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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM

RAxML-NG was called at 03-Jun-2021 02:06:44 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P78562/2_msa/P78562_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P78562/3_mltree/P78562.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P78562/4_raxmlng_ancestral/P78562 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622675204
  tip-inner: ON
  pattern compression: OFF
  per-rate scalers: OFF
  site repeats: OFF
  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
  SIMD kernels: AVX2
  parallelization: coarse-grained (auto), PTHREADS (4 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P78562/2_msa/P78562_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 749 sites

WARNING: Sequences tr_A0A2I3ST75_A0A2I3ST75_PANTR_9598 and tr_A0A2R8ZX15_A0A2R8ZX15_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A158Q1I1_A0A158Q1I1_BRUMA_6279 and tr_A0A0R3QJH4_A0A0R3QJH4_9BILA_42155 are exactly identical!
WARNING: Sequences tr_A0A1D5QKC2_A0A1D5QKC2_MACMU_9544 and tr_G7NZK8_G7NZK8_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A1D5QKC2_A0A1D5QKC2_MACMU_9544 and tr_A0A2K5MZ14_A0A2K5MZ14_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A1D5QKC2_A0A1D5QKC2_MACMU_9544 and tr_A0A2K6E3V2_A0A2K6E3V2_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A1D5QKC2_A0A1D5QKC2_MACMU_9544 and tr_A0A2K6A4Q3_A0A2K6A4Q3_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A1D5QMJ9_A0A1D5QMJ9_MACMU_9544 and tr_A0A2I3M7R5_A0A2I3M7R5_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A1D5QMJ9_A0A1D5QMJ9_MACMU_9544 and tr_A0A0D9S8B6_A0A0D9S8B6_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A1D5QMJ9_A0A1D5QMJ9_MACMU_9544 and tr_A0A2K6BPS4_A0A2K6BPS4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A1D5QMJ9_A0A1D5QMJ9_MACMU_9544 and tr_A0A2K6AIN5_A0A2K6AIN5_MANLE_9568 are exactly identical!
WARNING: Sequences tr_H9H3W2_H9H3W2_MACMU_9544 and tr_A0A2K6DWV5_A0A2K6DWV5_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A015L124_A0A015L124_9GLOM_1432141 and tr_U9UN95_U9UN95_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A0V1CNS6_A0A0V1CNS6_TRIBR_45882 and tr_A0A0V0WJN5_A0A0V0WJN5_9BILA_92179 are exactly identical!
WARNING: Sequences tr_A0A0V1CNS6_A0A0V1CNS6_TRIBR_45882 and tr_A0A0V1L7Z3_A0A0V1L7Z3_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V1CNS6_A0A0V1CNS6_TRIBR_45882 and tr_A0A0V1NQX7_A0A0V1NQX7_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V1CNS6_A0A0V1CNS6_TRIBR_45882 and tr_A0A0V0UBP1_A0A0V0UBP1_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A0V0WMT9_A0A0V0WMT9_9BILA_92179 and tr_A0A0V1A8C9_A0A0V1A8C9_9BILA_990121 are exactly identical!
WARNING: Sequences tr_A0A1S3HMA4_A0A1S3HMA4_LINUN_7574 and tr_A0A1S3HMB4_A0A1S3HMB4_LINUN_7574 are exactly identical!
WARNING: Sequences tr_A0A1S3HMA4_A0A1S3HMA4_LINUN_7574 and tr_A0A1S3HMH7_A0A1S3HMH7_LINUN_7574 are exactly identical!
WARNING: Sequences tr_A0A1S3HMA4_A0A1S3HMA4_LINUN_7574 and tr_A0A1S3HNW2_A0A1S3HNW2_LINUN_7574 are exactly identical!
WARNING: Sequences tr_A0A2D0SU77_A0A2D0SU77_ICTPU_7998 and tr_A0A2D0SUQ0_A0A2D0SUQ0_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0SU77_A0A2D0SU77_ICTPU_7998 and tr_A0A2D0SVA0_A0A2D0SVA0_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2K5LQG5_A0A2K5LQG5_CERAT_9531 and tr_A0A2K5ZAA4_A0A2K5ZAA4_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2K5M322_A0A2K5M322_CERAT_9531 and tr_A0A2K5ZQZ1_A0A2K5ZQZ1_MANLE_9568 are exactly identical!
WARNING: Duplicate sequences found: 24

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P78562/4_raxmlng_ancestral/P78562.raxml.reduced.phy

Alignment comprises 1 partitions and 749 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 749
Gaps: 9.13 %
Invariant sites: 0.40 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P78562/4_raxmlng_ancestral/P78562.raxml.rba

Parallelization scheme autoconfig: 1 worker(s) x 4 thread(s)

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

[00:00:00] Loading user starting tree(s) from: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P78562/3_mltree/P78562.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 188 / 15040
[00:00:00] Data distribution: max. searches per worker: 1

Starting ML tree search with 1 distinct starting trees

[00:00:00] Tree #1, initial LogLikelihood: -373808.602144

[00:00:00 -373808.602144] Initial branch length optimization
[00:00:01 -373320.986128] Model parameter optimization (eps = 0.100000)

[00:00:43] Tree #1, final logLikelihood: -372950.826898


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.140987,0.258875) (0.198481,0.407761) (0.407751,0.897580) (0.252781,2.043585) 
   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 

Marginal ancestral probabilities saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P78562/4_raxmlng_ancestral/P78562.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P78562/4_raxmlng_ancestral/P78562.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P78562/4_raxmlng_ancestral/P78562.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P78562/4_raxmlng_ancestral/P78562.raxml.log

Analysis started: 03-Jun-2021 02:06:44 / finished: 03-Jun-2021 02:07:34

Elapsed time: 50.660 seconds

Consumed energy: 3.472 Wh