25:17 -264282.275313] AUTODETECT spr round 4 (radius: 20)
[13:28:02 -238283.141202] AUTODETECT spr round 5 (radius: 25)
[13:30:38 -231016.872756] SPR radius for FAST iterations: 25 (autodetect)
[13:30:38 -231016.872756] Model parameter optimization (eps = 3.000000)
[13:30:57 -230840.919611] FAST spr round 1 (radius: 25)
[13:33:13 -189847.334557] FAST spr round 2 (radius: 25)
[13:35:03 -185756.977685] FAST spr round 3 (radius: 25)
[13:36:43 -185276.911175] FAST spr round 4 (radius: 25)
[13:38:21 -185232.034284] FAST spr round 5 (radius: 25)
[13:39:55 -185196.590688] FAST spr round 6 (radius: 25)
[13:41:27 -185196.589443] Model parameter optimization (eps = 1.000000)
[13:41:44 -185174.938649] SLOW spr round 1 (radius: 5)
[13:43:43 -185126.520188] SLOW spr round 2 (radius: 5)
[13:45:40 -185123.769889] SLOW spr round 3 (radius: 5)
[13:47:30 -185123.769529] SLOW spr round 4 (radius: 10)
[13:49:21 -185120.474511] SLOW spr round 5 (radius: 5)
[13:51:34 -185120.474481] SLOW spr round 6 (radius: 10)
[13:53:35 -185120.474477] SLOW spr round 7 (radius: 15)
[13:56:11 -185120.321726] SLOW spr round 8 (radius: 5)
[13:58:32 -185120.272893] SLOW spr round 9 (radius: 10)
[14:00:38 -185120.272883] SLOW spr round 10 (radius: 15)
[14:03:11 -185120.272883] SLOW spr round 11 (radius: 20)
[14:07:19 -185120.272883] SLOW spr round 12 (radius: 25)
[14:12:40 -185120.272883] Model parameter optimization (eps = 0.100000)

[14:12:46] ML tree search #20, logLikelihood: -185120.191647


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.202476,0.320013) (0.213690,0.470433) (0.333113,0.877857) (0.250721,2.162771) 
   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: -185111.451643

AIC score: 374232.903287 / AICc score: 8418292.903287 / BIC score: 382997.985040
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=585).
         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/Q15835/3_mltree/Q15835.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q15835/3_mltree/Q15835.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q15835/3_mltree/Q15835.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q15835/3_mltree/Q15835.raxml.log

Analysis started: 25-Jun-2021 04:54:51 / finished: 25-Jun-2021 19:07:37

Elapsed time: 51166.439 seconds (this run) / 71998.137 seconds (total with restarts)