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 04-Jul-2021 09:51:12 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NMN3/2_msa/A6NMN3_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NMN3/3_mltree/A6NMN3 --seed 2 --threads 5 --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 (5 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NMN3/2_msa/A6NMN3_trimmed_msa.fasta
[00:00:00] Loaded alignment with 153 taxa and 355 sites

WARNING: Sequences tr_F6SDR1_F6SDR1_MACMU_9544 and tr_G7NXC4_G7NXC4_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A096N1N6_A0A096N1N6_PAPAN_9555 and tr_A0A2K6AL59_A0A2K6AL59_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A096N4P3_A0A096N4P3_PAPAN_9555 and tr_A0A2K6D2G4_A0A2K6D2G4_MACNE_9545 are exactly identical!
WARNING: Duplicate sequences found: 3

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/A6NMN3/3_mltree/A6NMN3.raxml.reduced.phy

Alignment comprises 1 partitions and 355 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 355 / 355
Gaps: 26.73 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NMN3/3_mltree/A6NMN3.raxml.rba

Parallelization scheme autoconfig: 5 worker(s) x 1 thread(s)

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

[00:00:00] Generating 20 random starting tree(s) with 153 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 355 / 28400
[00:00:00] Data distribution: max. searches per worker: 4

Starting ML tree search with 20 distinct starting trees

[00:00:00 -84084.041857] Initial branch length optimization
[00:00:00 -68595.312686] Model parameter optimization (eps = 10.000000)
[00:00:12 -68165.940992] AUTODETECT spr round 1 (radius: 5)
[00:00:22 -44670.181961] AUTODETECT spr round 2 (radius: 10)
[00:00:34 -35027.126836] AUTODETECT spr round 3 (radius: 15)
[00:00:51 -33265.717753] AUTODETECT spr round 4 (radius: 20)
[00:01:09 -33256.934227] AUTODETECT spr round 5 (radius: 25)
[00:01:26 -33256.879846] SPR radius for FAST iterations: 20 (autodetect)
[00:01:26 -33256.879846] Model parameter optimization (eps = 3.000000)
[00:01:35 -33183.242312] FAST spr round 1 (radius: 20)
[00:01:49 -31023.158720] FAST spr round 2 (radius: 20)
[00:02:00 -30973.109049] FAST spr round 3 (radius: 20)
[00:02:09 -30967.607715] FAST spr round 4 (radius: 20)
[00:02:17 -30967.607367] Model parameter optimization (eps = 1.000000)
[00:02:22 -30960.894016] SLOW spr round 1 (radius: 5)
[00:02:44 -30955.133106] SLOW spr round 2 (radius: 5)
[00:03:03 -30955.120966] SLOW spr round 3 (radius: 10)
[00:03:22 -30955.120956] SLOW spr round 4 (radius: 15)
[00:03:55 -30955.120956] SLOW spr round 5 (radius: 20)
[00:04:26 -30955.120956] SLOW spr round 6 (radius: 25)
[00:04:47] [worker #3] ML tree search #4, logLikelihood: -30953.360742
[00:04:49 -30955.120956] Model parameter optimization (eps = 0.100000)

[00:04:50] [worker #0] ML tree search #1, logLikelihood: -30955.107804

[00:04:51 -80794.733030] Initial branch length optimization
[00:04:51 -66753.302933] Model parameter optimization (eps = 10.000000)
[00:04:54] [worker #2] ML tree search #3, logLikelihood: -30954.921853
[00:05:05 -66463.792168] AUTODETECT spr round 1 (radius: 5)
[00:05:15 -48929.163960] AUTODETECT spr round 2 (radius: 10)
[00:05:29 -35212.161023] AUTODETECT spr round 3 (radius: 15)
[00:05:35] [worker #4] ML tree search #5, logLikelihood: -30957.213135
[00:05:46 -33697.181772] AUTODETECT spr round 4 (radius: 20)
[00:06:06 -33449.862129] AUTODETECT spr round 5 (radius: 25)
[00:06:21 -33248.178822] SPR radius for FAST iterations: 25 (autodetect)
[00:06:21 -33248.178822] Model parameter optimization (eps = 3.000000)
[00:06:30 -33177.783618] FAST spr round 1 (radius: 25)
[00:06:30] [worker #1] ML tree search #2, logLikelihood: -30953.362174
[00:06:45 -31003.422298] FAST spr round 2 (radius: 25)
[00:06:55 -30974.175365] FAST spr round 3 (radius: 25)
[00:07:03 -30973.188318] FAST spr round 4 (radius: 25)
[00:07:12 -30970.463545] FAST spr round 5 (radius: 25)
[00:07:20 -30970.463537] Model parameter optimization (eps = 1.000000)
[00:07:27 -30965.945405] SLOW spr round 1 (radius: 5)
[00:07:47 -30960.677411] SLOW spr round 2 (radius: 5)
[00:08:07 -30954.932222] SLOW spr round 3 (radius: 5)
[00:08:26 -30954.932211] SLOW spr round 4 (radius: 10)
[00:08:46 -30954.932211] SLOW spr round 5 (radius: 15)
[00:09:19 -30954.932211] SLOW spr round 6 (radius: 20)
[00:09:50 -30954.932211] SLOW spr round 7 (radius: 25)
[00:10:13 -30954.932211] Model parameter optimization (eps = 0.100000)

[00:10:15] [worker #0] ML tree search #6, logLikelihood: -30954.921770

[00:10:15 -81573.635236] Initial branch length optimization
[00:10:16 -67468.991237] Model parameter optimization (eps = 10.000000)
[00:10:23] [worker #4] ML tree search #10, logLikelihood: -30953.360604
[00:10:26] [worker #3] ML tree search #9, logLikelihood: -30953.351901
[00:10:26 -67206.636740] AUTODETECT spr round 1 (radius: 5)
[00:10:36 -46441.205962] AUTODETECT spr round 2 (radius: 10)
[00:10:52 -35682.423741] AUTODETECT spr round 3 (radius: 15)
[00:11:11 -32716.491268] AUTODETECT spr round 4 (radius: 20)
[00:11:29 -32710.979509] AUTODETECT spr round 5 (radius: 25)
[00:11:42] [worker #2] ML tree search #8, logLikelihood: -30955.523698
[00:11:44 -32710.963195] SPR radius for FAST iterations: 20 (autodetect)
[00:11:44 -32710.963195] Model parameter optimization (eps = 3.000000)
[00:11:52] [worker #1] ML tree search #7, logLikelihood: -30955.131393
[00:11:53 -32659.861342] FAST spr round 1 (radius: 20)
[00:12:08 -31001.420927] FAST spr round 2 (radius: 20)
[00:12:17 -30983.193253] FAST spr round 3 (radius: 20)
[00:12:26 -30963.653358] FAST spr round 4 (radius: 20)
[00:12:35 -30960.934737] FAST spr round 5 (radius: 20)
[00:12:43 -30960.934722] Model parameter optimization (eps = 1.000000)
[00:12:48 -30956.747049] SLOW spr round 1 (radius: 5)
[00:13:09 -30953.393604] SLOW spr round 2 (radius: 5)
[00:13:28 -30953.393125] SLOW spr round 3 (radius: 10)
[00:13:48 -30953.393114] SLOW spr round 4 (radius: 15)
[00:14:21 -30953.393113] SLOW spr round 5 (radius: 20)
[00:14:52 -30953.393113] SLOW spr round 6 (radius: 25)
[00:15:15 -30953.393113] Model parameter optimization (eps = 0.100000)

[00:15:17] [worker #0] ML tree search #11, logLikelihood: -30953.351961

[00:15:17 -82049.714265] Initial branch length optimization
[00:15:18 -67896.223577] Model parameter optimization (eps = 10.000000)
[00:15:30 -67492.909796] AUTODETECT spr round 1 (radius: 5)
[00:15:36] [worker #4] ML tree search #15, logLikelihood: -30953.351909
[00:15:40 -43044.550113] AUTODETECT spr round 2 (radius: 10)
[00:15:54 -35224.560262] AUTODETECT spr round 3 (radius: 15)
[00:16:12 -33194.751148] AUTODETECT spr round 4 (radius: 20)
[00:16:32 -32751.345694] AUTODETECT spr round 5 (radius: 25)
[00:16:49 -32742.465279] SPR radius for FAST iterations: 25 (autodetect)
[00:16:49 -32742.465279] Model parameter optimization (eps = 3.000000)
[00:16:53] [worker #3] ML tree search #14, logLikelihood: -30955.131537
[00:16:57] [worker #2] ML tree search #13, logLikelihood: -30953.352021
[00:16:57 -32661.397103] FAST spr round 1 (radius: 25)
[00:16:59] [worker #1] ML tree search #12, logLikelihood: -30955.334428
[00:17:11 -31087.365122] FAST spr round 2 (radius: 25)
[00:17:23 -30966.363637] FAST spr round 3 (radius: 25)
[00:17:31 -30963.689221] FAST spr round 4 (radius: 25)
[00:17:39 -30963.677722] Model parameter optimization (eps = 1.000000)
[00:17:46 -30960.916723] SLOW spr round 1 (radius: 5)
[00:18:08 -30953.744534] SLOW spr round 2 (radius: 5)
[00:18:28 -30953.740760] SLOW spr round 3 (radius: 10)
[00:18:47 -30953.740611] SLOW spr round 4 (radius: 15)
[00:19:20 -30953.740596] SLOW spr round 5 (radius: 20)
[00:19:51 -30953.740594] SLOW spr round 6 (radius: 25)
[00:20:14 -30953.740594] Model parameter optimization (eps = 0.100000)

[00:20:18] [worker #0] ML tree search #16, logLikelihood: -30953.352053

[00:21:44] [worker #2] ML tree search #18, logLikelihood: -30953.352054
[00:21:49] [worker #4] ML tree search #20, logLikelihood: -30953.351964
[00:22:20] [worker #1] ML tree search #17, logLikelihood: -30953.352044
[00:23:16] [worker #3] ML tree search #19, logLikelihood: -30953.352824

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.102412,0.451529) (0.045840,0.649984) (0.286809,0.610207) (0.564938,1.325719) 
   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: -30953.351901

AIC score: 62524.703802 / AICc score: 66782.037135 / BIC score: 63721.188199
Free parameters (model + branch lengths): 309

Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NMN3/3_mltree/A6NMN3.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NMN3/3_mltree/A6NMN3.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NMN3/3_mltree/A6NMN3.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NMN3/3_mltree/A6NMN3.raxml.log

Analysis started: 04-Jul-2021 09:51:12 / finished: 04-Jul-2021 10:14:29

Elapsed time: 1396.254 seconds

Consumed energy: 128.834 Wh